Contacts of the helix formed by residues 122 - 142 (chain A) in PDB entry 4WMJ


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with VAL 122 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  LEU*     5.2     0.7    -      -       +      -
    106A  ALA*     3.9    27.4    -      -       +      -
    115A  ILE*     2.9    28.0    +      -       +      +
    117A  VAL*     3.5    37.7    -      -       +      -
    120A  LYS*     3.7    11.4    -      -       -      +
    121A  ASP*     1.3    73.9    -      -       -      +
    123A  THR*     1.3    69.7    +      -       +      +
    124A  PRO*     3.3     0.9    -      -       -      -
    125A  ASP*     3.0    10.1    +      -       +      +
    126A  VAL*     3.0    22.6    +      -       +      +
    272A  TRP*     3.7    28.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 123 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  ALA      5.9     0.9    -      -       -      +
    109A  ASN*     3.1    32.3    -      -       -      +
    112A  ASN*     4.3    12.3    +      -       -      +
    113A  ARG      3.1    13.9    -      -       -      +
    115A  ILE      4.3     1.8    -      -       -      +
    121A  ASP*     2.9    24.3    +      -       -      +
    122A  VAL*     1.3    80.2    -      -       +      +
    124A  PRO*     1.4    74.1    -      -       -      +
    126A  VAL*     3.2     6.9    +      -       -      +
    127A  ASN*     2.8    43.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 124 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121A  ASP*     3.3    26.0    -      -       +      +
    122A  VAL      3.5     0.9    -      -       -      -
    123A  THR*     1.4    99.0    -      -       -      +
    125A  ASP*     1.3    59.6    +      -       -      +
    127A  ASN*     3.5     6.8    +      -       +      +
    128A  ALA*     2.9    29.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 125 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  LYS*     2.6    41.3    +      -       -      +
    121A  ASP      4.7     0.6    -      -       -      +
    122A  VAL*     3.0    11.1    +      -       +      +
    124A  PRO*     1.3    78.2    -      -       -      +
    126A  VAL*     1.4    65.6    +      -       +      +
    128A  ALA*     3.4     6.4    +      -       -      +
    129A  VAL*     3.1    28.2    +      -       -      +
    270A  TRP*     3.7    27.3    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 126 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  ALA      3.6    26.7    -      -       -      +
    107A  LEU*     3.8    22.9    -      -       +      +
    109A  ASN*     5.7     0.4    -      -       +      +
    122A  VAL*     3.0    22.6    +      -       +      +
    123A  THR*     3.6     9.2    -      -       -      +
    125A  ASP*     1.4    74.4    -      -       -      +
    127A  ASN*     1.3    68.9    +      -       -      +
    129A  VAL*     3.3     4.3    +      -       -      +
    130A  LEU*     3.0    33.1    +      -       +      +
    270A  TRP*     3.7    13.9    -      -       +      -
    272A  TRP*     3.9    26.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 127 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109A  ASN      5.3     0.7    -      -       -      +
    110A  ARG*     5.3     2.9    +      -       -      -
    112A  ASN*     3.0    37.4    +      -       -      +
    123A  THR*     2.8    23.3    +      -       -      +
    124A  PRO*     4.0     6.1    -      -       +      +
    126A  VAL*     1.3    83.2    -      -       -      +
    128A  ALA*     1.3    56.6    +      -       -      +
    130A  LEU*     3.4    18.8    +      -       -      +
    131A  ALA*     2.9    28.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 128 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124A  PRO      2.9    18.6    +      -       -      +
    125A  ASP*     3.7     7.6    -      -       -      +
    126A  VAL      3.2     0.4    -      -       -      -
    127A  ASN*     1.3    75.1    -      -       -      +
    129A  VAL*     1.3    64.9    +      -       +      +
    131A  ALA*     3.3     7.4    +      -       -      +
    132A  HIS*     3.1    22.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 129 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125A  ASP      3.1    15.0    +      -       -      +
    126A  VAL      3.8     6.3    -      -       -      +
    128A  ALA*     1.3    75.9    -      -       +      +
    130A  LEU*     1.3    59.5    +      -       +      +
    132A  HIS*     3.1     9.5    +      -       +      +
    133A  MET*     2.9    37.6    +      -       +      +
    267A  PHE*     4.7     5.4    -      -       +      -
    268A  GLY*     3.6    38.8    -      -       -      +
    270A  TRP*     3.7    16.8    -      -       +      -
    282A  ALA*     4.0    20.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 130 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107A  LEU      4.3     3.8    -      -       -      +
    110A  ARG*     4.0    23.1    -      -       -      +
    126A  VAL*     3.0    30.2    +      -       +      +
    127A  ASN*     3.6    21.5    -      -       -      +
    128A  ALA      3.3     0.2    -      -       -      -
    129A  VAL*     1.3    78.1    -      -       +      +
    131A  ALA*     1.3    57.5    +      -       -      +
    133A  MET*     3.4    12.1    +      -       -      -
    134A  LYS*     2.9    25.3    +      -       -      +
    280A  TRP      4.8     6.5    -      -       -      +
    281A  SER*     5.8     1.1    -      -       -      -
    293A  PHE*     3.4    25.8    -      -       +      -
    296A  PHE*     4.0    16.6    -      -       +      -
    300A  LEU*     3.9    23.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 131 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127A  ASN      2.9    16.9    +      -       -      +
    128A  ALA*     3.3     8.7    +      -       -      +
    130A  LEU*     1.3    75.0    -      -       -      +
    132A  HIS*     1.3    56.8    +      -       -      +
    134A  LYS*     3.4    11.6    +      -       +      +
    135A  GLU*     3.0    28.8    +      -       -      +
    293A  PHE*     5.4     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 132 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  ALA      3.1    11.6    +      -       -      +
    129A  VAL*     3.1    12.9    +      -       -      +
    131A  ALA*     1.3    74.3    -      -       -      +
    133A  MET*     1.3    64.3    +      -       -      +
    135A  GLU*     3.3    19.7    +      -       -      +
    136A  PHE*     2.9    25.2    +      -       +      +
    264A  LYS*     3.2    29.0    +      -       -      +
    265A  ASN*     4.6     2.6    +      -       -      -
    266A  MET      3.7    19.3    +      -       -      -
    267A  PHE*     3.3    35.8    -      +       -      -
----------------------------------------------------------
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Residues in contact with MET 133 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129A  VAL*     2.9    22.5    +      -       +      +
    130A  LEU*     3.4    26.0    -      -       -      +
    132A  HIS*     1.3    77.7    -      -       -      +
    134A  LYS*     1.3    53.3    +      -       -      +
    136A  PHE*     4.0     0.7    -      -       -      +
    137A  SER*     2.7    39.4    +      -       -      -
    267A  PHE*     3.9    22.0    -      -       +      -
    281A  SER      3.6    14.4    -      -       -      +
    282A  ALA*     3.8    21.5    -      -       -      -
    284A  GLY      3.8     4.7    -      -       -      +
    285A  LEU*     3.6    42.1    -      -       +      +
    288A  SER*     4.7     3.1    -      -       -      +
    293A  PHE*     4.2     7.9    -      -       +      -
    296A  PHE*     3.8    16.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 134 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130A  LEU      2.9    17.5    +      -       -      +
    131A  ALA*     3.5    10.1    -      -       +      +
    132A  HIS      3.3     0.2    -      -       -      -
    133A  MET*     1.3    73.8    -      -       -      +
    135A  GLU*     1.3    59.7    +      -       -      +
    137A  SER*     3.4     2.3    +      -       -      -
    138A  THR*     3.0    43.8    +      -       +      +
    293A  PHE*     3.5    45.5    -      -       +      +
    297A  GLU*     4.9     4.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 135 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131A  ALA      3.0    16.0    +      -       -      +
    132A  HIS*     3.3    21.2    +      -       -      +
    134A  LYS*     1.3    75.1    -      -       -      +
    136A  PHE*     1.3    65.2    +      -       -      +
    138A  THR*     2.4    24.8    +      -       -      +
    139A  GLN*     3.0    37.9    +      -       +      +
    264A  LYS*     6.0     1.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 136 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132A  HIS*     2.9    20.9    +      -       +      +
    133A  MET      4.0     1.6    -      -       -      +
    135A  GLU*     1.3    78.6    +      -       -      +
    137A  SER*     1.3    64.3    +      -       -      +
    139A  GLN*     3.1    10.1    +      -       -      +
    140A  VAL*     2.9    44.0    +      -       +      +
    145A  TRP*     3.5    44.4    -      +       -      -
    208A  LEU*     3.8    23.1    -      -       +      -
    247A  VAL*     3.9    22.0    -      -       +      -
    265A  ASN*     5.0     3.6    -      -       -      -
    267A  PHE*     3.6    24.0    -      +       +      -
    285A  LEU*     4.1    26.5    -      -       +      -
    289A  LEU*     4.2     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 137 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133A  MET      2.7    22.0    +      -       -      -
    134A  LYS*     3.6     6.1    -      -       -      -
    136A  PHE*     1.3    77.6    -      -       -      +
    138A  THR*     1.3    58.3    +      -       -      +
    140A  VAL*     3.2     0.7    +      -       -      +
    141A  ILE*     2.8    42.0    +      -       -      +
    285A  LEU*     4.1     5.9    -      -       -      +
    288A  SER*     2.7    43.0    +      -       -      -
    289A  LEU*     3.8    14.0    +      -       -      +
    293A  PHE*     4.6     6.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 138 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134A  LYS*     3.0    25.4    +      -       +      +
    135A  GLU*     2.4    28.1    +      -       -      +
    137A  SER*     1.3    75.5    -      -       -      +
    139A  GLN*     1.3    56.7    +      -       -      +
    141A  ILE*     4.1     5.1    -      -       -      +
    142A  SER*     2.8    40.3    +      -       -      -
    293A  PHE*     6.0     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 139 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A  GLU*     3.0    41.9    +      -       +      +
    136A  PHE*     3.1    12.6    +      -       -      +
    138A  THR*     1.3    83.3    +      -       -      +
    140A  VAL*     1.3    61.6    +      -       -      +
    142A  SER*     3.9     3.8    -      -       -      -
    143A  GLY      3.3     1.4    +      -       -      -
    144A  ALA*     3.0    24.2    +      -       +      -
    145A  TRP*     3.0    54.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 140 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136A  PHE*     2.9    49.2    +      -       +      +
    139A  GLN*     1.3    77.8    -      -       -      +
    141A  ILE*     1.3    64.3    +      -       -      +
    143A  GLY*     3.2    11.6    +      -       -      -
    145A  TRP*     4.0    20.8    -      -       +      +
    152A  PRO*     5.6     0.3    -      -       -      +
    153A  ILE*     3.9    40.8    +      -       +      +
    156A  VAL*     5.0     0.7    -      -       +      -
    181A  HIS*     5.0     0.5    +      -       -      -
    182A  LEU*     4.1    11.9    -      -       +      +
    208A  LEU*     4.1     8.5    -      -       +      -
    289A  LEU*     3.6    21.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 141 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137A  SER*     2.8    32.1    +      -       -      +
    138A  THR*     4.1     4.3    -      -       -      +
    140A  VAL*     1.3    74.7    -      -       -      +
    142A  SER*     1.3    60.4    +      -       -      +
    143A  GLY*     3.5     0.9    +      -       -      -
    180A  ASN*     3.5    24.2    -      -       +      +
    181A  HIS*     3.2    34.8    +      -       +      -
    182A  LEU*     3.9    10.8    -      -       +      -
    288A  SER      4.1    12.6    -      -       -      +
    289A  LEU*     3.5    24.2    -      -       +      +
    292A  GLY*     4.2    10.3    -      -       -      -
    293A  PHE      5.2     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 142 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138A  THR*     2.8    24.5    +      -       -      -
    139A  GLN*     3.4     1.0    +      -       -      -
    141A  ILE*     1.3    77.2    -      -       -      +
    143A  GLY*     1.3    59.6    +      -       -      +
    144A  ALA*     3.4    19.4    +      -       -      +
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il