Contacts of the strand formed by residues 142 - 152 (chain D) in PDB entry 1MWA


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 LYS 142 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120C  ASN*     6.0     1.6    -      -       -      -
    145C  ASP*     5.3     1.3    -      -       -      +
    170C  MET*     3.2    34.6    -      -       -      +
    172C  ALA*     5.0     4.2    -      -       -      +
    175C  SER*     6.1     0.4    -      -       -      +
    136D  GLU      2.5    30.7    -      -       -      +
    137D  ILE*     4.3     1.8    +      -       -      -
    140D  LYS*     2.9    45.1    -      -       +      +
    141D  GLN*     1.3    82.1    -      -       -      +
    143D  ALA*     1.3    56.2    +      -       -      +
    197D  ARG*     2.9    47.1    -      -       +      +
    198D  VAL      3.7     4.5    -      -       -      -
    199D  SER*     5.2     4.2    +      -       -      +
    204D  HIS*     5.4     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 143 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132D  PRO*     4.2    18.8    -      -       +      -
    136D  GLU*     3.8    14.4    -      -       -      +
    137D  ILE*     5.2     2.2    -      -       +      -
    140D  LYS*     4.5     0.2    -      -       -      +
    142D  LYS*     1.3    78.4    -      -       -      +
    144D  THR*     1.3    61.2    +      -       -      +
    145D  LEU*     3.2     5.2    -      -       -      +
    197D  ARG*     3.2     8.6    -      -       -      +
    198D  VAL*     3.0    50.5    +      -       +      +
    203D  TRP*     5.3     1.6    -      -       +      -
    204D  HIS*     4.8     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 144 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128C  LEU*     5.8     0.3    -      -       -      +
    142C  LEU*     3.2    42.3    -      -       +      +
    143C  PHE      3.5    17.5    -      -       -      +
    144C  THR*     3.1    25.5    +      -       -      +
    168C  LEU*     3.5    29.8    -      -       +      +
    132D  PRO*     4.4    11.4    -      -       -      +
    136D  GLU*     3.6     9.5    +      -       -      -
    140D  LYS*     5.6     1.4    -      -       -      +
    143D  ALA*     1.3    70.4    -      -       -      +
    145D  LEU*     1.3    64.7    +      -       -      +
    195D  ARG*     4.8     4.3    -      -       +      -
    196D  LEU      3.7     3.8    -      -       -      +
    197D  ARG*     4.1     4.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 145 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128C  LEU*     6.4     0.2    -      -       -      -
    181C  ILE*     4.8     0.9    -      -       -      +
    129D  LEU*     6.2     1.8    -      -       +      -
    130D  PHE      4.8     4.3    -      -       -      +
    131D  GLU*     5.1     1.1    -      -       +      +
    132D  PRO*     4.1    22.7    -      -       +      -
    143D  ALA*     3.2    15.7    -      -       +      +
    144D  THR*     1.3    78.3    -      -       -      +
    146D  VAL*     1.3    65.1    +      -       -      +
    161D  TRP*     3.6    31.2    -      -       +      -
    195D  ARG*     3.1    23.2    -      -       -      +
    196D  LEU*     2.9    33.8    +      -       +      +
    198D  VAL*     3.6    31.4    -      -       +      -
    203D  TRP*     4.8    15.5    -      -       +      -
    210D  PHE*     4.6    10.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 146 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128C  LEU*     3.6    31.4    -      -       +      -
    142C  LEU*     5.6     0.2    -      -       +      -
    181C  ILE*     3.3    24.9    -      -       +      -
    183C  TRP*     6.2     0.9    -      -       +      -
    129D  LEU*     3.7     7.6    -      -       -      +
    130D  PHE*     3.2    41.3    +      -       +      +
    144D  THR      5.5     0.4    -      -       -      +
    145D  LEU*     1.3    82.1    -      -       -      +
    147D  CYS*     1.3    77.8    +      -       -      +
    148D  LEU*     4.6     4.7    -      -       +      -
    161D  TRP*     3.6    11.0    -      -       -      -
    193D  SER*     4.7     4.7    -      -       -      -
    194D  SER      2.8    27.4    -      -       -      +
    195D  ARG*     4.0     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 147 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127D  VAL*     3.5    16.4    -      -       -      -
    128D  SER      3.6     7.2    -      -       -      -
    129D  LEU*     4.4     8.5    -      -       +      +
    146D  VAL*     1.3    86.5    -      -       -      +
    148D  LEU*     1.3    76.7    +      -       -      +
    159D  LEU*     3.4    11.7    -      -       -      +
    161D  TRP*     3.5    20.0    -      -       +      -
    193D  SER*     4.1     1.7    -      -       -      -
    194D  SER*     3.5    13.1    +      -       -      +
    212D  CYS*     2.0    50.3    -      -       +      -
    239D  ALA      4.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 148 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183C  TRP*     3.6    34.1    -      -       +      -
    126D  LYS      4.9     0.2    -      -       -      +
    127D  VAL*     3.0    22.5    -      -       -      +
    128D  SER*     3.3    39.4    +      -       -      +
    129D  LEU*     3.8     1.1    -      -       -      +
    130D  PHE*     3.6    36.1    -      -       +      +
    146D  VAL*     4.6     6.3    -      -       +      -
    147D  CYS*     1.3    88.9    -      -       -      +
    149D  ALA*     1.3    67.9    +      -       -      +
    150D  ARG*     3.9    21.1    -      -       +      +
    159D  LEU*     3.3    11.8    -      -       -      +
    192D  LEU      4.5     7.0    -      -       -      +
    193D  SER*     5.6     0.7    -      -       -      -
    214D  VAL*     3.4     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 149 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126D  LYS      3.8     8.9    +      -       -      -
    148D  LEU*     1.3    77.7    -      -       -      +
    150D  ARG*     1.3    62.4    +      -       -      +
    152D  PHE*     2.9    23.6    -      -       -      -
    157D  VAL*     4.1     8.9    -      -       +      +
    159D  LEU*     3.5    26.2    -      -       +      +
    190D  TYR      4.7     0.3    -      -       -      +
    191D  CYS      5.5     0.2    -      -       -      -
    192D  LEU*     4.2    10.7    +      -       +      +
    214D  VAL*     3.2    34.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 150 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183C  TRP*     3.2    42.5    -      -       +      +
    185C  ASN*     5.9     2.9    -      -       -      +
    126D  LYS*     3.0    21.1    +      -       -      +
    128D  SER*     5.1     5.5    +      -       -      -
    130D  PHE*     5.8     2.0    -      -       -      -
    148D  LEU*     3.9    17.9    -      -       +      +
    149D  ALA*     1.3    78.3    -      -       -      +
    151D  GLY*     1.3    65.9    +      -       -      +
    152D  PHE*     3.7     2.0    -      -       -      -
    181D  GLU*     3.8    25.0    +      -       -      -
    189D  SER*     5.9     1.3    -      -       -      -
    190D  TYR      2.8    25.8    -      -       -      +
    191D  CYS*     3.2    27.6    -      -       +      -
    192D  LEU      3.9     9.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 151 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123D  THR*     4.3     1.6    +      -       -      -
    124D  PRO      3.7     7.1    -      -       -      +
    126D  LYS*     3.7    22.7    -      -       -      +
    150D  ARG*     1.3    92.1    -      -       -      +
    152D  PHE*     1.3    70.6    +      -       -      +
    189D  SER*     4.2     9.4    -      -       -      -
    190D  TYR      3.6     2.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 152 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123D  THR*     2.9    30.3    -      -       -      +
    124D  PRO      3.0     7.2    -      -       -      +
    125D  PRO*     3.6    24.0    -      -       +      -
    149D  ALA      2.9    33.9    -      -       -      -
    150D  ARG*     3.7     4.7    -      -       -      -
    151D  GLY*     1.3    83.2    -      -       -      +
    153D  PHE*     1.3    53.7    +      -       -      +
    154D  PRO*     3.0    43.3    -      -       +      -
    155D  ASP*     5.1     2.2    -      -       -      -
    157D  VAL*     3.5    31.6    -      -       +      -
    187D  TYR      2.7    11.1    -      -       -      +
    189D  SER*     2.6    35.6    +      -       -      +
    190D  TYR*     3.9     8.9    +      -       +      -
    216D  PHE*     3.8     4.5    -      +       -      -
----------------------------------------------------------
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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