Contacts of the strand formed by residues 135 - 145 (chain B) in PDB entry 4JZJ


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 THR 135 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150A  LYS*     4.7     9.0    -      -       -      -
    130B  GLN*     3.1    38.4    +      -       -      +
    131B  LEU*     3.2    17.0    -      -       -      +
    133B  SER*     3.6     7.8    +      -       -      +
    134B  GLY*     1.3    84.0    -      -       -      +
    136B  ALA*     1.3    61.8    +      -       -      +
    186B  THR*     6.4     1.3    -      -       -      -
    187B  LEU      3.7     4.3    -      -       -      +
    188B  SER*     4.2     2.7    -      -       -      +
    189B  LYS      3.7     9.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 136 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126B  PRO*     3.9     7.9    -      -       +      -
    130B  GLN*     4.1     1.6    -      -       -      -
    131B  LEU*     3.7    14.6    -      -       +      -
    135B  THR*     1.3    71.8    -      -       -      +
    137B  SER*     1.3    61.8    +      -       -      +
    138B  VAL*     4.9     1.6    -      -       +      -
    185B  LEU      3.9     0.6    -      -       -      +
    186B  THR*     3.3     4.9    -      -       -      +
    187B  LEU*     2.4    59.4    +      -       +      +
    188B  SER      4.1     1.6    -      -       -      +
    192B  TYR*     3.7    34.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 137 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131A  LEU*     5.9     1.6    -      -       -      +
    148A  LEU*     3.5    20.8    -      -       -      +
    150A  LYS*     3.1    28.6    +      -       -      -
    124B  PHE      4.5     0.2    -      -       -      +
    125B  PRO      4.1     0.9    -      -       -      -
    126B  PRO*     3.2    25.7    -      -       -      +
    130B  GLN*     3.1    24.3    +      -       -      -
    136B  ALA*     1.3    71.1    -      -       -      +
    138B  VAL*     1.3    62.8    +      -       -      +
    139B  VAL*     4.1     4.5    +      -       -      +
    184B  THR*     4.2     5.8    -      -       -      -
    185B  LEU      3.7     3.4    -      -       -      -
    186B  THR*     3.1    10.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 138 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123B  ILE*     4.5     0.9    -      -       +      -
    124B  PHE      3.5    15.9    -      -       -      +
    126B  PRO*     3.8    19.1    -      -       +      -
    136B  ALA*     4.9     2.7    -      -       +      +
    137B  SER*     1.3    80.3    -      -       -      +
    139B  VAL*     1.3    60.9    +      -       -      +
    154B  TRP*     3.2    33.6    -      -       +      -
    184B  THR*     4.6     0.4    -      -       -      +
    185B  LEU*     2.9    45.5    +      -       +      +
    187B  LEU*     5.3     3.4    -      -       +      -
    192B  TYR*     4.4    13.0    -      -       +      -
    198B  TYR*     4.9     6.5    -      -       +      -
    215B  PHE*     3.7    21.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 139 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131A  LEU*     3.9    32.3    -      -       +      -
    148A  LEU*     4.3    14.4    -      -       +      -
    186A  SER*     5.2     3.4    -      -       -      +
    188A  VAL*     5.7     2.2    -      -       +      -
    123B  ILE*     3.6     0.7    -      -       -      -
    124B  PHE*     3.0    53.4    +      -       +      +
    137B  SER      4.8     3.1    -      -       -      +
    138B  VAL*     1.3    78.1    -      -       -      +
    140B  CYS*     1.3    66.8    +      -       -      +
    141B  LEU*     5.0     2.9    -      -       +      -
    154B  TRP*     3.9     3.4    -      -       -      -
    182B  SER*     5.1     7.9    -      -       -      -
    183B  SER      3.3     9.6    -      -       -      +
    184B  THR*     3.8    23.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 140 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121B  VAL*     3.8    15.7    -      -       -      -
    122B  PHE      3.4     4.7    -      -       -      -
    123B  ILE*     4.5     1.6    -      -       -      +
    139B  VAL*     1.3    77.3    -      -       -      +
    141B  LEU*     1.3    65.9    +      -       -      +
    142B  LEU*     3.9    12.8    -      -       -      -
    152B  VAL*     4.4     3.4    -      -       +      -
    154B  TRP*     3.3    19.8    -      -       +      -
    182B  SER*     3.5     3.1    -      -       -      -
    183B  SER*     3.0    36.9    +      -       -      +
    200B  CYS*     2.0    46.7    -      -       +      -
    202B  VAL*     4.4     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 141 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144A  ALA*     4.4     8.3    -      -       +      -
    173A  PHE*     3.8    23.1    -      -       +      -
    188A  VAL*     3.8    33.4    -      -       +      -
    190A  THR*     5.8     1.1    -      -       +      -
    120B  SER      3.4     2.3    -      -       -      +
    121B  VAL*     3.2     8.1    -      -       -      +
    122B  PHE*     2.8    55.6    +      -       +      +
    124B  PHE*     4.2    17.5    -      -       +      -
    139B  VAL*     5.0     2.9    -      -       +      -
    140B  CYS*     1.3    77.2    -      -       -      +
    142B  LEU*     1.3    73.7    +      -       -      +
    143B  ASN*     4.3    13.7    -      -       +      +
    181B  LEU      3.4    14.8    -      -       -      +
    182B  SER*     5.0     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 142 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119B  PRO*     3.7    13.9    -      -       +      -
    120B  SER      3.8     3.6    -      -       -      -
    121B  VAL*     4.0     1.6    -      -       +      +
    140B  CYS*     3.9    12.3    -      -       -      -
    141B  LEU*     1.3    82.2    -      -       -      +
    143B  ASN*     1.3    58.7    +      -       -      +
    145B  PHE*     3.3    19.0    -      -       +      -
    150B  ALA*     4.1    18.8    -      -       +      -
    152B  VAL*     3.6    27.4    -      -       +      -
    180B  SER*     3.4     1.9    -      -       -      -
    181B  LEU*     2.8    51.4    +      -       +      +
    202B  VAL*     3.4    47.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 143 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169A  GLY      5.2     1.4    +      -       -      -
    171A  HIS*     3.1    17.0    -      -       -      -
    188A  VAL*     5.0     1.8    -      -       -      +
    190A  THR*     3.5    31.9    +      -       -      +
    118B  ALA      4.4     0.2    -      -       -      +
    119B  PRO*     3.4     2.8    -      -       -      +
    120B  SER*     3.1    41.4    +      -       -      +
    122B  PHE*     4.4     8.3    -      -       +      -
    141B  LEU*     4.3    15.4    -      -       +      +
    142B  LEU*     1.3    75.1    -      -       -      +
    144B  ASN*     1.3    89.0    +      -       -      +
    145B  PHE*     3.6     1.8    -      -       -      -
    180B  SER*     2.9    19.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 144 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171A  HIS*     3.3    16.5    +      -       -      -
    117B  ALA*     3.9    14.2    -      -       -      +
    118B  ALA      4.0     5.0    -      -       -      +
    143B  ASN*     1.3    97.8    +      -       -      +
    145B  PHE*     1.3    58.7    +      -       -      +
    173B  ASP*     6.1     0.2    -      -       -      -
    176B  ASP*     2.9    25.6    +      -       -      +
    178B  THR*     3.2    26.6    +      -       +      +
    179B  TYR      3.3     2.8    +      -       -      -
    180B  SER*     3.1     8.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 145 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117B  ALA*     3.3    15.0    -      -       -      +
    119B  PRO*     3.5    31.6    -      -       +      -
    142B  LEU*     3.3    35.0    -      -       +      -
    144B  ASN*     1.3    75.3    -      -       -      +
    146B  TYR*     1.3    62.6    +      -       -      +
    147B  PRO      3.2    20.0    -      -       -      -
    148B  ARG*     3.5    28.9    -      -       -      -
    150B  ALA*     4.2     9.9    -      -       +      -
    169B  VAL*     5.2     2.2    -      -       +      -
    178B  THR*     3.6     2.1    -      -       -      -
    179B  TYR*     3.0    47.4    +      -       +      -
    180B  SER      4.4     1.6    -      -       -      -
    181B  LEU*     3.5    30.5    -      -       +      -
    204B  HIS*     3.8     9.2    -      +       -      +
----------------------------------------------------------
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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