Contacts of the strand formed by residues 116 - 122 (chain B) in PDB entry 3ZWG


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 TRP 116 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103B  LEU*     5.1     2.2    -      -       +      -
    104B  PHE*     3.5     0.3    -      -       -      -
    105B  SER*     2.8    45.3    +      -       -      +
    114B  SER*     2.9    41.5    +      -       -      +
    115B  ASN*     1.3    76.6    -      -       -      +
    117B  TRP*     1.3    63.9    +      -       -      +
    137B  TYR*     4.0    30.9    +      +       +      -
    142B  PRO*     3.5    42.0    -      -       +      -
    143B  PHE      3.3    22.4    -      -       -      -
    144B  ARG*     3.5    46.0    -      -       +      -
    145B  GLY      4.2     0.7    -      -       -      +
    164B  MET*     3.5     8.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 117 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103B  LEU*     3.2    15.9    -      -       -      +
    116B  TRP*     1.3    75.8    -      -       -      +
    118B  ASN*     1.3    69.5    +      -       -      +
    119B  VAL*     3.4    34.5    -      -       +      -
    142B  PRO*     3.2     4.8    -      -       -      +
    143B  PHE*     2.9    78.4    +      +       +      +
    144B  ARG      4.1     6.7    +      -       -      -
    150B  HIS*     3.7    16.2    -      +       +      -
    160B  SER*     5.0     3.4    -      -       -      -
    161B  ARG      4.5     0.2    -      -       -      -
    162B  GLY*     3.3    48.5    -      -       -      -
    164B  MET*     3.4    40.8    -      -       +      +
    172B  LEU*     3.7    17.3    -      -       +      -
    174B  ILE*     4.1    11.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 118 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101B  ALA      4.4     0.7    -      -       -      -
    102B  VAL*     3.3     6.2    -      -       -      +
    103B  LEU*     2.9    48.7    +      -       +      +
    117B  TRP*     1.3    76.9    -      -       -      +
    119B  VAL*     1.3    80.2    +      -       -      +
    120B  ARG*     4.9     0.4    -      -       -      -
    136B  LEU*     2.8    36.7    +      -       +      +
    140B  ARG*     3.7    21.0    +      -       -      +
    142B  PRO*     3.6    18.8    -      -       +      +
    143B  PHE*     4.6     2.8    -      -       -      -
    152B  ARG*     3.4    21.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 119 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100B  LEU*     4.1    14.1    -      -       +      -
    101B  ALA      3.5     6.1    -      -       -      +
    102B  VAL*     4.2     6.7    -      -       +      -
    117B  TRP*     3.4    28.3    -      -       +      -
    118B  ASN*     1.3    90.5    +      -       -      +
    120B  ARG*     1.3    66.2    +      -       -      +
    143B  PHE*     5.1     2.4    -      -       +      -
    152B  ARG*     4.2    10.9    +      -       -      -
    154B  LEU*     3.3    25.0    -      -       +      +
    160B  SER*     3.7    27.7    +      -       -      +
    174B  ILE*     3.8    23.8    -      -       +      -
    176B  VAL*     4.6     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 120 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99B  THR      3.8     0.2    -      -       -      +
    100B  LEU*     3.9     2.6    -      -       -      +
    101B  ALA*     3.0    33.4    +      -       -      +
    118B  ASN*     4.3     1.4    +      -       -      +
    119B  VAL*     1.3    77.5    +      -       -      +
    121B  VAL*     1.3    76.2    +      -       -      +
    122B  TYR*     3.9    22.2    -      -       +      -
    136B  LEU*     3.6    22.9    -      -       +      +
    140B  ARG*     2.9    62.3    +      -       -      +
    152B  ARG*     2.5    43.8    -      -       -      +
    153B  GLY      4.8     6.3    +      -       -      -
    154B  LEU*     3.9    10.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 121 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94B  MET*     4.0    16.6    -      -       +      -
     98B  ASN*     4.2     1.6    -      -       +      -
     99B  THR      3.4     8.5    -      -       -      +
    100B  LEU*     4.0    11.4    -      -       +      -
    120B  ARG*     1.3    87.8    -      -       -      +
    122B  TYR*     1.3    70.5    +      -       -      +
    154B  LEU*     3.6    44.0    +      -       +      +
    156B  TYR*     3.3    45.2    +      -       +      -
    158B  LEU*     4.5    11.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 122 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98B  ASN*     3.1     7.8    -      -       -      +
     99B  THR*     2.8    44.8    +      -       +      +
    101B  ALA*     3.9    28.0    -      -       +      -
    120B  ARG*     3.9    18.0    -      -       +      +
    121B  VAL*     1.3    78.8    -      -       -      +
    123B  LYS*     1.3    61.7    +      -       -      +
    126B  LYS*     3.9    33.7    -      -       +      -
    132B  MET*     4.0    21.6    -      -       +      +
    135B  GLU*     2.6    41.2    +      -       -      +
    136B  LEU*     3.8    15.6    -      -       +      +
    140B  ARG*     4.3    20.2    +      -       -      -
    156B  TYR*     4.5     0.9    -      -       -      -
----------------------------------------------------------
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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