Contacts of the strand formed by residues 116 - 120 (chain B) in PDB entry 3GSB


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 MET 116 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  GLN      4.3     7.2    -      -       -      +
     21A  LYS*     3.9    22.0    -      -       -      +
     22A  LEU      3.3    22.0    -      -       -      +
     23A  MET*     3.9     7.4    -      -       -      +
     24A  PRO*     4.0    21.8    -      -       +      -
    108B  ASN*     4.1     1.6    -      -       -      +
    114B  ILE*     3.5     1.0    -      -       -      +
    115B  GLU*     1.3    80.6    -      -       -      +
    117B  VAL*     1.3    62.7    +      -       -      +
    285B  GLY*     3.0    23.0    -      -       -      -
    286B  GLY      3.3     6.3    +      -       -      +
    288B  ARG*     3.5    37.0    -      -       +      +
    291B  MET*     3.5    27.9    -      -       +      +
    292B  GLN*     3.8    20.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 117 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  LEU      3.2     5.9    +      -       -      +
     23A  MET*     3.4    27.0    -      -       -      +
     24A  PRO*     3.4     4.0    -      -       -      +
    104B  ALA*     3.9    28.0    -      -       +      +
    107B  VAL*     3.8    18.4    -      -       +      -
    108B  ASN*     3.6    13.9    -      -       -      +
    114B  ILE*     3.2    34.8    -      -       +      -
    116B  MET*     1.3    70.1    -      -       -      +
    118B  ARG*     1.3    64.1    +      -       -      +
    119B  PHE*     4.3    14.6    -      -       +      -
    283B  ALA*     5.2     5.6    -      -       +      -
    284B  TYR      3.6     6.3    -      -       -      +
    285B  GLY*     4.1     4.3    -      -       -      +
    291B  MET*     4.2     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 118 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  MET*     5.4     1.8    -      -       -      +
     24A  PRO*     3.2    34.1    +      -       +      +
     27A  VAL*     2.9    29.2    +      -       -      +
     28A  SER*     3.5    24.4    +      -       -      +
     30A  PRO*     4.2     2.6    -      -       -      +
    117B  VAL*     1.3    76.4    -      -       -      +
    119B  PHE*     1.3    70.7    +      -       -      +
    283B  ALA*     3.2     3.9    -      -       -      -
    284B  TYR*     3.0    58.4    +      -       +      +
    291B  MET*     4.2     6.1    -      -       +      -
    294B  VAL*     3.8     7.9    -      -       +      +
    295B  ALA      3.3    24.8    +      -       -      -
    296B  PRO*     4.3     2.0    -      -       -      +
    302B  GLN*     2.9    50.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 119 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  MET*     4.5     9.9    -      -       -      -
     28A  SER*     3.9    21.3    +      -       -      +
    100B  GLU*     3.7    13.2    -      -       +      -
    103B  LEU*     3.6    29.2    -      -       +      -
    104B  ALA*     3.7    25.6    -      -       +      -
    107B  VAL*     4.9     3.8    -      -       +      -
    117B  VAL*     4.3    11.4    -      -       +      -
    118B  ARG*     1.3    86.8    -      -       -      +
    120B  VAL*     1.3    66.8    +      -       -      +
    275B  ILE*     4.0    16.2    -      -       +      -
    281B  VAL*     5.3     5.6    -      -       +      -
    282B  GLY      3.5     5.2    -      -       -      +
    283B  ALA*     3.6    17.3    -      -       +      -
    302B  GLN*     4.7     0.2    +      -       -      -
    307B  SER*     3.8    14.6    +      -       -      -
    308B  GLY*     4.4    11.7    -      -       -      +
    313B  MET*     3.3    29.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 120 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118B  ARG*     4.3     0.2    -      -       +      -
    119B  PHE*     1.3    80.8    -      -       -      +
    121B  ASN*     1.3    69.4    +      -       -      +
    122B  SER      3.3    22.7    -      -       -      +
    125B  GLU*     3.5    15.0    -      -       +      +
    126B  ALA*     3.7    13.5    -      -       +      +
    281B  VAL*     3.6     5.5    -      -       -      +
    282B  GLY      2.7    36.9    +      -       -      +
    283B  ALA*     3.8     3.6    -      -       -      +
    284B  TYR*     3.7    23.6    -      -       +      -
    302B  GLN*     3.5    25.6    -      -       +      +
    307B  SER*     3.8    10.5    -      -       -      -
    308B  GLY      5.4     0.7    +      -       -      -
----------------------------------------------------------
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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