Contacts of the strand formed by residues 496 - 501 (chain A) in PDB entry 3GEB


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 496 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    267A  MET*     4.2    17.9    -      -       +      -
    268A  GLU      2.8    20.2    +      -       -      +
    269A  ARG*     3.2    41.4    -      -       +      +
    270A  VAL      3.1    19.8    +      -       -      +
    494A  LYS      4.9     3.4    -      -       -      +
    495A  ALA*     1.3    73.1    -      -       -      +
    497A  TYR*     1.3    63.5    +      -       -      +
    498A  VAL*     3.9     2.2    +      -       +      +
    516A  PRO*     6.0     3.1    -      -       +      -
    269D  ARG*     3.2    31.2    -      -       -      +
    537D  TYR      5.5     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 497 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    270A  VAL*     3.4    33.9    -      -       +      +
    272A  VAL*     4.6    11.7    -      -       +      -
    487A  ILE*     4.2     5.4    -      -       +      -
    488A  MET*     3.4    49.6    +      -       +      -
    491A  PHE*     3.0    26.2    +      -       +      +
    492A  GLY      2.6    33.5    +      -       -      -
    493A  ARG*     5.2     0.9    -      -       -      -
    495A  ALA*     3.4    20.4    -      -       +      -
    496A  VAL*     1.3    72.3    -      -       -      +
    498A  VAL*     1.3    60.9    +      -       -      +
    499A  VAL*     4.2     0.9    -      -       +      -
    515A  MET*     4.2    21.7    -      -       +      +
    516A  PRO*     2.9    34.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 498 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    269A  ARG*     4.5     9.4    -      -       +      +
    270A  VAL      3.0     6.5    +      -       -      +
    271A  PHE*     3.6    26.5    -      -       +      -
    272A  VAL*     2.9    27.9    +      -       -      +
    496A  VAL*     4.2     9.2    -      -       +      +
    497A  TYR*     1.3    78.9    -      -       -      +
    499A  VAL*     1.3    63.5    +      -       -      +
    500A  ILE*     3.7     9.1    +      -       +      +
    516A  PRO*     3.5    16.8    -      -       +      +
    517A  PHE      5.2     0.2    -      -       -      -
    518A  TRP*     4.3    21.3    -      -       +      +
    537D  TYR*     3.7    37.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 499 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    272A  VAL*     3.6    13.9    -      -       +      +
    484A  PHE*     3.9    21.5    -      -       +      -
    497A  TYR*     5.6     0.2    -      -       +      -
    498A  VAL*     1.3    72.9    -      -       -      +
    500A  ILE*     1.3    58.6    +      -       -      +
    506A  GLU*     3.8    19.1    -      -       +      +
    510A  ALA*     3.6    19.5    -      -       +      -
    515A  MET*     4.0    27.1    -      -       +      -
    516A  PRO      2.8    13.4    +      -       -      +
    517A  PHE*     3.1    28.8    -      -       +      -
    518A  TRP      2.6    33.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 500 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    271A  PHE*     3.8    25.6    -      -       +      -
    272A  VAL      3.1    11.4    +      -       -      +
    273A  TRP*     3.7    34.9    -      -       +      +
    274A  ASP*     3.1    24.9    +      -       -      +
    278A  THR*     4.1     1.1    -      -       +      -
    498A  VAL*     4.0    10.8    -      -       +      +
    499A  VAL*     1.3    80.3    -      -       -      +
    501A  GLY*     1.3    58.8    +      -       -      +
    506A  GLU*     4.9     0.9    -      -       -      +
    517A  PHE*     4.3     2.0    -      -       -      -
    518A  TRP*     3.4    16.6    -      -       +      +
    520A  ILE*     3.1    35.2    -      -       +      -
    529A  LEU*     3.5    27.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 501 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    274A  ASP*     3.9     0.7    -      -       -      -
    278A  THR*     3.3    14.6    -      -       -      -
    500A  ILE*     1.3    78.2    -      -       -      +
    502A  ASP*     1.3    59.9    +      -       -      -
    503A  GLY      3.7     0.4    -      -       -      -
    506A  GLU*     3.4    17.0    -      -       -      -
    517A  PHE*     3.5    10.7    -      -       -      -
    518A  TRP      3.3     6.1    +      -       -      -
    519A  ARG*     3.3     9.0    -      -       -      +
    520A  ILE*     2.9    23.0    +      -       -      -
----------------------------------------------------------
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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