Contacts of the strand formed by residues 135 - 139 (chain B) in PDB entry 3SN6


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 135 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93B  ILE*     6.0     0.6    -      -       +      +
     96B  ARG*     5.5    12.1    -      -       +      +
    122B  SER*     4.6     2.5    -      -       -      +
    123B  ILE      4.1     3.6    -      -       -      +
    124B  TYR*     3.3    35.8    -      -       +      +
    134B  ARG*     1.3    99.5    +      -       +      +
    136B  SER*     1.3    65.1    +      -       -      +
    137B  ARG      4.2     7.2    -      -       -      +
    138B  GLU*     4.3    28.0    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 136 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111B  TYR*     4.3     6.5    -      -       -      -
    123B  ILE*     2.5    43.1    +      -       -      +
    125B  ASN*     3.7    27.6    -      -       -      -
    134B  ARG      3.0     3.4    +      -       -      -
    135B  VAL*     1.3    76.9    -      -       -      +
    137B  ARG*     1.3    69.8    +      -       -      +
    171B  ILE*     5.0     1.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 137 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121B  CYS      3.6     0.9    -      -       -      +
    123B  ILE*     2.9    34.0    +      -       -      +
    135B  VAL*     4.3     2.7    -      -       -      -
    136B  SER*     1.3    87.9    +      -       -      +
    138B  GLU*     1.3    66.0    +      -       -      +
    139B  LEU*     3.9    12.1    +      -       +      +
    171B  ILE*     3.0    40.9    +      -       +      +
    172B  GLU*     3.7    12.1    +      -       -      +
    173B  THR      3.8    14.6    +      -       -      -
    174B  GLY*     3.4    13.3    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 138 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96B  ARG*     5.7     5.5    -      -       -      +
    120B  ILE*     3.7    30.7    -      -       +      +
    121B  CYS      3.4     3.8    -      -       -      -
    122B  SER*     4.0    18.4    +      -       -      +
    135B  VAL*     4.3    14.8    -      -       +      +
    137B  ARG*     1.3    80.5    +      -       -      +
    139B  LEU*     1.3    63.7    +      -       -      +
    140B  ALA      3.8     2.5    +      -       -      +
    174B  GLY      5.5     0.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 139 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119B  ASN      4.4     0.5    -      -       -      +
    120B  ILE*     3.3     2.7    -      -       -      +
    121B  CYS*     2.9    48.3    +      -       +      +
    123B  ILE*     4.6     7.0    -      -       +      -
    137B  ARG*     3.9    22.2    -      -       +      +
    138B  GLU*     1.3    72.5    -      -       -      +
    140B  ALA*     1.3    59.3    +      -       -      +
    141B  GLY      4.0     1.3    +      -       -      -
    142B  HIS*     5.7     1.7    -      -       -      -
    157B  ILE*     3.8    18.6    -      -       +      -
    169B  TRP*     3.5    51.2    -      -       +      -
    170B  ASP      4.6     0.2    -      -       -      +
    171B  ILE*     4.2    12.1    -      -       +      +
    174B  GLY*     3.7    33.7    -      -       -      +
----------------------------------------------------------
 Back to top of page


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