Contacts of the strand formed by residues 22 - 28 (chain B) in PDB entry 3GBN


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 TYR 22 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  GLY      3.4     9.2    -      -       -      +
     17A  TYR*     4.6     0.7    -      -       +      -
    320A  LEU*     4.7     3.6    -      -       +      -
     17B  MET*     3.5     4.7    -      -       -      -
     20B  GLY      3.5     0.2    -      -       -      -
     21B  TRP*     1.3   100.0    -      -       +      +
     23B  GLY*     1.3    60.1    +      -       -      +
     36B  ALA*     3.6     4.2    -      -       -      +
     37B  ASP*     2.7    23.5    +      -       -      +
     40B  SER*     3.4    47.3    -      -       -      +
     41B  THR*     3.7     5.9    +      -       -      -
     44B  ALA*     3.3    12.1    -      -       +      +
    111B  HIS*     2.6    46.7    +      -       +      -
    114B  ASN*     2.9    35.2    +      -       +      -
    115B  VAL*     3.5    24.9    -      -       +      -
    118B  LEU*     4.0    10.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 23 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  ILE*     3.4     9.0    -      -       -      +
     16A  GLY      2.9    32.8    +      -       -      -
     14B  TRP*     3.9     1.6    -      -       -      -
     17B  MET*     3.4     9.7    -      -       -      -
     22B  TYR*     1.3    77.9    -      -       -      +
     24B  TYR*     1.3    67.7    +      -       -      -
     35B  ALA      3.4    10.5    -      -       -      -
     37B  ASP*     3.5     9.9    -      -       -      -
    118B  LEU*     4.0     3.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 24 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  ILE*     4.1    18.4    -      -       +      -
     14A  CYS      3.1     7.4    -      -       -      +
     15A  ILE*     3.5    29.8    -      -       +      -
     14B  TRP*     3.6     8.9    -      -       -      -
     17B  MET*     4.0     0.5    -      -       -      +
     23B  GLY*     1.3    72.1    -      -       -      -
     25B  HIS*     1.3    58.1    -      -       -      +
     34B  TYR*     3.2     7.6    -      -       -      +
     35B  ALA      2.8    42.6    +      -       -      +
     36B  ALA      4.5     1.1    -      -       -      -
     37B  ASP*     2.8    45.0    +      -       +      -
    118B  LEU*     3.6    16.5    -      -       +      +
    122B  VAL*     3.9    15.3    -      -       +      +
    152B  VAL*     4.6     1.4    +      -       +      -
    153B  ARG*     3.4    45.9    +      -       +      -
    181B  GOL      5.1     0.9    -      -       -      -
    182B   CL      3.6    16.4    -      -       +      -
    183B  EDO      3.7     3.5    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 25 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  THR*     5.5     1.2    +      -       -      -
     13A  ILE*     3.3     3.6    -      -       -      +
     14A  CYS*     2.7    49.7    +      -       +      +
     14B  TRP*     3.4    23.5    -      +       +      -
     24B  TYR*     1.3    73.5    -      -       -      +
     26B  HIS*     1.3    78.1    +      -       -      +
     27B  GLN*     4.8     5.8    -      -       +      -
     32B  SER*     4.0    12.4    -      -       -      -
     33B  GLY*     3.1    30.2    +      -       -      -
     34B  TYR*     3.4    35.5    +      +       +      -
    182B   CL      3.9     1.8    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 26 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  THR*     3.3    13.5    -      -       -      +
     13A  ILE*     4.5     3.4    -      -       +      -
     25B  HIS*     1.3    82.8    -      -       -      +
     27B  GLN*     1.3    62.2    +      -       -      +
     28B  ASN*     4.0    19.3    -      -       -      -
     31B  GLY      3.7    18.4    +      -       -      -
     32B  SER*     3.1    29.1    -      -       -      -
     33B  GLY*     3.0    32.9    +      -       -      -
     34B  TYR      6.0     0.2    -      -       -      -
    146B  ASP*     3.7    15.7    +      -       -      -
    149B  MET*     3.7    18.4    -      -       +      -
    153B  ARG*     3.4    15.8    +      -       -      +
    182B   CL      2.9    24.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 27 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  GLY      5.4     5.8    -      -       -      +
     11A  ASP*     3.2     6.9    -      -       -      +
     12A  THR*     3.0    42.7    +      -       -      +
     25B  HIS*     5.0     6.1    -      -       +      -
     26B  HIS*     1.3    76.1    -      -       -      +
     28B  ASN*     1.3    70.7    +      -       -      +
     31B  GLY      3.6     4.9    -      -       -      +
     32B  SER*     3.7    17.3    +      -       -      +
    149B  MET*     3.9     0.8    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 28 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  ASP*     3.4    10.5    -      -       -      -
     26B  HIS*     4.0     2.5    -      -       -      -
     27B  GLN*     1.3    83.6    +      -       -      +
     29B  GLU*     1.3    58.6    +      -       -      +
     30B  GLN*     3.1    13.5    +      -       -      +
     31B  GLY*     2.9    31.6    +      -       -      +
    144B  CYS      3.2    27.7    +      -       -      +
    145B  ASP      3.5     7.1    -      -       -      -
    146B  ASP*     3.0    23.0    +      -       -      +
    149B  MET*     3.8    11.5    -      -       +      +
    185B  EDO      3.3    19.1    +      -       -      +
----------------------------------------------------------
 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