Contacts of the strand formed by residues 93 - 101 (chain A) in PDB entry 3B93


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 GLY 93 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  GLN      3.4     1.2    +      -       -      -
     92A  ASN*     1.3    79.1    -      -       -      +
     94A  LEU*     1.3    61.5    +      -       -      -
     95A  TYR*     3.5    15.3    -      -       -      -
    141A  GLU*     3.4     3.1    -      -       -      -
    142A  LEU      2.7    38.0    +      -       -      -
    169A  LEU*     4.0     1.3    -      -       -      -
    171A  ALA      3.5     8.5    -      -       -      -
    172A  ASN*     4.0     7.1    -      -       -      +
    176A  ILE*     3.9    11.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 94 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  GLY*     1.3    70.5    -      -       -      -
     95A  TYR*     1.3    60.2    +      -       -      +
    139A  THR*     3.5    26.0    -      -       +      -
    140A  TYR      3.7    13.5    -      -       -      +
    141A  GLU*     4.1     4.0    -      -       +      +
    169A  LEU*     3.7     3.1    -      -       -      +
    170A  LEU*     2.8    59.4    +      -       +      -
    171A  ALA*     2.7    26.4    +      -       +      +
    173A  PRO*     4.5     7.9    -      -       +      -
    176A  ILE*     4.2     3.4    -      -       +      +
     59C  MET*     4.2    10.3    -      -       +      -
     98C  TYR*     3.8    35.9    -      -       +      +
    168C  ILE*     4.0    23.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 95 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  CYS*     3.3    24.6    +      -       +      +
     79A  VAL*     4.3    16.2    -      -       +      -
     89A  ILE*     4.1     7.2    -      -       +      -
     91A  GLN*     2.6    39.1    +      -       -      +
     93A  GLY*     3.5    25.4    -      -       -      -
     94A  LEU*     1.3    74.3    -      -       -      +
     96A  LEU*     1.3    61.5    +      -       -      +
     97A  ILE*     4.1     1.3    +      -       +      -
    138A  GLY      4.0     0.3    -      -       -      +
    139A  THR*     3.3     6.2    -      -       -      +
    140A  TYR*     2.8    34.6    +      -       -      +
    142A  LEU*     3.6    27.8    -      -       +      -
    167A  ILE*     3.7    31.0    -      -       +      -
    168A  ILE      3.2    14.6    -      -       -      +
    169A  LEU*     3.6    26.3    -      -       +      +
    170A  LEU*     4.4     0.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 96 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95A  TYR*     1.3    75.1    -      -       -      +
     97A  ILE*     1.3    88.6    +      -       -      +
     98A  TYR*     4.2     2.8    +      -       +      -
    138A  GLY*     3.5     9.4    -      -       -      +
    139A  THR*     3.7    16.2    -      -       -      +
    167A  ILE*     3.2     3.0    -      -       -      -
    168A  ILE*     2.8    50.4    +      -       +      +
    170A  LEU*     3.9    10.9    -      -       +      +
     96B  LEU*     4.0    14.4    -      -       +      -
    139B  THR*     3.5    24.0    -      -       +      +
    170B  LEU*     3.9    22.7    -      -       +      -
     96C  LEU*     3.9    18.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 97 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95A  TYR      5.0     2.0    -      -       -      +
     96A  LEU*     1.3    84.4    -      -       -      +
     98A  TYR*     1.4    63.4    +      -       -      +
    117A  LEU*     4.3    11.0    -      -       +      -
    124A  ILE*     4.6     7.0    -      -       +      -
    136A  VAL*     3.9     0.8    -      -       +      +
    137A  GLY*     3.2    16.3    -      -       -      -
    138A  GLY      2.6    35.3    +      -       -      +
    140A  TYR*     3.8    26.2    -      -       +      -
    142A  LEU*     4.7     4.9    -      -       +      -
    148A  ILE*     3.9    34.1    -      -       +      -
    165A  TRP*     3.8    17.9    -      -       +      -
    166A  GLY      3.4    11.0    -      -       -      +
    167A  ILE*     4.0    18.6    -      -       +      -
    139B  THR*     5.1     0.3    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 98 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  MET*     5.6     2.7    -      -       -      -
     60A  ALA      4.4     1.1    +      -       -      -
     61A  LYS*     4.2     2.6    -      -       -      +
     96A  LEU*     4.3     4.3    -      -       +      -
     97A  ILE*     1.4    77.4    -      -       -      +
     99A  GLY*     1.3    64.8    +      -       -      +
    136A  VAL      3.2    12.3    -      -       -      -
    164A  TYR*     4.3    11.0    -      +       -      -
    165A  TRP*     3.3     7.0    -      -       -      +
    166A  GLY*     2.8    61.3    +      -       -      +
    167A  ILE*     3.5    10.3    -      -       -      -
     94B  LEU*     3.8    36.5    -      -       +      +
    139B  THR*     3.7    30.3    -      -       +      +
    140B  TYR*     5.7     0.2    -      -       -      -
    141B  GLU*     2.9    40.6    +      -       +      -
    173B  PRO*     5.6     0.2    -      -       -      +
    175B  PHE*     4.0    17.8    -      -       -      -
    176B  ILE*     4.3     2.8    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 99 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98A  TYR*     1.3    88.5    -      -       -      +
    100A  GLN*     1.3    61.4    +      -       -      +
    135A  ASN*     3.2    14.6    -      -       -      +
    136A  VAL*     3.0    30.9    +      -       -      -
    164A  TYR*     3.3    16.2    -      -       -      -
    165A  TRP*     3.8     2.7    -      -       -      -
    139B  THR      5.2     2.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 100 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99A  GLY*     1.3    75.8    -      -       -      +
    101A  VAL*     1.3    61.4    +      -       -      +
    133A  ILE*     3.4    31.0    -      -       +      +
    134A  GLN      3.5     6.1    -      -       -      +
    135A  ASN*     5.0     6.9    +      -       -      +
    136A  VAL*     4.1     0.4    -      -       -      +
    162A  ASN*     2.9    42.5    +      -       -      +
    163A  THR*     3.3     6.4    -      -       -      +
    164A  TYR*     2.7    69.7    +      -       +      +
    119B  LYS*     5.9     2.8    -      -       -      +
    140B  TYR*     6.3     1.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 101 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100A  GLN*     1.3    79.0    -      -       -      +
    102A  ALA*     1.3    60.1    +      -       -      +
    103A  PRO*     3.1    23.8    -      -       +      +
    115A  VAL*     4.0    19.5    -      -       +      -
    127A  LEU*     3.5    25.8    -      -       +      -
    133A  ILE*     3.4     1.2    -      -       -      -
    134A  GLN      2.8    31.2    +      -       -      +
    136A  VAL*     3.6    24.6    -      -       +      +
    150A  LEU*     4.0    19.7    -      -       +      -
    152A  PHE*     5.4     0.2    -      -       +      -
    158A  VAL*     4.1    21.3    -      -       +      -
    163A  THR*     3.9     3.4    -      -       +      -
----------------------------------------------------------
 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