Contacts of the strand formed by residues 164 - 171 (chain A) in PDB entry 3B94


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 164 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  LYS*     3.6    14.8    -      -       -      -
     62A  PHE      3.3    15.9    -      -       -      +
     63A  GLY      3.6    12.6    -      -       -      -
     64A  PRO*     3.9    19.7    -      -       +      -
     85A  TRP*     4.2     5.2    -      -       -      -
     98A  TYR*     4.0    12.3    -      +       -      -
     99A  GLY*     3.3    20.4    -      -       -      -
    100A  GLN*     3.2    59.0    +      -       +      +
    136A  VAL*     5.2     0.5    -      -       -      +
    150A  LEU*     4.7     3.1    -      -       -      +
    162A  ASN*     5.3     4.3    -      -       -      -
    163A  THR*     1.4    82.8    -      -       -      +
    165A  TRP*     1.3    71.4    +      -       -      +
    140B  TYR*     5.1     0.9    -      -       -      -
    141B  GLU*     3.6    46.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 165 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  LYS*     3.5     4.7    -      -       -      +
     62A  PHE*     2.9    30.7    +      -       +      +
     69A  TRP*     3.6    17.8    -      +       -      -
     85A  TRP*     3.5    29.9    -      +       -      +
     87A  LEU*     2.8    36.1    -      -       +      -
     97A  ILE*     4.1    11.9    -      -       +      -
     98A  TYR      3.2    12.8    -      -       -      +
     99A  GLY*     4.5     0.7    -      -       -      -
    117A  LEU*     5.2     2.7    -      -       +      -
    136A  VAL*     5.4     4.9    -      -       +      -
    148A  ILE*     3.5    41.1    -      -       +      -
    149A  ASP      4.6     0.4    -      -       -      -
    150A  LEU*     3.0    47.6    -      -       +      +
    164A  TYR*     1.3    81.7    -      -       -      +
    166A  GLY*     1.3    87.6    +      -       -      +
    167A  ILE*     4.4    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 166 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  ALA      3.0    14.8    -      -       -      -
     61A  LYS*     3.8     3.8    -      -       -      -
     69A  TRP*     5.2     0.7    -      -       -      -
     97A  ILE*     3.5     7.8    -      -       -      +
     98A  TYR*     2.8    44.2    +      -       -      +
    165A  TRP*     1.3    82.6    -      -       -      +
    167A  ILE*     1.3    64.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 167 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  MET*     3.2     7.3    -      -       -      +
     60A  ALA*     2.8    52.2    +      -       +      +
     78A  CYS*     6.2     0.4    -      -       -      -
     79A  VAL*     4.3    13.5    -      -       +      -
     87A  LEU*     4.7     4.5    -      -       +      -
     89A  ILE*     4.3    19.7    -      -       +      -
     95A  TYR*     3.7    31.9    -      -       +      -
     96A  LEU      3.3    14.1    -      -       -      +
     97A  ILE*     4.0    19.5    -      -       +      -
     98A  TYR*     3.5     5.9    -      -       -      -
    142A  LEU*     4.5     2.7    -      -       +      -
    148A  ILE*     5.1     2.7    -      -       +      -
    165A  TRP*     4.4    15.0    -      -       +      -
    166A  GLY*     1.3    76.9    -      -       -      +
    168A  ILE*     1.3    62.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 168 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57A  PRO*     3.1    35.0    -      -       +      -
     58A  CYS      3.7     6.3    -      -       -      +
     59A  MET*     3.9     8.7    -      -       +      -
     95A  TYR*     3.3     7.9    -      -       -      -
     96A  LEU*     2.8    56.7    +      -       +      +
     98A  TYR*     5.2     1.1    -      -       +      -
    167A  ILE*     1.3    74.6    -      -       -      +
    169A  LEU*     1.3    68.7    +      -       -      +
    170A  LEU*     3.9    12.5    +      -       +      -
     94B  LEU*     4.3    20.6    -      -       +      -
    170B  LEU*     4.6    10.5    -      -       +      +
    171B  ALA*     3.9    20.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 169 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57A  PRO*     3.9    18.4    -      -       +      +
     58A  CYS*     3.3    33.1    +      -       +      +
     78A  CYS*     4.2    12.8    -      -       +      -
     91A  GLN*     4.3    15.3    -      -       -      +
     92A  ASN      4.7     2.9    -      -       -      +
     93A  GLY*     4.1     8.3    -      -       -      -
     94A  LEU      3.7     9.9    -      -       -      +
     95A  TYR*     3.4    36.3    -      -       +      +
    168A  ILE*     1.3    77.6    -      -       -      +
    170A  LEU*     1.3    60.8    +      -       -      +
    171A  ALA*     3.8    23.1    -      -       -      +
    172A  ASN*     4.9     0.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 170 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  LEU*     2.8    43.5    +      -       +      +
     95A  TYR      4.6     0.4    -      -       -      -
     96A  LEU*     4.1    24.7    -      -       +      +
    139A  THR*     4.5     3.6    -      -       +      -
    168A  ILE*     4.3    24.0    -      -       +      -
    169A  LEU*     1.3    77.0    -      -       -      +
    171A  ALA*     1.3    65.6    +      -       +      +
    170B  LEU*     5.5     8.5    -      -       +      -
     57C  PRO*     5.8     0.3    -      -       -      +
     96C  LEU*     4.1    26.0    -      -       +      -
    168C  ILE*     4.7     7.9    -      -       +      +
    170C  LEU*     5.1    11.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 171 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  GLY*     3.6     2.6    -      -       -      -
     94A  LEU*     2.9    27.7    +      -       +      -
    169A  LEU*     3.5    12.2    -      -       -      +
    170A  LEU*     1.3    86.6    -      -       +      +
    172A  ASN*     1.3    60.6    +      -       -      +
    173A  PRO*     3.5     2.2    -      -       -      +
     57C  PRO*     4.6    17.9    -      -       +      -
     59C  MET*     4.0    25.6    -      -       -      -
    168C  ILE*     4.8     6.1    -      -       +      -
----------------------------------------------------------
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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