Contacts of the strand formed by residues 164 - 169 (chain A) in PDB entry 3I7L


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 164 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  GLU      4.2     2.3    -      -       -      +
    118A  THR*     3.5     7.6    +      -       -      +
    121A  ILE*     5.3     0.9    -      -       +      -
    134A  ARG*     3.0    39.0    +      -       +      +
    137A  ASP*     5.0     0.4    +      -       -      -
    159A  LEU*     4.3    16.6    -      -       +      -
    161A  GLU      3.9    16.6    -      -       -      +
    162A  LEU      4.0     1.0    -      -       -      -
    163A  HIS*     1.3    80.0    +      -       -      +
    165A  ILE*     1.3    62.9    +      -       -      +
    166A  ASP*     3.7     7.4    -      -       -      +
    167A  VAL*     3.3    33.0    -      -       +      -
    180A  PHE*     3.7    26.2    -      -       +      -
    181A  VAL      3.7    11.7    -      -       -      +
    182A  TYR*     4.2     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 165 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  GLU*     5.8     0.9    -      -       -      +
    118A  THR*     3.5    31.9    +      -       +      +
    121A  ILE*     4.0     6.4    -      -       -      +
    163A  HIS*     3.9    15.5    -      -       +      -
    164A  VAL*     1.3    72.8    -      -       -      +
    166A  ASP*     1.3    60.2    +      -       +      +
    181A  VAL*     3.0    19.0    +      -       +      +
    182A  TYR      4.2     2.2    -      -       -      -
    183A  GLN*     3.8    26.2    -      -       +      +
    188A  ARG*     3.4    44.2    -      -       -      +
    216A  ALA      3.8     4.0    -      -       -      +
    217A  SER*     3.4    42.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 166 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121A  ILE*     4.0    16.4    -      -       -      +
    164A  VAL*     3.7     1.0    -      -       -      +
    165A  ILE*     1.3    81.9    -      -       +      +
    167A  VAL*     1.3    77.7    +      -       -      +
    168A  LYS*     3.0    17.9    +      -       -      -
    180A  PHE*     3.1    25.8    -      -       -      +
    181A  VAL      3.2     6.7    +      -       -      +
    217A  SER      3.5    15.7    -      -       -      +
    218A  MET*     3.6    13.6    -      -       -      +
    219A  VAL*     2.9    35.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 167 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121A  ILE*     4.2    14.6    -      -       +      +
    123A  ILE*     3.7    30.3    -      -       +      +
    134A  ARG*     5.4     8.7    -      -       +      -
    140A  PHE*     5.0     8.1    -      -       +      -
    159A  LEU*     6.3     1.8    -      -       +      -
    164A  VAL*     3.3    23.1    -      -       +      -
    166A  ASP*     1.3    82.6    +      -       -      +
    168A  LYS*     1.3    77.5    +      -       -      +
    178A  ILE*     3.2    33.7    -      -       +      -
    179A  CYS      3.3     5.6    -      -       -      +
    180A  PHE*     3.2    19.5    -      -       +      -
    219A  VAL*     4.9     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 168 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121A  ILE*     6.0     0.4    -      -       -      -
    123A  ILE*     3.8    22.0    -      -       +      -
    166A  ASP*     3.0    27.5    +      -       -      -
    167A  VAL*     1.3    80.5    -      -       -      +
    169A  PHE*     1.3    67.1    +      -       -      +
    178A  ILE*     3.4     1.8    -      -       -      -
    179A  CYS*     2.8    35.8    +      -       +      +
    219A  VAL*     2.3    51.1    +      -       +      +
    220A  ILE*     5.0     0.7    -      -       -      -
    221A  ALA*     4.0    19.1    -      -       +      +
    261A  HIS*     4.4    15.1    +      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 169 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123A  ILE*     3.5    40.1    -      -       +      +
    124A  ILE      3.6     5.2    -      -       -      +
    125A  ASP*     3.3    44.9    -      -       +      -
    126A  PRO*     3.8    10.9    -      -       +      +
    130A  MET*     3.4    35.2    -      -       +      -
    132A  GLY*     3.7    22.0    -      -       -      -
    140A  PHE*     4.3     9.0    -      +       -      -
    168A  LYS*     1.3    71.7    -      -       -      +
    170A  LEU*     1.3    61.9    +      -       -      +
    171A  TYR*     3.9     2.3    +      -       -      -
    176A  PRO*     4.4     3.8    -      -       +      -
    177A  THR      3.3    20.4    -      -       -      -
    178A  ILE*     4.2    14.6    -      -       +      -
    195A  VAL*     4.2     7.9    -      -       +      -
    221A  ALA*     3.3    19.2    -      -       -      +
----------------------------------------------------------
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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