Contacts of the strand formed by residues 180 - 182 (chain A) in PDB entry 1Q62


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 ILE 180 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101A  PRO      4.5     1.2    -      -       -      +
    102A  PHE*     3.5    27.0    -      -       +      +
    128A  MET*     3.6    17.0    -      -       +      -
    146A  TYR*     3.5    38.6    -      -       +      +
    149A  GLN*     3.0    19.7    +      -       +      +
    150A  ILE*     4.1    12.1    -      -       +      -
    172A  LEU*     4.0    23.6    -      -       +      -
    173A  MET      3.3     4.3    -      -       -      +
    174A  ILE*     3.5    29.2    -      -       +      -
    175A  ASP*     5.2     0.2    -      -       -      -
    179A  TYR*     1.3    74.3    -      -       -      +
    181A  GLN*     1.3    73.3    +      -       -      +
    182A  VAL*     4.1     5.2    -      -       +      +
    308A  ARG*     4.8     2.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 181 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101A  PRO      6.0     0.4    -      -       -      +
    102A  PHE*     3.6     4.5    -      -       -      -
    103A  LEU      4.4     1.6    -      -       -      -
    104A  VAL*     3.0    47.5    -      -       +      +
    121A  GLU*     3.8    28.4    +      -       -      +
    122A  TYR      4.6     0.6    -      -       -      -
    123A  ALA*     3.4    32.2    +      -       +      +
    171A  ASN      3.6     0.9    -      -       -      +
    172A  LEU*     3.7     0.7    -      -       -      -
    173A  MET*     2.8    43.8    +      -       +      +
    175A  ASP*     4.9     9.7    -      -       +      +
    179A  TYR      5.1     1.3    -      -       -      +
    180A  ILE*     1.3    77.2    -      -       -      +
    182A  VAL*     1.3    60.1    +      -       -      +
    183A  THR*     3.3    15.1    +      -       -      +
    308A  ARG*     6.3     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 182 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102A  PHE*     2.8    21.7    +      -       +      +
    103A  LEU*     3.7     9.5    -      -       +      -
    104A  VAL*     2.9    24.8    +      -       -      +
    150A  ILE*     4.3    13.0    -      -       +      -
    153A  THR*     4.1    21.5    -      -       +      +
    154A  PHE*     6.2     2.7    -      -       +      -
    157A  LEU*     5.9     0.2    -      -       +      -
    164A  TYR*     3.4    44.0    -      -       +      +
    167A  LEU*     5.8     1.3    -      -       +      -
    171A  ASN      3.9     3.6    -      -       -      -
    172A  LEU*     3.9    20.4    -      -       +      -
    180A  ILE*     4.4     2.7    -      -       +      -
    181A  GLN*     1.3    69.0    -      -       -      +
    183A  THR*     1.3    59.9    +      -       -      +
    185A  PHE*     3.9    10.5    -      -       +      -
----------------------------------------------------------
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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