Contacts of the strand formed by residues 120 - 124 (chain A) in PDB entry 3QPV


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 120 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  THR*     3.3    20.6    -      -       +      +
     37A  ILE*     3.6    31.9    -      -       +      -
     58A  LEU*     4.5     8.5    -      -       +      -
     63A  VAL*     3.7    14.1    -      -       +      -
     64A  PRO      2.9     3.0    +      -       -      -
     65A  THR*     3.1    31.7    -      -       +      +
     66A  LYS      3.0    23.6    +      -       -      -
    112A  TYR*     3.4     4.9    -      -       -      -
    113A  LEU*     3.9     2.7    -      -       -      -
    119A  GLN*     1.4    84.2    -      -       +      +
    121A  ALA*     1.3    66.3    +      -       -      +
    122A  VAL*     4.2     1.3    -      -       +      -
    230A  ILE*     4.0    33.9    -      -       +      -
    234A  ILE*     4.8     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 121 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  THR      2.8     6.5    +      -       -      -
     36A  VAL*     3.4     4.7    -      -       +      +
     37A  ILE*     2.7    34.1    +      -       -      +
     66A  LYS      3.5     4.5    -      -       -      -
     68A  PHE*     3.7    22.9    -      -       +      -
    109A  VAL*     3.8    26.7    -      -       +      -
    112A  TYR*     4.4     0.2    -      -       +      -
    113A  LEU*     3.9    16.6    -      -       +      +
    120A  ILE*     1.3    74.4    -      -       -      +
    122A  VAL*     1.3    56.8    +      -       -      +
    123A  PHE      3.7     0.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 122 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  ILE*     3.5    21.5    -      -       +      +
     39A  MET*     3.9    21.8    -      -       +      -
     51A  SER*     3.6    32.1    -      -       -      +
     54A  LEU*     5.2     7.2    -      -       +      -
     55A  THR*     3.6    22.7    -      -       -      +
     65A  THR*     4.0    13.0    -      -       +      -
     66A  LYS      2.8    13.0    +      -       -      +
     67A  VAL*     3.7     7.3    -      -       +      +
     68A  PHE*     2.8    31.3    +      -       -      -
    120A  ILE*     4.4     3.6    -      -       +      -
    121A  ALA*     1.3    75.8    -      -       -      +
    123A  PHE*     1.3    60.3    +      -       -      +
    124A  ASP      3.4     3.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 123 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  VAL*     4.2    15.5    -      -       +      -
     37A  ILE      2.6    16.0    +      -       -      +
     38A  VAL*     4.5     2.5    -      -       +      -
     39A  MET*     3.0    27.4    +      -       -      -
     68A  PHE*     3.9     5.4    -      -       +      -
     70A  VAL*     3.6    21.3    -      -       +      -
    102A  ALA*     3.9    18.4    -      -       +      -
    105A  ALA*     3.6    26.7    -      -       +      -
    106A  LEU*     3.7    29.2    -      -       +      -
    109A  VAL*     4.3    12.3    -      -       +      -
    121A  ALA      3.7     0.8    +      -       -      -
    122A  VAL*     1.3    69.1    -      -       -      +
    124A  ASP*     1.3    59.9    +      -       -      +
    125A  ALA*     4.4     0.7    -      -       +      -
    127A  ASN*     3.4    36.7    +      -       -      -
    132A  ARG*     4.5     3.6    -      -       -      -
    136A  ILE*     3.4    30.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 124 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  MET*     3.8     9.0    -      -       +      +
     47A  LYS*     3.9    15.8    -      -       -      +
     48A  THR*     2.8    32.4    +      -       -      +
     51A  SER*     3.5    24.3    +      -       -      +
     67A  VAL*     4.1    11.7    -      -       +      +
     68A  PHE      2.8    15.5    +      -       -      +
     69A  ASN*     3.1    21.9    -      -       -      +
     70A  VAL*     3.1    26.1    +      -       -      +
     71A  GLY      4.7     0.7    +      -       -      -
    122A  VAL      4.3     1.1    -      -       -      +
    123A  PHE*     1.3    69.1    -      -       -      +
    125A  ALA*     1.3    62.6    +      -       -      +
    524A  FDP      5.0     3.1    +      -       -      -
    700A  ADP      4.8     0.3    +      -       -      -
----------------------------------------------------------
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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