Contacts of the strand formed by residues 624 - 628 (chain A) in PDB entry 3QER


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 SER 624 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    409A  SER*     6.1     0.4    -      -       -      -
    410A  PHE      3.2    11.0    -      -       -      -
    411A  ASP*     4.0    13.7    -      -       -      -
    594A  LEU*     3.2     9.1    -      -       -      +
    620A  GLY*     3.0    19.1    -      -       -      -
    621A  ASP*     3.3    23.4    +      -       -      +
    623A  ASP*     1.3    80.3    -      -       -      +
    625A  ILE*     1.3    63.4    +      -       -      +
    626A  TYR*     3.6    23.3    +      -       -      -
    683A  MET*     4.4     0.4    -      -       -      -
    686A  GLU*     5.8     2.0    -      -       -      -
    906A   CA      4.0     4.9    -      -       -      -
    115P  DOC      5.3     3.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 625 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    408A  MET      4.1     0.7    -      -       -      +
    409A  SER*     3.2     5.5    -      -       -      -
    410A  PHE*     2.9    57.6    +      -       +      +
    594A  LEU*     3.6    21.1    -      -       +      +
    597A  ILE*     4.3    13.2    -      -       +      -
    598A  GLU*     4.7     5.8    -      -       +      -
    601A  VAL*     3.8    31.6    -      -       +      -
    617A  VAL*     4.0    20.9    -      -       +      -
    619A  TYR      3.5     4.5    -      -       -      +
    620A  GLY*     5.0     0.7    -      -       -      -
    624A  SER*     1.3    78.1    -      -       -      +
    626A  TYR*     1.3    64.1    +      -       -      +
    627A  VAL*     3.8    19.3    -      -       +      -
    663A  ILE*     4.7     0.7    -      -       +      -
    683A  MET*     4.0    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 626 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    407A  VAL*     3.9     9.2    -      -       +      -
    408A  MET      3.8     1.6    -      -       -      -
    409A  SER*     3.5    24.2    -      -       -      -
    617A  VAL*     3.4     2.8    -      -       -      -
    618A  LEU*     2.8    39.1    +      -       +      +
    619A  TYR*     2.8    40.5    +      +       +      +
    624A  SER*     3.6    27.7    +      -       -      -
    625A  ILE*     1.3    75.2    -      -       -      +
    627A  VAL*     1.3    62.3    +      -       -      +
    686A  GLU*     4.5     7.3    +      -       -      -
    687A  ALA*     5.8     0.2    -      -       +      -
    702A  TRP*     3.6    30.3    -      +       +      -
    708A  TYR*     2.7    32.5    +      +       -      -
    710A  LEU*     3.9    17.9    -      -       +      -
    726A  LYS*     4.1    11.3    -      -       -      -
    115P  DOC      4.2     2.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 627 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    407A  VAL*     3.3     2.8    -      -       -      +
    408A  MET*     2.8    51.0    +      -       +      +
    410A  PHE*     4.1    11.9    -      -       +      -
    601A  VAL*     4.2    11.2    -      -       +      -
    605A  LEU*     3.5    29.4    -      -       +      -
    616A  PHE*     3.5    10.5    -      -       +      +
    617A  VAL*     4.4     4.0    -      -       +      -
    618A  LEU*     4.1     2.7    -      -       -      -
    625A  ILE*     3.8    27.6    -      -       +      -
    626A  TYR*     1.3    75.7    -      -       -      +
    628A  SER*     1.3    73.9    +      -       -      +
    629A  ALA*     3.3     1.5    +      -       +      -
    632A  ILE*     5.1     5.2    -      -       +      -
    659A  MET*     4.2     6.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 628 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    404A  TYR*     4.8    11.3    -      -       -      +
    406A  TYR      3.5     6.4    +      -       -      -
    615A  ALA      5.1     3.6    -      -       -      -
    616A  PHE*     2.8    45.3    +      -       -      -
    618A  LEU*     3.7    19.3    -      -       -      +
    627A  VAL*     1.3    73.1    -      -       -      +
    629A  ALA*     1.3    59.6    +      -       -      +
    630A  ASP*     3.4    25.6    +      -       -      +
    631A  LYS*     4.9     0.9    +      -       -      +
    632A  ILE*     4.7     0.7    -      -       -      +
----------------------------------------------------------
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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