Contacts of the strand formed by residues 631 - 637 (chain B) in PDB entry 3U11


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 LYS 631 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    612B  ARG*     6.4     0.4    -      -       -      -
    614B  GLU*     3.3    28.1    +      -       -      -
    630B  LYS*     1.3    83.1    -      -       +      +
    632B  MET*     1.3    60.8    +      -       -      +
    633B  TYR*     3.6    31.0    +      -       +      +
    659B  GLY      3.7     1.2    -      -       -      +
    663B  LEU*     3.6     8.4    -      -       -      +
    669B  ARG*     2.9    32.4    +      -       -      +
    683B  SER*     4.0    18.6    -      -       -      -
    684B  LEU      3.4     7.6    -      -       -      +
    685B  SER*     4.4     9.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 632 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    631B  LYS*     1.3    74.0    -      -       -      +
    633B  TYR*     1.3    60.6    +      -       -      +
    634B  PHE*     3.5    25.1    -      -       +      -
    657B  TYR*     3.4    37.0    -      -       +      -
    658B  PHE      3.6    10.3    -      -       -      +
    659B  GLY      4.1     0.9    -      -       -      -
    660B  GLU*     3.8    19.5    -      -       +      +
    663B  LEU*     3.4    11.4    -      -       +      +
    682B  TYR      4.6     0.2    -      -       -      -
    683B  SER*     3.0     9.4    -      -       -      -
    684B  LEU*     2.5    64.1    +      -       +      +
    689B  PHE*     4.0    18.8    -      -       -      -
    703B  PHE*     3.7    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 633 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    614B  GLU*     3.9    20.6    +      -       -      -
    616B  PHE*     4.1     7.0    -      +       -      -
    622B  ILE*     3.5    31.4    +      -       +      +
    623B  ILE*     4.1    12.5    -      -       +      +
    631B  LYS*     3.6    38.7    +      -       +      +
    632B  MET*     1.3    78.5    -      -       -      +
    634B  PHE*     1.3    65.4    +      -       -      +
    657B  TYR*     3.1     7.8    -      -       -      +
    658B  PHE*     2.9    77.7    +      +       +      +
    669B  ARG*     4.5     2.8    +      -       -      -
    681B  LEU*     3.9    23.3    -      -       +      -
    682B  TYR      3.6     2.9    -      -       -      -
    683B  SER*     4.0    14.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 634 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    589B  LEU*     4.4    17.7    -      -       +      -
    593B  MET*     3.8    17.9    -      -       +      -
    595B  LEU*     4.3     8.3    -      -       +      -
    596B  PHE*     4.2    18.2    -      +       -      -
    607B  MET*     3.9    20.0    -      -       +      -
    611B  LEU*     4.1    17.3    -      -       +      -
    632B  MET*     3.5    26.2    -      -       +      -
    633B  TYR*     1.3    75.6    -      -       -      +
    635B  ILE*     1.3    63.5    +      -       -      +
    636B  GLN      3.3     0.9    +      -       -      -
    656B  SER      3.7     2.5    -      -       -      -
    657B  TYR*     3.7    24.7    -      +       +      -
    681B  LEU*     3.2     7.3    -      -       -      -
    682B  TYR*     2.8    50.2    +      -       +      +
    684B  LEU*     4.0    23.3    -      -       +      -
    703B  PHE*     4.9     2.2    -      +       -      -
----------------------------------------------------------
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Residues in contact with ILE 635 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    589B  LEU*     3.4     9.3    -      -       -      +
    634B  PHE*     1.3    70.5    -      -       -      +
    636B  GLN*     1.3    63.3    +      -       -      +
    637B  HIS      3.7    16.2    -      -       -      +
    638B  GLY      3.5    15.3    -      -       -      +
    640B  VAL*     4.7     6.7    -      -       +      -
    652B  LEU*     3.9    25.8    -      -       +      +
    653B  ALA      3.1    34.5    -      -       -      +
    654B  ASP      3.7     0.7    -      -       -      +
    655B  GLY*     3.1    20.1    +      -       -      -
    656B  SER      2.9    17.2    +      -       -      +
    658B  PHE*     3.6    36.1    -      -       +      -
    679B  CYS*     5.7     0.2    -      -       -      -
    681B  LEU*     3.7    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 636 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    585B  ASN      3.3    23.8    +      -       -      -
    586B  CSO      4.1    10.3    -      -       -      -
    588B  LYS*     3.8    37.1    -      -       +      +
    589B  LEU*     4.0    16.4    -      -       +      +
    592B  SER*     5.7     0.2    +      -       -      -
    613B  PHE*     4.4     8.7    -      -       -      -
    634B  PHE      3.3     4.2    +      -       -      -
    635B  ILE*     1.3    74.6    -      -       -      +
    637B  HIS*     1.3    64.9    +      -       +      +
    654B  ASP*     3.7    16.3    -      -       -      +
    655B  GLY      4.8     0.2    +      -       -      -
    680B  ARG*     2.8    28.6    +      -       +      +
    682B  TYR*     3.2    38.2    +      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 637 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    644A  THR*     6.4     0.7    -      -       +      -
    645A  LYS*     6.5     0.4    -      -       -      -
    714A  ILE      3.3    18.5    +      -       -      -
    715A  GLY      3.8     1.7    +      -       -      -
    716A  LYS*     3.2    44.5    -      -       +      +
    588B  LYS*     4.1    19.0    +      -       -      +
    635B  ILE*     3.4     7.8    -      -       -      +
    636B  GLN*     1.3    84.9    -      -       +      +
    638B  GLY*     1.3    77.1    +      -       -      +
    654B  ASP*     3.7     7.7    +      -       -      -
    678B  TYR*     4.3     9.4    -      -       +      -
    679B  CYS*     3.3     2.6    -      -       -      -
    680B  ARG*     2.7    56.0    +      -       +      +
----------------------------------------------------------
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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