Contacts of the strand formed by residues 460 - 468 (chain B) in PDB entry 3R2W


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 460 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    440B  ASP*     2.7    32.5    +      -       -      -
    458B  ASN      3.4     3.8    +      -       -      -
    459B  VAL*     1.3    74.0    -      -       -      +
    461B  LEU*     1.3    63.5    +      -       -      +
    462B  LYS*     4.6     7.6    -      -       -      +
    481B  ALA      2.8    10.2    +      -       -      +
    482B  VAL*     3.2    26.5    -      -       -      +
    483B  LEU*     2.8    28.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 461 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    435B  PHE*     5.9     0.4    -      -       +      -
    439B  PRO*     4.0    22.2    -      -       +      -
    440B  ASP*     3.1    15.8    +      -       -      +
    441B  MET*     3.1    31.0    -      -       -      +
    444B  LEU*     3.6    14.7    -      -       +      +
    447B  LEU*     3.8    34.3    -      -       +      -
    455B  PHE*     4.7    12.3    -      -       +      -
    459B  VAL*     4.1    16.2    -      -       +      -
    460B  SER*     1.3    75.8    +      -       -      +
    462B  LYS*     1.3    64.4    +      -       -      +
    465B  VAL*     3.9    26.9    -      -       +      -
    483B  LEU*     3.8    21.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 462 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    440B  ASP*     5.6     2.0    -      -       -      +
    443B  GLU*     3.2    56.9    +      -       +      +
    444B  LEU*     3.8     3.4    -      -       -      +
    460B  SER*     4.6     9.2    -      -       -      +
    461B  LEU*     1.3    78.0    -      -       -      +
    463B  GLY*     1.3    62.4    +      -       -      +
    465B  VAL*     4.1     2.4    -      -       -      +
    482B  VAL*     3.8    24.6    -      -       -      +
    483B  LEU      2.9    24.5    +      -       -      +
    484B  GLU*     3.2    31.7    -      -       +      +
    485B  ASN      3.4     1.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 463 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    443B  GLU*     2.7    18.6    +      -       -      +
    444B  LEU*     3.7     3.5    -      -       -      +
    445B  ASP*     2.8    31.8    +      -       -      -
    446B  HIS      3.3     6.2    -      -       -      +
    462B  LYS*     1.3    74.7    -      -       -      +
    464B  THR*     1.3    59.6    +      -       -      -
    485B  ASN*     3.8    17.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 464 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    445B  ASP*     3.8    14.8    -      -       +      +
    446B  HIS*     3.3    37.2    -      -       +      +
    463B  GLY*     1.3    74.7    -      -       -      -
    465B  VAL*     1.3    58.9    +      -       -      +
    466B  ILE*     4.2     7.2    -      -       -      -
    485B  ASN*     2.9    49.1    +      -       -      +
    486B  LYS      3.1     4.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 465 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    444B  LEU*     5.0     1.6    -      -       +      -
    446B  HIS      3.1     7.7    +      -       -      +
    447B  LEU*     3.4    24.6    -      -       +      +
    448B  THR*     3.1    23.2    +      -       -      +
    461B  LEU*     3.9    21.8    -      -       +      -
    462B  LYS      4.1     4.9    -      -       -      +
    464B  THR*     1.3    77.8    -      -       -      +
    466B  ILE*     1.3    62.7    +      -       -      +
    467B  ILE*     3.9    20.2    -      -       +      -
    483B  LEU*     3.4    44.9    -      -       +      +
    485B  ASN      4.7     0.4    -      -       -      +
    486B  LYS      3.4     7.4    -      -       -      +
    488B  VAL*     5.7     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 466 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    446B  HIS*     5.4     4.3    -      -       +      +
    448B  THR*     3.5    28.0    -      -       +      +
    464B  THR*     5.4     4.7    -      -       -      -
    465B  VAL*     1.3    78.7    -      -       -      +
    467B  ILE*     1.3    58.0    +      -       -      +
    468B  ILE*     4.1    26.0    -      -       +      -
    486B  LYS      2.8    13.1    +      -       -      +
    487B  ILE*     3.3    26.2    -      -       +      -
    488B  VAL*     2.7    33.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 467 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    447B  LEU*     4.9     0.4    -      -       +      -
    448B  THR      2.8    10.8    +      -       -      +
    449B  VAL*     3.4    16.6    -      -       +      +
    450B  SER      3.1    26.2    +      -       -      +
    453B  VAL*     4.4     9.0    -      -       +      -
    455B  PHE*     3.5    39.9    -      -       +      -
    461B  LEU*     5.1     0.2    -      -       +      -
    465B  VAL*     3.9    22.4    -      -       +      -
    466B  ILE*     1.3    76.9    -      -       -      +
    468B  ILE*     1.3    63.1    +      -       -      +
    475B  ILE*     4.2    13.2    -      -       +      -
    477B  ILE*     4.0    15.3    -      -       +      -
    483B  LEU*     4.8     4.3    -      -       +      -
    488B  VAL*     3.4    31.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 468 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    448B  THR      5.3     1.1    -      -       -      +
    450B  SER*     3.4    22.7    -      -       -      +
    466B  ILE*     4.1    21.5    -      -       +      -
    467B  ILE*     1.3    78.8    -      -       -      +
    469B  ALA*     1.3    64.5    +      -       -      +
    470B  ASN*     3.9    20.1    +      -       -      +
    475B  ILE*     3.4     4.8    -      -       -      +
    487B  ILE*     6.2     2.0    -      -       +      -
    488B  VAL      2.9     8.9    +      -       -      +
    489B  SER*     3.3    29.2    -      -       -      -
    490B  GLY      3.8     1.6    +      -       -      -
----------------------------------------------------------
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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