Contacts of the strand formed by residues 38 - 45 (chain B) in PDB entry 4OWW


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 VAL 38 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28B  ARG      4.1     0.9    -      -       -      +
     29B  VAL*     3.6     2.6    -      -       -      +
     30B  THR*     2.9    60.4    +      -       -      +
     31B  LYS      5.2     0.2    -      -       -      +
     32B  THR      5.0     5.8    -      -       -      +
     36B  HIS      5.0     2.9    -      -       -      +
     37B  GLU*     1.3    75.5    -      -       -      +
     39B  ARG*     1.3    70.9    +      -       -      +
     53B  SER*     4.3     7.4    -      -       -      +
     54B  VAL      3.4    11.2    -      -       -      +
     55B  TRP*     4.1    39.7    -      -       +      +
      7L    T      3.6    26.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 39 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26B  THR*     4.5    10.8    +      -       -      -
     27B  GLY      3.9    15.7    +      -       -      +
     28B  ARG      3.8    16.6    -      -       -      +
     29B  VAL*     3.3    46.3    -      -       -      +
     37B  GLU*     4.2     4.0    +      -       -      +
     38B  VAL*     1.3    79.3    -      -       -      +
     40B  THR*     1.3    63.1    +      -       -      +
     41B  CYS*     3.9    21.5    +      -       -      -
     52B  ILE      3.8     0.2    -      -       -      +
     53B  SER*     3.6     1.7    -      -       -      -
     54B  VAL*     2.9    32.5    +      -       +      +
     56B  ASP      4.8     1.8    +      -       -      -
     59B  GLY*     3.0    35.0    +      -       -      -
     60B  ASN*     2.7    31.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 40 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27B  GLY*     2.9    29.2    +      -       -      +
     28B  ARG      4.8     2.5    +      -       -      -
     39B  ARG*     1.3    72.3    -      -       -      +
     41B  CYS*     1.3    62.0    +      -       -      +
     42B  LYS      4.2     0.3    +      -       -      -
     51B  ASN*     4.1    27.6    -      -       +      +
     52B  ILE      3.4     8.7    -      -       -      +
     53B  SER*     3.4    24.5    -      -       -      +
     78B  PHE*     6.3     2.5    -      -       +      -
     83B  THR*     4.7     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 41 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23B  VAL*     4.5     3.8    -      -       +      -
     25B  GLU      3.2     8.7    -      -       -      +
     26B  THR*     3.6    25.8    -      -       +      -
     39B  ARG*     4.1    17.9    -      -       -      -
     40B  THR*     1.3    76.9    -      -       -      +
     42B  LYS*     1.3    60.9    +      -       -      +
     43B  VAL*     3.7     8.4    +      -       +      -
     51B  ASN*     3.4     5.8    -      -       -      -
     52B  ILE*     2.8    47.4    +      -       +      +
     54B  VAL*     4.3    15.0    -      -       -      -
     62B  ILE*     3.9    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 42 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23B  VAL*     3.6     0.7    -      -       -      -
     24B  LEU*     2.7    44.6    +      -       +      -
     25B  GLU*     2.8    51.4    +      -       +      +
     40B  THR      4.2     0.6    +      -       -      -
     41B  CYS*     1.3    72.1    -      -       -      +
     43B  VAL*     1.3    55.1    +      -       -      +
     49B  SER*     3.4    30.0    +      -       -      -
     50B  ILE      3.8     3.8    -      -       -      +
     51B  ASN*     4.4    12.7    +      -       -      +
    104B  GLU*     3.9    27.2    +      -       -      +
    107B  ASN*     3.7    25.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 43 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  VAL*     5.5     0.2    -      -       +      -
     21B  PHE*     3.3    50.5    -      -       +      -
     22B  ILE      3.3     5.4    -      -       -      +
     23B  VAL*     3.9    17.5    -      -       +      -
     24B  LEU*     4.6     1.1    -      -       -      -
     41B  CYS*     4.3     3.1    -      -       +      +
     42B  LYS*     1.3    78.6    -      -       -      +
     44B  ALA*     1.3    63.3    +      -       -      +
     49B  SER*     3.2     5.1    -      -       -      -
     50B  ILE*     2.9    53.9    +      -       +      +
     52B  ILE*     3.7    25.1    -      -       +      -
     62B  ILE*     6.4     0.2    -      -       +      -
     84B  LEU*     4.9     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 44 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  VAL*     4.6     2.2    -      -       -      -
     21B  PHE*     3.4     7.8    -      -       -      +
     22B  ILE*     2.8    37.2    +      -       -      +
     24B  LEU*     3.6    22.0    -      -       +      -
     43B  VAL*     1.3    79.5    -      -       -      +
     45B  ASP*     1.3    61.3    +      -       -      +
     48B  GLY      3.4    14.4    -      -       -      +
     49B  SER*     3.8     2.7    -      -       -      -
    100B  MET*     4.1     0.3    -      -       -      +
    102B  TYR*     4.1     9.4    -      -       +      -
    103B  SER      3.6    15.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 45 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5B  THR      4.8     0.7    -      -       -      +
      6B  PHE*     3.5    22.9    -      -       +      -
      7B  VAL*     2.9    32.3    +      -       +      +
     19B  LEU*     4.9     1.0    -      -       -      +
     20B  ILE      3.9    10.8    -      -       -      +
     44B  ALA*     1.3    74.5    -      -       -      +
     46B  LYS*     1.3    62.7    +      -       +      +
     47B  THR*     2.6    27.9    +      -       -      -
     48B  GLY      3.1    11.6    +      -       -      +
    100B  MET*     3.8    23.6    -      -       +      -
    102B  TYR*     3.5     8.2    -      -       -      -
    103B  SER      2.9    17.3    +      -       -      +
----------------------------------------------------------
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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