Contacts of the strand formed by residues 37 - 46 (chain B) in PDB entry 6W4E


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 GLU 37 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36B  ILE*     1.3    86.5    -      -       +      +
     38B  ASP*     1.3    61.7    +      -       -      +
     39B  SER*     4.0     3.1    +      -       -      -
     56B  LEU*     3.6    27.8    -      -       +      +
     57B  ASP      3.5     5.8    -      -       -      -
     58B  THR*     4.0     6.3    -      -       +      -
     67B  MET*     4.1    16.7    -      -       +      +
     70B  GLN*     5.5     5.4    +      -       -      -
     71B  TYR*     4.1    23.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 38 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35B  THR*     3.4    28.3    +      -       +      +
     36B  ILE      5.1     0.9    +      -       -      -
     37B  GLU*     1.3    74.1    -      -       -      +
     39B  SER*     1.3    61.8    +      -       -      +
     40B  TYR*     3.3    40.4    +      -       +      +
     55B  ILE      4.0     0.2    -      -       -      +
     56B  LEU*     3.3     4.2    -      -       -      -
     57B  ASP*     2.8    37.1    +      -       +      -
----------------------------------------------------------
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Residues in contact with SER 39 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  GLU      4.0     2.8    +      -       -      -
     38B  ASP*     1.3    74.5    +      -       -      +
     40B  TYR*     1.3    70.0    +      -       -      +
     41B  ARG*     3.4    37.6    +      -       -      -
     54B  ASP*     6.0     0.2    -      -       -      -
     55B  ILE      3.3     6.3    -      -       -      -
     56B  LEU*     3.8    16.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 40 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  SER*     5.7     3.1    +      -       -      -
     20B  THR*     3.6    24.7    -      -       +      -
     21B  ILE*     4.7    19.8    -      -       +      +
     24B  ILE*     3.7    39.5    -      -       +      -
     25B  GLN*     6.3     2.0    -      -       -      -
     35B  THR*     5.6     0.3    -      -       -      +
     38B  ASP*     3.3    48.5    +      -       +      -
     39B  SER*     1.3    79.1    -      -       -      +
     41B  ARG*     1.3    66.6    +      -       -      +
     53B  LEU      3.4     1.4    -      -       -      +
     55B  ILE*     2.8    46.1    +      -       +      +
     57B  ASP*     4.9     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 41 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  ILE*     4.2     8.4    -      -       -      +
     39B  SER*     3.4    41.9    +      -       -      -
     40B  TYR*     1.3    79.9    -      -       -      +
     42B  LYS*     1.3    62.4    +      -       -      +
     52B  LEU*     4.4    24.5    -      -       +      -
     53B  LEU      3.3     9.9    -      -       -      +
     54B  ASP*     2.7    40.9    +      -       -      +
     55B  ILE      5.2     0.2    +      -       -      -
----------------------------------------------------------
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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  LEU*     3.3    51.2    +      -       +      +
     24B  ILE*     3.8    22.0    +      -       +      +
     26B  ASN*     4.8     6.2    -      -       -      +
     41B  ARG*     1.3    75.6    -      -       -      +
     43B  GLN*     1.3    70.3    +      -       -      +
     44B  VAL*     4.2    21.1    -      -       +      -
     52B  LEU*     3.5     6.5    -      -       -      +
     53B  LEU*     2.7    52.1    +      -       +      +
     55B  ILE*     5.0     1.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 43 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1B  SER      5.9     0.6    -      -       -      +
     42B  LYS*     1.3    79.3    +      -       -      +
     44B  VAL*     1.3    70.3    +      -       -      +
     45B  VAL*     6.1     0.7    -      -       +      -
     50B  THR*     3.7    29.9    -      -       +      +
     51B  CYS      3.4     7.4    -      -       -      +
     52B  LEU*     4.6    11.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 44 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23B  LEU*     6.1     1.8    -      -       +      -
     42B  LYS*     4.2    24.0    -      -       +      -
     43B  GLN*     1.3    78.8    -      -       -      +
     45B  VAL*     1.3    66.5    +      -       -      +
     46B  ILE*     3.5    33.0    -      -       +      -
     50B  THR*     3.4     4.0    -      -       -      +
     51B  CYS*     2.8    33.8    +      -       -      +
     53B  LEU*     3.6    26.2    -      -       +      -
    157B  TYR*     4.3    21.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 45 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43B  GLN*     6.1     0.7    -      -       +      -
     44B  VAL*     1.3    77.0    -      -       -      +
     46B  ILE*     1.3    62.1    +      -       -      +
     48B  GLY*     3.5    27.9    +      -       -      +
     49B  GLU      3.4     8.5    -      -       -      +
     50B  THR*     4.3    13.2    -      -       +      +
    157B  TYR*     6.4     0.2    -      -       -      -
    128C  LYS*     3.3    25.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 46 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44B  VAL*     3.5    28.0    -      -       +      -
     45B  VAL*     1.3    69.0    -      -       -      +
     47B  ASP*     1.3    61.6    +      -       -      +
     48B  GLY      2.9    10.8    +      -       -      -
     49B  GLU      2.9    14.7    +      -       -      +
     51B  CYS*     3.6     5.6    -      -       -      -
     53B  LEU*     4.2     1.3    -      -       +      -
    157B  TYR*     3.5    38.8    -      -       +      +
    160B  VAL*     3.6    35.0    -      -       +      -
    161B  ARG*     3.6    39.3    -      -       -      +
    164B  ARG*     2.7    24.2    +      -       -      +
    128C  LYS*     4.6     3.4    -      -       +      +
----------------------------------------------------------
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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