Contacts of the strand formed by residues 118 - 124 (chain B) in PDB entry 1W4R


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 THR 118 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18B  ARG      4.4     8.1    +      -       -      -
     19B  GLY      4.8     0.2    +      -       -      -
     20B  GLN*     3.6    31.0    +      -       +      +
     22B  GLN*     4.0    16.8    -      -       -      +
     43B  PHE*     4.2    22.2    -      -       +      -
     92B  ALA      3.0    11.2    +      -       -      -
     93B  VAL*     3.3    13.0    -      -       +      +
     94B  ILE*     2.9    27.2    +      -       -      +
    116B  GLY      3.9     1.1    +      -       -      -
    117B  LYS*     1.3    72.2    -      -       -      +
    119B  VAL*     1.3    60.1    +      -       -      +
    120B  ILE*     4.1    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 119 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20B  GLN      2.8    15.5    +      -       -      +
     21B  ILE*     3.3     7.9    -      -       +      +
     22B  GLN*     2.8    26.9    +      -       -      +
     94B  ILE*     3.3    13.5    -      -       +      +
     96B  ILE*     4.0    16.2    -      -       +      -
    108B  PHE*     5.5     0.9    -      -       +      -
    109B  CYS*     3.7    34.8    -      -       +      +
    112B  MET*     3.8    28.9    -      -       +      -
    113B  ALA      4.0     9.4    -      -       -      +
    117B  LYS*     4.1     7.0    -      -       +      +
    118B  THR*     1.3    78.8    -      -       -      +
    120B  ILE*     1.3    64.0    +      -       -      +
    121B  VAL*     4.0     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 120 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22B  GLN*     3.5    25.8    -      -       +      +
     24B  ILE*     3.8    20.6    -      -       +      -
     36B  LEU*     3.4    21.8    -      -       +      +
     39B  ARG*     3.8    33.0    -      -       +      -
     40B  VAL*     4.3     7.6    -      -       +      -
     43B  PHE*     4.2    20.9    -      -       +      -
     93B  VAL*     4.3    11.7    -      -       +      -
     94B  ILE      2.8    13.3    +      -       -      +
     95B  GLY*     3.2     3.0    -      -       -      -
     96B  ILE*     2.8    31.2    +      -       -      +
    118B  THR*     4.1     9.4    -      -       +      +
    119B  VAL*     1.3    77.9    -      -       -      +
    121B  VAL*     1.3    57.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 121 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21B  ILE*     4.7     2.5    -      -       +      -
     22B  GLN      2.8    15.7    +      -       -      +
     23B  VAL*     3.5     4.8    -      -       +      +
     24B  ILE*     2.8    36.9    +      -       -      +
     96B  ILE*     3.4    12.1    -      -       +      +
     99B  GLY*     3.9    20.2    -      -       -      -
    105B  ILE*     4.1     7.4    -      -       +      -
    109B  CYS*     3.7    29.2    -      -       -      -
    119B  VAL*     4.0     9.0    -      -       +      -
    120B  ILE*     1.3    77.6    -      -       -      +
    122B  ALA*     1.3    68.5    +      -       -      +
    123B  ALA*     4.4     0.9    -      -       +      -
    136B  ILE*     4.2     5.8    -      -       +      -
    139B  LEU*     4.0    19.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 122 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  ILE*     3.4     8.5    -      -       +      +
     32B  LYS*     3.8    34.8    -      -       +      +
     36B  LEU*     4.1    12.2    -      -       +      +
     96B  ILE      2.9    10.4    +      -       -      +
     97B  ASP*     3.8    18.8    -      -       -      +
     98B  GLU      2.9    12.1    +      -       -      -
     99B  GLY      2.9    21.1    +      -       -      -
    120B  ILE      4.2     0.6    -      -       -      -
    121B  VAL*     1.3    71.8    -      -       -      +
    123B  ALA*     1.3    62.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 123 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23B  VAL*     5.5     0.2    -      -       +      -
     24B  ILE      3.0     7.1    +      -       -      +
     25B  LEU*     3.3    28.7    -      -       +      +
     32B  LYS*     3.4    13.8    -      -       -      +
     98B  GLU*     4.7     1.3    -      -       -      +
     99B  GLY*     3.9     3.6    -      -       -      +
    100B  GLN*     3.2    14.8    -      -       -      +
    121B  VAL*     4.4     2.5    -      -       +      +
    122B  ALA*     1.3    76.5    -      -       -      +
    124B  LEU*     1.3    63.1    +      -       -      +
    136B  ILE*     3.5    39.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 124 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26B  GLY      3.3    17.7    -      -       -      +
     27B  PRO*     3.4     3.8    -      -       +      -
     28B  MET*     3.4    26.2    -      -       +      +
     32B  LYS*     3.6     2.2    -      -       -      +
    100B  GLN*     3.0    20.4    +      -       -      +
    123B  ALA*     1.3    74.9    -      -       -      +
    125B  ASP*     1.3    63.1    +      -       -      +
    126B  GLY      3.8    11.9    -      -       -      +
    133B  PHE*     3.7    23.9    -      -       +      +
    136B  ILE*     3.6    16.8    -      -       -      +
    163B  THR*     4.3     3.4    -      -       -      +
    300B  TTP      3.5    66.4    -      -       +      +
----------------------------------------------------------
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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