Contacts of the strand formed by residues 53 - 59 (chain B) in PDB entry 1SKW


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 LEU 53 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22B  ALA*     3.5    20.6    -      -       +      +
     24B  LEU*     4.2    10.1    -      -       +      +
     46B  ALA*     5.4     2.6    -      -       -      +
     49B  TYR*     2.9    33.2    +      -       +      +
     50B  GLN*     4.4     4.5    -      -       -      -
     51B  GLY      4.4     1.6    +      -       -      +
     52B  LYS*     1.3    81.9    -      -       -      +
     54B  THR*     1.3    80.9    +      -       -      +
     55B  VAL*     3.7    19.2    +      -       +      +
     80B  LEU*     4.3     9.9    -      -       +      -
    103B  LEU*     3.8    25.6    -      -       +      -
    107B  LEU*     3.5    35.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 54 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3B  LYS      5.2     3.8    -      -       -      +
      5B  ILE*     3.4    38.6    -      -       +      -
     22B  ALA      3.0     7.7    +      -       -      -
     23B  ILE*     3.3    28.6    -      -       +      +
     24B  LEU      2.8    26.5    +      -       -      -
     53B  LEU*     1.3    78.1    +      -       -      +
     55B  VAL*     1.3    66.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 55 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3B  LYS      5.3     1.6    +      -       -      -
      4B  ILE*     3.4    20.9    -      -       +      +
      5B  ILE      3.0    21.3    +      -       -      -
     24B  LEU*     3.5    14.6    -      -       +      +
     26B  ASP*     5.8     0.4    -      -       +      -
     42B  LEU*     4.0    34.1    -      -       +      +
     45B  ILE*     3.9    22.4    -      -       +      -
     46B  ALA*     4.1    24.9    -      -       +      +
     53B  LEU*     3.7    21.7    +      -       +      +
     54B  THR*     1.3    78.3    -      -       -      +
     56B  ALA*     1.3    64.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 56 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4B  ILE*     4.2     0.4    -      -       -      -
      5B  ILE*     3.0    22.2    -      -       +      +
      7B  LEU*     3.8    25.4    -      -       +      -
     23B  ILE*     4.2    16.8    -      -       +      -
     24B  LEU      2.7    13.2    +      -       -      +
     25B  VAL*     3.1     6.9    -      -       +      -
     26B  ASP*     2.7    31.5    +      -       -      +
     54B  THR*     3.9     1.3    +      -       +      -
     55B  VAL*     1.3    74.6    -      -       -      +
     57B  LYS*     1.3    60.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 57 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4B  ILE*     3.7    24.4    -      -       +      +
      5B  ILE      2.8    10.6    +      -       -      +
      6B  HIS*     3.7    28.7    -      -       -      +
      7B  LEU*     2.8    34.2    +      -       -      +
     26B  ASP*     3.4    28.2    +      -       +      +
     28B  TRP*     3.7    33.2    -      -       +      +
     39B  ALA*     4.6    19.2    +      -       -      +
     42B  LEU*     4.2    14.1    -      -       +      -
     43B  ASP*     5.8     0.6    +      -       -      -
     55B  VAL*     5.0     0.4    -      -       +      -
     56B  ALA*     1.3    79.0    -      -       -      +
     58B  LEU*     1.3    60.6    +      -       -      +
     59B  ASN      4.2     0.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 58 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  LEU*     3.6    34.5    -      -       +      -
      8B  THR      3.8     9.9    -      -       -      +
      9B  ASP      4.3     0.2    -      -       -      +
     12B  PHE*     4.5     4.7    -      -       +      -
     25B  VAL*     4.4     2.9    -      -       +      +
     26B  ASP      3.0     9.4    +      -       -      +
     27B  PHE*     3.3    42.0    -      -       +      -
     28B  TRP*     3.1    22.8    +      -       -      -
     57B  LYS*     1.3    75.1    -      -       -      +
     59B  ASN*     1.3    64.6    +      -       -      +
     60B  ILE*     3.3     4.3    +      -       +      +
     63B  ASN*     3.6    38.1    -      -       +      +
     66B  THR*     3.6    24.7    -      -       +      +
     67B  ALA      4.6     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 59 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  LEU      5.2     0.6    +      -       -      -
     28B  TRP*     3.2    52.4    +      -       +      +
     29B  ALA*     4.2     0.8    -      -       -      +
     30B  GLU*     4.0    16.2    -      -       -      +
     57B  LYS      4.2     0.2    -      -       -      -
     58B  LEU*     1.3    70.2    -      -       -      +
     60B  ILE*     1.3    57.5    +      -       -      +
     61B  ASP*     2.7    35.5    +      -       -      +
     62B  GLN*     2.9    35.4    +      -       +      +
     63B  ASN*     3.1    30.7    +      -       -      +
----------------------------------------------------------
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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