Contacts of the strand formed by residues 24 - 31 (chain B) in PDB entry 6RIN


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 ALA 24 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16B  ILE*     5.7     5.6    -      -       +      -
     17B  GLU      3.7     6.5    -      -       -      +
     18B  GLN*     4.2    14.6    -      -       +      +
     22B  THR      2.6     8.6    +      -       -      +
     23B  HIS*     1.3    77.6    -      -       -      +
     25B  LYS*     1.3    65.9    +      -       -      +
     26B  VAL*     5.4     6.5    -      -       +      -
    204B  GLU*     3.9     6.9    -      -       -      +
    205B  MET*     3.0    24.6    +      -       +      +
    213B  PRO*     3.6    33.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 25 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  ASP      4.1     0.3    -      -       -      +
     16B  ILE*     3.7     1.6    -      -       -      +
     17B  GLU*     2.9    53.5    +      -       +      +
     23B  HIS*     5.0     5.8    -      -       +      +
     24B  ALA*     1.3    80.3    -      -       -      +
     26B  VAL*     1.3    63.9    +      -       -      +
     27B  THR*     4.3     7.4    +      -       +      +
    202B  VAL*     4.0    23.8    -      -       +      -
    203B  ILE      3.5    12.6    -      -       -      +
    204B  GLU*     4.5    21.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 26 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231A  PHE*     5.9     2.0    -      -       +      -
    234A  LEU*     5.3    12.1    -      -       +      -
     14B  VAL*     4.6     7.6    -      -       +      -
     15B  ASP      3.4     9.4    -      -       -      +
     16B  ILE*     4.4    21.5    -      -       +      -
     24B  ALA*     5.4     4.5    -      -       +      -
     25B  LYS*     1.3    80.2    -      -       -      +
     27B  THR*     1.3    72.1    +      -       -      +
     28B  LEU*     4.5    15.9    -      -       +      -
    201B  LEU      4.0     0.2    -      -       -      +
    202B  VAL*     3.4     4.0    -      -       -      +
    203B  ILE*     2.9    47.7    +      -       +      +
    213B  PRO*     6.5     0.9    -      -       +      -
    217B  ILE*     4.4    20.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 27 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  LEU      4.0     0.8    -      -       -      +
     14B  VAL*     3.5     4.0    -      -       -      -
     15B  ASP*     2.9    57.0    +      -       -      +
     25B  LYS*     5.2     9.2    -      -       +      +
     26B  VAL*     1.3    80.7    -      -       -      +
     28B  LEU*     1.3    65.2    +      -       -      +
     29B  GLU*     6.5     0.2    -      -       -      -
    200B  LYS*     4.5    17.7    -      -       -      +
    201B  LEU      3.4     5.6    -      -       -      -
    202B  VAL*     4.2    20.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 28 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231A  PHE*     3.3    42.6    -      -       +      -
     11B  PRO*     5.1     8.1    -      -       +      -
     13B  LEU      3.7     1.8    -      -       -      -
     14B  VAL*     3.6    40.8    -      -       +      -
     26B  VAL*     4.5    10.1    -      -       +      -
     27B  THR*     1.3    77.5    -      -       -      +
     29B  GLU*     1.3    68.0    +      -       -      +
     31B  LEU*     4.3    16.7    -      -       +      +
     39B  LEU*     6.1     0.7    -      -       +      -
    200B  LYS*     3.4     5.0    -      -       -      +
    201B  LEU*     2.9    59.7    +      -       +      +
    203B  ILE*     5.5     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 29 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  PRO*     4.0     2.7    -      -       -      +
     12B  ARG      3.3     3.8    +      -       -      -
     13B  LEU*     3.0    65.6    +      -       +      +
     28B  LEU*     1.3    78.0    -      -       -      +
     30B  PRO*     1.3    78.2    -      -       +      +
     31B  LEU*     4.3     1.1    -      -       -      +
    190B  ALA*     3.7    15.9    -      -       +      +
    199B  ASP      4.7     0.2    -      -       -      -
    200B  LYS*     3.3    39.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 30 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  LEU*     4.2    10.3    -      -       +      +
     10B  LYS      4.2     4.2    -      -       -      +
     11B  PRO*     3.6    12.6    -      -       -      +
     12B  ARG*     3.8    31.6    -      -       +      +
     13B  LEU*     4.5     4.9    -      -       +      -
     29B  GLU*     1.3    87.2    -      -       +      +
     31B  LEU*     1.3    72.6    +      -       -      +
    190B  ALA*     5.4     6.1    -      -       +      +
    192B  VAL*     3.8    31.2    -      -       +      -
    198B  LEU*     4.4    13.7    -      -       +      -
    199B  ASP      4.0     3.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 31 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    227A  GLN*     4.8     7.9    -      -       -      +
      9B  LEU*     4.7     7.2    -      -       -      +
     11B  PRO*     4.1    20.2    -      -       +      -
     28B  LEU*     4.3    22.7    -      -       +      +
     29B  GLU*     4.3     1.6    -      -       -      -
     30B  PRO*     1.3    92.0    -      -       +      +
     32B  GLU*     1.3    70.7    +      -       -      +
     35B  PHE*     4.1    19.1    -      -       +      -
     36B  GLY*     4.6     5.8    -      -       -      +
     39B  LEU*     4.0    27.4    -      -       +      -
    198B  LEU*     3.3    13.3    -      -       -      +
    199B  ASP*     3.0    41.8    +      -       +      +
    201B  LEU*     5.0    12.8    -      -       +      -
----------------------------------------------------------
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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