Contacts of the strand formed by residues 180 - 190 (chain B) in PDB entry 6RI7


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 180 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47B  LEU*     3.6    50.0    -      -       +      +
     48B  LEU*     4.6     5.6    -      -       +      -
     51B  MET*     6.3     0.2    -      -       +      -
    178B  SER*     2.7    41.0    +      -       -      +
    179B  PRO*     1.3    86.6    -      -       +      +
    181B  GLU*     1.3    61.9    +      -       -      +
    183B  ILE*     4.7     9.2    -      -       +      -
    205B  MET*     4.3    11.0    -      -       -      -
    206B  GLU      3.6     8.1    -      -       -      +
    207B  THR*     3.8     9.9    -      -       +      +
    216B  ALA*     4.7     7.2    -      -       +      -
    535D  ARG*     3.3    13.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 181 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48B  LEU*     5.9     0.2    -      -       -      +
     87B  GLY      5.8     0.5    -      -       -      +
    179B  PRO      4.7     0.2    -      -       -      +
    180B  VAL*     1.3    77.0    -      -       -      +
    182B  ARG*     1.3    61.5    +      -       +      +
    206B  GLU*     2.9    11.7    +      -       +      +
    207B  THR*     3.7    23.2    -      -       -      +
    208B  ASN*     4.0    12.6    -      -       +      +
    531D  LYS*     3.4    45.3    +      -       +      +
    532D  GLU*     5.6     1.6    -      -       +      +
    535D  ARG*     3.8    37.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 182 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23B  HIS*     6.5     0.2    -      -       -      -
    181B  GLU*     1.3    80.6    -      -       -      +
    183B  ILE*     1.3    77.1    +      -       -      +
    184B  ALA*     4.5    16.3    -      -       -      +
    204B  GLU*     4.7    22.3    +      -       +      +
    205B  MET*     3.4     1.6    -      -       -      -
    206B  GLU*     2.8    46.4    +      -       +      +
    531D  LYS*     4.3    19.7    -      -       +      +
    534D  GLU*     2.2    40.5    +      -       +      +
    581D  MET*     3.3    36.7    +      -       -      +
    582D  ILE*     6.0     4.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 183 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43B  LEU*     4.4     0.9    -      -       +      +
     44B  ARG*     3.5    52.8    -      -       +      +
     47B  LEU*     3.5    30.1    -      -       +      -
     48B  LEU*     5.0    12.5    -      -       +      +
    180B  VAL*     4.7     8.7    -      -       +      -
    182B  ARG*     1.3    86.6    -      -       -      +
    184B  ALA*     1.3    68.0    +      -       -      +
    185B  TYR*     6.2     1.1    -      -       +      -
    203B  ILE*     5.6     4.3    -      -       +      -
    204B  GLU*     3.4    10.5    -      -       -      +
    205B  MET*     3.4    22.9    -      -       +      -
    534D  GLU*     4.5     8.8    -      -       -      +
    538D  ARG*     5.8     3.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 184 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44B  ARG*     5.4     4.0    -      -       -      +
    182B  ARG*     4.5    18.8    -      -       -      +
    183B  ILE*     1.3    80.4    -      -       -      +
    185B  TYR*     1.3    77.1    +      -       -      +
    203B  ILE*     3.8     4.5    -      -       -      +
    204B  GLU*     3.1    34.9    +      -       +      +
    534D  GLU*     4.8     7.6    -      -       -      +
    538D  ARG*     5.9     3.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 185 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  HIS*     4.2    26.8    +      +       -      -
     40B  GLY*     3.7    32.5    -      -       -      -
     41B  ASN*     3.5    20.4    +      -       -      +
     44B  ARG*     4.2    33.5    +      -       +      -
    183B  ILE*     6.2     0.9    -      -       +      -
    184B  ALA*     1.3    87.5    -      -       -      +
    186B  ASN*     1.3    68.1    +      -       -      +
    187B  VAL*     4.2    13.9    -      -       +      -
    201B  LEU*     4.6     3.4    -      -       +      -
    202B  VAL      3.0    18.8    -      -       -      +
    203B  ILE*     3.6    16.8    -      -       +      -
    204B  GLU*     4.7     1.6    -      -       -      +
   1216C  ARG*     5.3     3.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 186 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185B  TYR*     1.3    81.5    -      -       -      +
    187B  VAL*     1.3    70.7    +      -       -      +
    188B  GLU*     3.9     5.4    -      -       +      +
    200B  LYS      4.0     0.3    -      -       -      +
    201B  LEU*     3.8     3.6    -      -       -      +
    202B  VAL*     3.3    41.2    +      -       +      +
    204B  GLU*     5.9     0.8    +      -       -      -
    626D  TYR*     5.8     9.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 187 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36B  GLY*     4.6     4.3    -      -       -      -
     37B  HIS*     3.6    59.0    -      -       +      +
    185B  TYR*     4.2    12.3    -      -       +      -
    186B  ASN*     1.3    80.5    -      -       -      +
    188B  GLU*     1.3    60.6    +      -       -      +
    189B  ALA      4.1     0.3    +      -       -      -
    199B  ASP*     3.9    30.5    -      -       +      +
    200B  LYS      3.9     5.2    -      -       -      +
    201B  LEU*     4.6     3.8    -      -       +      -
    360D  TYR*     6.0     2.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 188 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186B  ASN*     3.9     6.0    -      -       +      -
    187B  VAL*     1.3    76.6    -      -       -      +
    189B  ALA*     1.3    61.6    +      -       -      +
    199B  ASP*     3.6     2.0    -      -       -      -
    200B  LYS*     2.7    79.4    +      -       +      +
    202B  VAL*     4.7    10.4    -      -       +      +
    360D  TYR*     5.5    12.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 189 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187B  VAL      4.1     0.8    +      -       -      -
    188B  GLU*     1.3    80.4    -      -       -      +
    190B  ALA*     1.3    61.6    +      -       -      +
    197B  ASP*     5.3    11.2    -      -       +      -
    198B  LEU      3.5     8.5    -      -       -      +
    199B  ASP*     4.6     5.8    -      -       -      +
    200B  LYS*     4.5     0.8    -      -       -      +
    360D  TYR*     5.4    15.7    -      -       +      +
    442D  ILE*     5.9     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 190 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29B  GLU*     4.0    18.4    -      -       +      +
     30B  PRO*     5.6     4.0    -      -       +      -
    188B  GLU      3.4     1.4    +      -       -      -
    189B  ALA*     1.3    76.6    -      -       -      +
    191B  ARG*     1.3    66.2    +      -       -      +
    196B  THR      4.7     1.6    -      -       -      +
    197B  ASP*     4.4     2.6    -      -       -      -
    198B  LEU*     2.6    36.0    +      -       +      +
    199B  ASP      4.9     0.4    -      -       -      -
    200B  LYS*     3.6    27.8    -      -       +      +
----------------------------------------------------------
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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