Contacts of the strand formed by residues 174 - 183 (chain B) in PDB entry 2O5J


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 174 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44B  LEU*     3.5    23.0    -      -       +      +
     45B  LEU*     5.2     5.3    -      -       -      +
     48B  ILE*     5.1     5.8    -      -       +      -
    172B  SER*     3.1    18.8    +      -       -      +
    173B  PRO*     1.3    81.8    -      -       +      +
    175B  ARG*     1.3    63.6    +      -       -      +
    176B  ARG*     4.1     4.5    -      -       -      +
    177B  VAL*     3.9    15.0    -      -       +      -
    199B  ILE*     3.4    21.8    -      -       +      -
    200B  TRP      2.9    18.8    -      -       -      +
    201B  THR*     3.8    12.1    -      -       +      +
    205B  VAL*     4.8     3.1    -      -       +      -
    210B  ALA*     3.8    28.0    -      -       +      -
    851D  LEU*     5.3     2.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 175 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45B  LEU*     5.2     4.0    -      -       -      +
     83B  LYS      4.9     7.5    +      -       -      -
     84B  GLU*     5.2     8.5    +      -       -      +
     86B  VAL*     6.3     1.4    -      -       -      +
    170B  VAL*     5.5     9.1    +      -       -      +
    172B  SER      3.0    24.7    +      -       -      +
    173B  PRO      4.1     0.4    -      -       -      -
    174B  VAL*     1.3    75.6    +      -       -      +
    176B  ARG*     1.3    65.7    +      -       +      +
    200B  TRP*     3.1    11.3    +      -       +      +
    201B  THR      4.7     1.8    -      -       -      -
    202B  ASP*     3.4    41.2    +      -       +      +
    845D  ASN*     5.8     4.8    -      -       -      +
    847D  ASP*     3.9    30.8    +      -       +      +
    848D  GLU*     2.8    29.3    +      -       -      -
    851D  LEU*     3.1    39.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 176 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41B  ARG*     5.9     1.3    -      -       -      +
     45B  LEU*     6.3     1.1    -      -       -      -
    174B  VAL*     3.6     1.7    -      -       -      -
    175B  ARG*     1.3    85.7    -      -       +      +
    177B  VAL*     1.3    69.1    +      -       -      +
    200B  TRP*     3.0    83.0    +      -       +      +
    846D  PRO*     6.1     1.2    -      -       -      +
    847D  ASP*     2.8    31.3    +      -       +      +
    851D  LEU*     5.3     3.1    -      -       +      -
    884D  ARG*     4.2    38.9    -      -       -      +
    888D  GLU*     4.0    18.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 177 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41B  ARG*     3.3    62.1    +      -       +      +
     44B  LEU*     3.6    37.9    -      -       +      -
     45B  LEU*     5.3     9.4    -      -       +      -
    174B  VAL*     3.9     5.4    -      -       +      -
    176B  ARG*     1.3    81.1    -      -       -      +
    178B  ALA*     1.3    63.4    +      -       -      +
    197B  LEU*     5.1     3.8    -      -       +      -
    198B  ARG      3.5     5.2    -      -       -      +
    199B  ILE*     3.7    19.7    -      -       +      -
    200B  TRP*     4.7     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 178 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41B  ARG*     5.8     2.0    -      -       -      +
    177B  VAL*     1.3    79.1    -      -       -      +
    179B  PHE*     1.3    61.2    +      -       -      +
    180B  GLN*     6.5     0.4    -      -       +      -
    196B  THR      3.8     0.7    -      -       -      +
    197B  LEU*     3.0     4.7    -      -       -      +
    198B  ARG*     2.6    73.4    +      -       -      +
    200B  TRP*     4.2     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 179 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34B  VAL*     3.9    32.1    -      -       +      -
     37B  GLY*     4.0    15.0    -      -       -      +
     38B  ASN*     3.9    20.4    -      -       +      -
     41B  ARG*     5.3    10.8    -      -       +      -
    178B  ALA*     1.3    76.8    -      -       -      +
    180B  GLN*     1.3    69.1    +      -       -      +
    181B  VAL*     3.4    32.3    -      -       +      -
    195B  LEU*     3.7    16.6    -      -       +      -
    196B  THR      3.3     5.6    -      -       -      +
    197B  LEU*     3.9    17.7    -      -       +      -
    936D  TYR*     5.0     5.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 180 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178B  ALA      6.0     0.4    -      -       -      -
    179B  PHE*     1.3    79.5    -      -       -      +
    181B  VAL*     1.3    64.0    +      -       -      +
    182B  GLU*     3.0    40.6    +      -       +      +
    194B  LYS      3.1     6.4    -      -       -      +
    195B  LEU*     3.5     2.4    -      -       -      -
    196B  THR*     3.0    26.9    +      -       -      +
    198B  ARG*     4.3    20.4    +      -       -      -
    936D  TYR*     5.0    15.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 181 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  GLY*     3.6    24.0    -      -       -      -
     34B  VAL*     3.7    11.2    -      -       +      +
    179B  PHE*     3.4    29.9    -      -       +      -
    180B  GLN*     1.3    74.4    -      -       -      +
    182B  GLU*     1.3    61.2    +      -       -      +
    183B  ASP*     4.0     4.1    +      -       -      +
    193B  ASP*     3.4    43.3    -      -       +      +
    194B  LYS      3.2     7.2    -      -       -      +
    195B  LEU*     4.5     1.3    -      -       +      -
    636D  GLN*     4.1    16.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 182 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180B  GLN*     3.0    37.9    +      -       +      +
    181B  VAL*     1.3    75.5    -      -       -      +
    183B  ASP*     1.3    70.8    +      -       -      +
    192B  LEU      4.6     0.4    -      -       -      -
    194B  LYS*     2.7    55.4    +      -       +      +
    196B  THR*     3.4    24.1    +      -       -      +
    636D  GLN*     4.6    10.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 183 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181B  VAL*     4.4     5.5    -      -       -      +
    182B  GLU*     1.3    81.2    -      -       -      +
    184B  THR*     1.3    58.5    -      -       -      +
    190B  THR*     4.5    12.7    -      -       +      +
    191B  ASP*     4.8     3.5    -      -       -      -
    192B  LEU      3.4    22.2    +      -       -      +
    193B  ASP*     4.6     4.7    -      -       -      +
    194B  LYS*     5.2     1.2    -      -       -      +
    636D  GLN*     5.0     8.3    +      -       -      +
----------------------------------------------------------
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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