Contacts of the strand formed by residues 58 - 64 (chain B) in PDB entry 1RUO


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 GLU 58 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136A  PHE*     3.8     6.5    -      -       -      -
     50B  LEU*     3.5    22.1    -      -       +      +
     51B  ILE      3.2    13.2    -      -       -      +
     52B  LYS*     3.1    39.1    -      -       +      +
     56B  GLY      3.6     7.9    -      -       -      +
     57B  LYS*     1.3    93.8    -      -       -      +
     59B  MET*     1.3    66.3    +      -       -      +
     87B  ARG*     4.3     9.2    +      -       -      -
    174B  GLN*     4.0    32.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with MET 59 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131A  VAL*     3.9    23.6    -      -       +      +
    132A  GLY*     5.6     0.7    -      -       -      -
    135A  ALA*     4.0    16.4    -      -       +      -
    136A  PHE*     4.1    13.7    -      -       +      -
     50B  LEU*     3.0    30.6    -      -       -      +
     51B  ILE*     2.8    24.0    +      -       +      -
     57B  LYS*     6.1     0.7    -      -       -      -
     58B  GLU*     1.3    79.1    -      -       -      +
     60B  ILE*     1.3    74.5    +      -       -      +
     61B  LEU*     3.8     2.5    -      -       +      +
    130B  LYS*     3.9    16.8    -      -       -      -
    134B  LEU*     5.2     4.0    -      -       +      -
    174B  GLN*     3.7     9.2    -      -       -      +
    175B  ILE      3.8     9.0    -      -       -      +
    176B  VAL      3.7     7.2    -      -       -      +
    177B  GLY*     3.3    39.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 60 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48B  ALA*     4.8    10.1    -      -       +      -
     49B  VAL      4.7     0.7    -      -       -      +
     50B  LEU*     4.1     9.9    -      -       +      -
     59B  MET*     1.3    84.2    -      -       -      +
     61B  LEU*     1.3    58.4    +      -       -      +
     62B  SER      3.7    24.2    +      -       -      +
     63B  TYR*     4.4    19.3    -      -       +      +
    130B  LYS*     3.3    13.9    +      -       -      -
    171B  GLU*     2.9    33.9    -      -       -      +
    174B  GLN*     2.9    38.2    +      -       +      +
    175B  ILE*     4.0    18.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 61 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  SER*     3.7    25.4    -      -       -      +
    131A  VAL*     4.7    15.0    -      -       +      -
     49B  VAL*     2.9    20.2    +      -       +      +
     50B  LEU*     5.0     0.4    -      -       -      -
     51B  ILE*     3.5    44.9    -      -       +      -
     59B  MET*     3.8     1.9    -      -       +      -
     60B  ILE*     1.3    73.1    -      -       -      +
     62B  SER*     1.3    64.2    +      -       -      +
     84B  ALA*     5.5     2.5    -      -       +      -
    127B  THR*     4.9     4.7    +      -       +      -
    130B  LYS*     4.4    15.1    -      -       +      +
    210B  CMP      2.9    45.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 62 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49B  VAL*     3.1    26.6    +      -       -      -
     60B  ILE*     3.6    11.6    -      -       -      +
     61B  LEU*     1.3    82.3    -      -       -      +
     63B  TYR*     1.3    84.8    +      -       -      +
     64B  LEU*     4.1     3.2    -      -       -      +
    123B  ARG*     5.7     1.4    -      -       -      +
    126B  VAL*     6.1     1.0    -      -       -      +
    210B  CMP      3.1    27.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 63 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46B  SER*     6.3     0.9    -      -       -      -
     47B  VAL      3.3     6.1    -      -       -      +
     48B  ALA*     3.7    19.1    -      -       +      -
     49B  VAL*     5.5     0.2    -      -       -      -
     60B  ILE*     4.4    10.0    -      -       +      +
     62B  SER*     1.3    88.7    +      -       -      +
     64B  LEU*     1.3    82.1    +      -       -      +
     65B  ASN*     4.9     3.8    -      -       -      +
     89B  LYS*     2.9    48.8    +      -       +      -
    150B  LEU*     5.1    10.3    -      -       +      -
    153B  GLN*     3.6    40.4    +      -       -      +
    167B  ILE*     4.0    12.8    -      -       +      +
    171B  GLU*     2.9    20.1    +      -       -      -
    175B  ILE*     4.4    20.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 64 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42B  ILE*     4.2     4.7    -      -       +      -
     46B  SER*     3.5     0.7    -      -       -      -
     47B  VAL*     2.9    43.1    +      -       +      -
     49B  VAL*     3.9    26.5    -      -       +      -
     62B  SER*     4.1     5.4    -      -       -      +
     63B  TYR*     1.3    90.1    -      -       -      +
     65B  ASN*     1.3    72.4    +      -       -      +
     68B  ASP*     3.5    22.7    -      -       +      +
     69B  PHE      4.5     3.8    -      -       -      +
     70B  ILE*     5.4     4.5    -      -       +      -
    123B  ARG*     3.1    42.6    -      -       +      +
    210B  CMP      4.3    12.3    -      -       -      +
----------------------------------------------------------
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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