Contacts of the strand formed by residues 207 - 212 (chain A) in PDB entry 1OKM


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 207 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  ARG*     3.0    10.8    +      -       -      +
    141A  LEU*     3.4    18.6    -      -       +      +
    143A  VAL*     3.6    28.3    -      -       +      +
    195A  PRO      3.7     0.2    -      -       -      -
    196A  GLY      2.7    34.2    +      -       -      -
    197A  SER*     3.7    23.6    -      -       -      -
    198A  LEU*     3.9    19.5    -      -       +      +
    206A  CYS*     1.3    83.7    -      -       -      +
    208A  THR*     1.3    69.1    +      -       -      +
    209A  TRP*     3.6    28.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 208 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  ARG*     5.3     0.7    +      -       -      -
     83A  PRO*     4.2    11.2    -      -       +      +
     84A  LEU*     3.8    28.4    -      -       +      +
     88A  TYR*     5.0     2.8    +      -       -      -
    138A  PRO      4.9     2.1    +      -       -      -
    139A  ASP*     4.9    12.6    -      -       -      +
    141A  LEU      2.9    13.8    +      -       -      -
    142A  ALA*     3.4     5.2    -      -       -      +
    143A  VAL      3.4    19.6    +      -       -      -
    193A  THR*     3.9    18.4    -      -       -      +
    194A  TYR      4.0     5.8    -      -       -      +
    195A  PRO*     4.7     4.4    -      -       +      +
    207A  VAL*     1.3    72.5    +      -       -      +
    209A  TRP*     1.3    61.3    +      -       -      +
    210A  ILE*     3.7     3.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 209 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  SER*     3.1    19.4    +      -       -      -
    107A  HIS*     3.5    21.8    -      +       -      -
    117A  GLU*     4.4     0.9    -      -       -      -
    119A  HIS*     3.5    39.9    -      +       -      -
    143A  VAL*     3.5    42.2    -      -       +      -
    145A  GLY*     4.5     4.7    -      -       -      -
    192A  TRP      4.3     0.2    -      -       -      -
    193A  THR*     2.9    32.6    +      -       -      -
    194A  TYR*     3.0    34.7    +      -       +      +
    196A  GLY*     3.8    11.7    -      -       -      -
    197A  SER      2.9    24.4    +      -       -      -
    199A  THR*     3.9     9.6    -      -       +      -
    207A  VAL*     3.6    18.4    -      -       +      +
    208A  THR*     1.3    72.5    -      -       -      +
    210A  ILE*     1.3    61.7    +      -       -      +
    211A  VAL*     3.9     8.3    -      -       +      -
    555A  SAB      3.5    19.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 210 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47A  LEU*     3.7    38.1    -      -       +      -
     79A  LEU*     4.2    11.4    -      -       +      -
     83A  PRO*     4.3     7.4    -      -       +      -
     84A  LEU*     4.0    32.3    -      -       +      -
    142A  ALA*     4.9     1.8    -      -       +      -
    143A  VAL      3.1    10.8    +      -       -      +
    144A  LEU*     3.4    13.9    -      -       +      +
    145A  GLY      2.8    23.7    +      -       -      -
    191A  TYR*     3.7    31.6    -      -       +      -
    192A  TRP      3.5     3.6    -      -       -      -
    193A  THR*     4.2     8.3    -      -       -      +
    208A  THR*     4.1     9.0    -      -       +      +
    209A  TRP*     1.3    78.4    -      -       -      +
    211A  VAL*     1.3    59.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 211 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  ILE*     4.0    18.6    -      -       +      -
    107A  HIS*     4.0    36.6    -      -       +      +
    117A  GLU*     5.5     0.7    -      -       -      +
    145A  GLY*     3.6    12.1    -      -       -      +
    147A  PHE*     3.4    39.5    -      -       +      -
    191A  TYR*     3.2     2.5    -      -       -      -
    192A  TRP*     2.8    43.5    +      -       +      +
    194A  TYR*     4.8     3.4    -      -       +      -
    209A  TRP*     4.4    11.7    -      -       +      -
    210A  ILE*     1.3    75.0    -      -       -      +
    212A  LEU*     1.3    65.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 212 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47A  LEU*     4.0     7.2    -      -       +      -
    144A  LEU*     3.9    26.9    -      -       +      -
    145A  GLY      3.0    17.6    +      -       -      +
    146A  ILE*     3.7    24.9    -      -       +      -
    147A  PHE*     3.8    21.5    +      -       -      -
    185A  LEU*     4.9     1.3    -      -       +      -
    186A  PRO*     3.6    29.6    -      -       +      -
    188A  SER      5.1     0.7    -      -       -      +
    189A  LEU*     3.8    28.5    -      -       +      +
    190A  ASP      3.5    13.2    -      -       -      +
    191A  TYR*     4.0     8.5    -      -       +      -
    192A  TRP*     4.0     0.8    -      -       -      -
    211A  VAL*     1.3    74.9    -      -       -      +
    213A  LYS*     1.3    63.3    +      -       -      +
    214A  GLU      3.7    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