Contacts of the strand formed by residues 160 - 166 (chain 6) in PDB entry 1O1F


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 THR 160 (chain 6).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1536  LEU*     4.4     6.7    -      -       +      -
    1546  ASP      3.2     9.4    -      -       -      +
    1556  SER*     2.6    25.8    +      -       -      +
    1596  VAL*     1.4    71.1    -      -       -      +
    1616  HIS*     1.3    74.0    +      -       -      +
    1626  ASN*     5.0     2.7    -      -       -      +
    1776  ARG*     3.3     6.9    -      -       -      +
    1786  LEU*     2.9    46.0    +      -       +      +
    1806  LEU      3.1    16.3    +      -       -      -
    1816  ALA*     4.3     0.2    -      -       -      +
    2616  LEU*     5.1     0.3    -      -       -      +
    2746  ILE*     3.6    30.6    -      -       +      +
    2776  THR*     6.1     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 161 (chain 6). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     736  HIS      5.2     0.7    -      -       -      -
    1086  ALA*     4.9     7.6    -      -       +      -
    1096  PRO*     3.6    42.1    -      -       +      +
    1106  LEU*     5.2     3.2    +      -       -      +
    1526  VAL      4.1     0.4    -      -       -      -
    1536  LEU*     3.4     4.9    -      -       -      -
    1546  ASP*     2.7    41.3    +      -       +      +
    1596  VAL*     4.0    32.6    -      -       +      +
    1606  THR*     1.3    80.3    +      -       -      +
    1626  ASN*     1.3    66.0    +      -       -      +
    1636  VAL*     4.2    11.7    -      -       +      -
    1756  ILE*     4.0     8.0    -      -       +      +
    1766  MET      3.0    17.0    -      -       -      -
    1776  ARG*     3.7    28.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 162 (chain 6). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1516  ILE*     4.5     5.6    -      -       +      +
    1526  VAL      3.2     6.7    -      -       -      -
    1536  LEU*     3.6    21.0    -      -       -      +
    1606  THR*     5.0     2.3    -      -       -      +
    1616  HIS*     1.3    75.8    +      -       -      +
    1636  VAL*     1.3    63.5    +      -       -      +
    1646  PRO*     3.5     1.4    -      -       -      +
    1756  ILE*     3.2    24.3    -      -       -      +
    1766  MET*     2.9    15.1    +      -       +      +
    1786  LEU*     5.8     0.7    +      -       -      +
    2776  THR*     2.9    31.6    -      -       -      +
    2786  THR*     3.4    34.1    +      -       -      +
    2816  SER*     3.6    20.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 163 (chain 6). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1096  PRO*     3.5    34.3    -      -       +      -
    1366  ILE*     5.1     2.2    -      -       +      -
    1386  ALA*     3.4    22.2    -      -       +      -
    1396  VAL*     5.0     1.1    -      -       +      -
    1516  ILE*     4.2     1.1    -      -       -      +
    1526  VAL      2.9    28.4    +      -       -      +
    1546  ASP*     5.8     0.4    -      -       +      -
    1616  HIS*     4.2     9.4    -      -       +      -
    1626  ASN*     1.3    79.4    -      -       -      +
    1646  PRO*     1.3    61.7    -      -       -      +
    1656  ILE*     3.5    18.0    +      -       +      +
    1706  ALA*     3.6    30.7    -      -       +      -
    1756  ILE*     3.9    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 164 (chain 6). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1506  GLY      3.7     7.2    -      -       -      +
    1516  ILE*     3.9    16.2    -      -       +      -
    1626  ASN      3.5     7.6    -      -       -      +
    1636  VAL*     1.3    82.4    -      -       -      +
    1656  ILE*     1.3    59.8    +      -       -      +
    1706  ALA*     3.6     0.2    -      -       -      -
    1716  LEU*     2.8    37.0    +      -       +      +
    1746  ALA*     3.7    15.3    -      -       +      -
    1756  ILE*     4.0    17.0    -      -       +      +
    2816  SER*     3.4    20.6    -      -       -      +
    2856  CYS*     3.8    21.3    -      -       -      -
    2936  LEU*     4.4     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 165 (chain 6). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1386  ALA*     3.7     9.2    -      -       +      +
    1396  VAL*     3.5    40.4    -      -       +      +
    1426  LEU*     3.9    18.8    -      -       +      -
    1486  THR*     3.4    17.0    -      -       -      +
    1496  THR*     3.1    23.6    -      -       -      +
    1506  GLY      2.9    13.3    +      -       -      +
    1526  VAL*     4.5     2.5    -      -       +      -
    1636  VAL*     3.6    21.1    -      -       +      +
    1646  PRO*     1.3    76.0    -      -       -      +
    1666  TYR*     1.3    61.0    +      -       -      +
    1686  GLY*     3.6    25.4    -      -       -      +
    1696  TYR      3.7     2.9    -      -       -      +
    1706  ALA*     3.6    15.7    -      -       +      -
    1716  LEU*     4.7     1.1    -      -       -      -
    2936  LEU*     4.3     2.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 166 (chain 6). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1496  THR*     3.6    18.4    -      -       +      -
    1656  ILE*     1.3    73.6    -      -       -      +
    1676  GLU*     1.3    90.8    +      -       +      +
    1686  GLY      2.9     4.6    +      -       -      -
    1696  TYR*     3.1    25.9    +      -       +      +
    1716  LEU*     4.3    20.4    -      -       +      +
    2896  ILE*     3.7    36.1    -      -       +      -
    2926  ASP*     4.0    17.0    +      -       -      -
     448  MET*     5.9     1.6    -      -       +      -
     608  SER      4.8     9.4    +      -       -      -
     618  LYS*     6.1     1.9    -      -       +      +
----------------------------------------------------------
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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