Contacts of the strand formed by residues 160 - 166 (chain Z) in PDB entry 1O18


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 Z).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153Z  LEU*     4.4     6.3    -      -       +      -
    154Z  ASP      3.2     9.0    -      -       -      +
    155Z  SER*     2.6    25.6    +      -       -      +
    159Z  VAL*     1.4    71.6    -      -       -      +
    161Z  HIS*     1.3    74.8    +      -       -      +
    162Z  ASN*     5.0     2.7    -      -       -      +
    177Z  ARG*     3.3     6.9    -      -       -      +
    178Z  LEU*     2.9    47.1    +      -       +      -
    180Z  LEU      3.1    15.9    +      -       -      -
    181Z  ALA*     4.3     0.2    -      -       -      +
    261Z  LEU*     5.1     0.2    -      -       -      +
    274Z  ILE*     3.6    31.9    -      -       +      +
    277Z  THR*     6.1     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 161 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73Z  HIS      5.2     0.9    -      -       -      -
    108Z  ALA*     4.9     7.6    -      -       +      -
    109Z  PRO*     3.6    42.1    -      -       +      +
    110Z  LEU*     5.2     3.2    +      -       -      +
    152Z  VAL      4.1     0.4    -      -       -      -
    153Z  LEU*     3.4     5.4    -      -       -      -
    154Z  ASP*     2.7    41.2    +      -       +      +
    159Z  VAL*     4.0    30.9    -      -       +      +
    160Z  THR*     1.3    80.7    +      -       -      +
    162Z  ASN*     1.3    66.5    +      -       -      +
    163Z  VAL*     4.2    11.9    -      -       +      -
    175Z  ILE*     4.0     9.1    -      -       +      +
    176Z  MET      3.0    17.3    -      -       -      -
    177Z  ARG*     3.7    28.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 162 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151Z  ILE*     4.5     6.3    -      -       +      +
    152Z  VAL      3.2     6.9    -      -       -      -
    153Z  LEU*     3.6    21.2    -      -       -      +
    160Z  THR*     5.0     2.4    -      -       -      +
    161Z  HIS*     1.3    74.6    +      -       -      +
    163Z  VAL*     1.3    63.4    +      -       -      +
    164Z  PRO*     3.5     2.2    -      -       -      +
    175Z  ILE*     3.2    24.4    -      -       -      +
    176Z  MET*     2.9    13.7    +      -       +      +
    178Z  LEU*     5.8     0.3    +      -       -      +
    277Z  THR*     2.9    31.2    -      -       -      +
    278Z  THR*     3.4    34.2    +      -       -      +
    281Z  SER*     3.6    20.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 163 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109Z  PRO*     3.5    33.2    -      -       +      -
    136Z  ILE*     5.1     2.2    -      -       +      -
    138Z  ALA*     3.4    21.1    -      -       +      -
    139Z  VAL*     5.0     1.1    -      -       +      -
    151Z  ILE*     4.2     0.6    -      -       -      +
    152Z  VAL      2.9    28.6    +      -       -      +
    154Z  ASP*     5.8     0.4    -      -       +      -
    161Z  HIS*     4.2     9.4    -      -       +      -
    162Z  ASN*     1.3    79.2    -      -       -      +
    164Z  PRO*     1.3    62.4    -      -       -      +
    165Z  ILE*     3.5    18.2    +      -       +      +
    170Z  ALA*     3.6    30.5    -      -       +      -
    175Z  ILE*     3.9    15.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 164 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150Z  GLY      3.7     6.7    -      -       -      +
    151Z  ILE*     3.9    16.4    -      -       +      -
    162Z  ASN      3.5     7.2    -      -       -      +
    163Z  VAL*     1.3    83.0    -      -       -      +
    165Z  ILE*     1.3    59.0    +      -       -      +
    170Z  ALA*     3.6     0.2    -      -       -      -
    171Z  LEU*     2.8    37.0    +      -       +      +
    174Z  ALA*     3.7    15.7    -      -       +      -
    175Z  ILE*     4.0    17.5    -      -       +      +
    281Z  SER*     3.4    20.4    -      -       -      +
    285Z  CYS*     3.8    21.3    -      -       -      -
    293Z  LEU*     4.4     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 165 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138Z  ALA*     3.7     9.2    -      -       +      +
    139Z  VAL*     3.5    40.6    -      -       +      +
    142Z  LEU*     3.9    18.4    -      -       +      -
    148Z  THR      3.4    16.6    -      -       -      +
    149Z  THR*     3.1    23.9    -      -       -      +
    150Z  GLY      2.9    12.6    +      -       -      +
    152Z  VAL*     4.5     2.7    -      -       +      -
    163Z  VAL*     3.6    21.5    -      -       +      +
    164Z  PRO*     1.3    75.3    -      -       -      +
    166Z  TYR*     1.3    62.8    +      -       -      +
    168Z  GLY*     3.6    25.8    -      -       -      +
    169Z  TYR      3.7     3.1    -      -       -      +
    170Z  ALA*     3.6    15.7    -      -       +      -
    171Z  LEU*     4.7     1.3    -      -       -      -
    293Z  LEU*     4.3     1.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 166 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     442  MET*     4.7    10.7    -      -       -      +
     602  SER      5.7     0.2    +      -       -      -
     612  LYS*     5.0    11.4    -      -       -      +
     642  ILE*     3.8    42.9    -      -       +      +
    149Z  THR*     3.6    18.2    -      -       +      -
    165Z  ILE*     1.3    73.6    -      -       -      +
    167Z  GLU*     1.3    91.6    +      -       +      +
    168Z  GLY      2.9     4.2    +      -       -      -
    169Z  TYR*     3.1    26.4    +      -       +      +
    171Z  LEU*     4.3    21.0    -      -       +      +
    289Z  ILE*     3.7    34.8    -      -       +      -
    292Z  ASP*     4.0    17.0    +      -       -      -
----------------------------------------------------------
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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