Contacts of the strand formed by residues 131 - 136 (chain X) 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 ALA 131 (chain X).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102X  PRO*     3.2    11.9    -      -       +      +
    103X  THR      2.9    21.4    +      -       -      -
    124X  PHE*     3.8     3.4    -      -       -      -
    129X  VAL*     3.4     6.9    -      -       -      +
    130X  PRO*     1.3    82.7    -      -       +      +
    132X  MET*     1.3    64.6    +      -       -      +
    356X  TRP*     4.0    22.7    -      -       +      -
    357X  ILE      3.0    20.9    -      -       -      +
    358X  THR*     3.9     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 132 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103X  THR*     3.2    18.2    -      -       -      +
    105X  LEU*     3.7    16.4    -      -       +      -
    119X  MET      4.0     0.9    -      -       -      +
    120X  THR*     3.8    27.8    -      -       -      +
    123X  MET*     3.6    35.9    -      -       +      -
    124X  PHE*     3.4    33.7    -      -       +      -
    129X  VAL*     4.2     7.6    -      -       +      -
    131X  ALA*     1.3    74.1    -      -       -      +
    133X  TYR*     1.3    63.5    +      -       -      +
    134X  VAL*     4.1    10.3    -      -       +      -
    356X  TRP*     3.4     7.6    -      -       -      -
    357X  ILE*     2.8    30.7    +      -       -      +
    370X  VAL*     4.3    11.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 133 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103X  THR      3.3     2.0    +      -       -      +
    104X  LEU*     3.5    16.0    -      -       +      +
    105X  LEU*     2.8    27.5    +      -       -      +
    132X  MET*     1.3    82.5    -      -       -      +
    134X  VAL*     1.3    75.4    +      -       -      +
    135X  ALA*     4.2    12.6    -      -       +      -
    346X  LEU*     4.5     5.1    -      -       +      +
    352X  PHE*     3.3    31.4    -      +       +      -
    355X  MET*     3.5    41.5    -      -       +      +
    356X  TRP*     3.9    15.9    -      -       +      -
    357X  ILE*     5.1     3.4    -      -       +      -
    370X  VAL*     4.7     4.5    -      -       -      -
    372X  ARG*     2.9    43.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 134 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105X  LEU*     3.4     4.7    -      -       +      +
    106X  THR      4.4     2.7    -      -       -      -
    107X  GLU*     3.6    48.5    -      -       +      +
    116X  ARG*     3.2    42.4    +      -       +      +
    119X  MET*     4.3    18.8    -      -       +      -
    120X  THR*     4.5     6.5    -      -       -      +
    132X  MET*     4.1    20.4    -      -       +      -
    133X  TYR*     1.3    87.7    -      -       -      +
    135X  ALA*     1.3    57.9    +      -       -      +
    370X  VAL*     4.6     9.2    -      -       +      +
    372X  ARG*     4.5     3.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 135 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104X  LEU*     4.2     7.0    -      -       +      -
    105X  LEU      2.9    11.0    +      -       -      +
    106X  THR*     3.3     4.5    -      -       -      -
    107X  GLU*     3.0    23.4    +      -       -      +
    116X  ARG*     4.9     0.4    -      -       -      +
    133X  TYR*     4.0    18.0    -      -       +      -
    134X  VAL*     1.3    73.3    -      -       -      +
    136X  ILE*     1.3    62.9    +      -       -      +
    139X  VAL*     6.1     1.8    -      -       +      -
    140X  LEU*     3.6    38.4    -      -       +      -
    346X  LEU*     4.7     1.1    -      -       +      -
    372X  ARG*     5.9     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 136 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107X  GLU*     3.7    25.8    -      -       +      +
    108X  ALA      4.6     2.2    -      -       -      +
    109X  PRO*     4.2    32.8    -      -       +      +
    116X  ARG*     4.0    14.8    -      -       -      +
    135X  ALA*     1.3    73.1    -      -       -      +
    137X  GLN*     1.3    70.5    +      -       -      +
    138X  ALA*     4.2     7.6    -      -       +      +
    139X  VAL*     3.2    38.4    +      -       +      +
    140X  LEU*     3.2    10.8    +      -       -      +
    163X  VAL*     5.1     1.1    -      -       +      -
    170X  ALA*     4.8    15.3    -      -       +      -
----------------------------------------------------------
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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