Contacts of the strand formed by residues 175 - 182 (chain L) in PDB entry 1OAK


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 MET 175 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    389H  PHE*     3.0    12.5    -      -       -      -
    135L  PHE      3.9     0.2    -      -       -      -
    136L  LEU*     2.9    49.0    +      -       +      +
    139L  PHE*     3.9     8.9    -      -       +      -
    144L  ILE*     4.1    13.9    -      -       -      +
    146L  VAL*     3.2    33.4    -      -       +      -
    161L  ASN*     3.8    25.1    -      -       +      +
    162L  SER      3.1     6.3    -      -       -      +
    163L  TRP*     3.2    36.6    -      -       +      +
    174L  SER*     1.3    76.6    -      -       -      +
    176L  SER*     1.3    78.5    +      -       -      +
    177L  SER*     3.9     5.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 176 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    389H  PHE*     3.3    28.9    -      -       -      -
    401H  SER*     4.1     7.3    -      -       -      -
    133L  VAL*     3.9     8.3    -      -       -      +
    134L  CYS      3.5     5.3    +      -       -      -
    135L  PHE*     3.5    21.8    -      -       -      -
    160L  LEU      4.4     0.9    -      -       -      -
    161L  ASN*     3.2     4.5    -      -       -      -
    162L  SER*     2.7    36.1    +      -       -      -
    175L  MET*     1.3    81.3    -      -       -      +
    177L  SER*     1.3    62.1    +      -       -      +
    178L  THR*     4.2     5.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 177 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133L  VAL*     3.7     0.3    -      -       -      +
    134L  CYS*     2.8    39.5    +      -       -      -
    136L  LEU*     5.0     0.4    -      -       -      -
    146L  VAL*     4.3    14.4    -      -       -      +
    148L  TRP*     2.7    33.6    +      -       -      -
    159L  VAL*     3.4     4.5    -      -       -      +
    160L  LEU      3.4     0.9    -      -       -      -
    161L  ASN*     2.9    22.3    +      -       -      -
    175L  MET*     3.9    11.0    -      -       -      -
    176L  SER*     1.3    74.6    +      -       -      +
    178L  THR*     1.3    63.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 178 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    364H  LEU*     4.8     8.5    -      -       +      +
    394H  GLN*     5.6     3.1    -      -       -      +
    399H  THR*     6.0     2.9    -      -       +      +
    401H  SER*     4.9     4.2    +      -       -      -
    131L  SER*     4.0    24.7    -      -       -      -
    132L  VAL      3.4     9.2    -      -       -      +
    133L  VAL*     4.1    16.1    -      -       +      +
    158L  GLY      3.1     3.6    -      -       -      +
    159L  VAL*     3.1     7.5    -      -       -      -
    160L  LEU*     2.9    48.3    +      -       -      +
    176L  SER*     4.2     9.0    +      -       -      -
    177L  SER*     1.3    80.4    +      -       -      +
    179L  LEU*     1.3    60.4    +      -       -      +
    180L  THR*     3.7    10.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 179 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130L  ALA      3.6     1.7    -      -       -      +
    131L  SER*     3.3     1.3    -      -       -      -
    132L  VAL*     2.7    48.3    +      -       +      +
    148L  TRP*     3.7    40.2    -      -       +      -
    150L  ILE*     3.8    30.3    -      -       +      -
    155L  ARG*     3.6    22.9    -      -       +      +
    157L  ASN      3.8     8.3    -      -       -      +
    158L  GLY      3.6     0.9    -      -       -      -
    159L  VAL*     3.5    24.7    -      -       +      +
    178L  THR*     1.3    71.8    -      -       -      +
    180L  THR*     1.3    64.2    +      -       -      +
    181L  LEU*     4.2    15.7    -      -       +      -
    192L  TYR*     4.6     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 180 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    366H  LYS*     4.4    10.8    -      -       -      +
    394H  GLN*     3.8    27.2    +      -       -      +
    124L  GLN*     5.5     0.2    -      -       -      +
    129L  GLY*     6.3     0.4    -      -       -      -
    130L  ALA      3.6     4.0    -      -       -      +
    131L  SER*     3.0    23.4    +      -       -      +
    158L  GLY*     2.9    29.6    +      -       -      +
    160L  LEU*     5.6     1.8    -      -       -      +
    178L  THR*     4.0     7.8    +      -       -      +
    179L  LEU*     1.3    74.4    -      -       -      +
    181L  LEU*     1.3    78.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 181 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128L  GLY      4.3     0.2    -      -       -      +
    129L  GLY*     4.0     2.3    -      -       -      -
    130L  ALA*     2.7    40.3    +      -       +      +
    132L  VAL*     5.6     1.3    -      -       +      -
    150L  ILE*     4.1    21.5    -      -       +      -
    155L  ARG*     2.9    37.7    -      -       -      +
    157L  ASN      5.1     0.7    -      -       -      +
    179L  LEU*     4.2    15.3    -      -       +      -
    180L  THR*     1.3    87.0    -      -       -      +
    182L  THR*     1.3    66.8    +      -       -      +
    185L  GLU*     3.8    16.8    -      -       +      +
    186L  TYR*     4.4    12.1    -      -       +      +
    189L  HIS*     5.4     2.2    -      -       +      +
    192L  TYR*     4.2    23.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 182 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128L  GLY      3.7     8.1    -      -       -      +
    130L  ALA*     4.2     0.7    -      -       -      -
    181L  LEU*     1.3    77.4    -      -       -      +
    183L  LYS*     1.3    66.9    +      -       -      +
    184L  ASP*     3.6     9.3    +      -       -      +
    185L  GLU*     2.9    43.6    +      -       -      +
    186L  TYR*     2.9    20.3    +      -       -      +
----------------------------------------------------------
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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