Contacts of the strand formed by residues 132 - 137 (chain B) in PDB entry 1NOY


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 132 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114B  GLU*     2.6    44.2    +      -       +      +
    130B  ILE*     3.5     2.4    -      -       -      +
    131B  ASP*     1.3    82.5    -      -       +      +
    133B  ILE*     1.3    71.1    +      -       -      +
    145B  VAL*     5.5     0.4    -      -       +      -
    146B  PHE      2.9    13.0    -      -       -      +
    194B  MET*     5.1     0.7    -      -       -      -
    317B  TYR*     5.0     0.4    -      -       +      -
    318B  ILE*     3.4    27.1    -      -       +      -
    321B  ASN*     3.9    14.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 133 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111B  CYS*     4.4     2.0    -      -       -      -
    112B  ASP      3.8     4.5    -      -       -      +
    113B  ILE*     3.7    20.6    -      -       +      -
    130B  ILE*     3.5    27.6    -      -       +      -
    132B  ALA*     1.3    81.1    -      -       -      +
    134B  THR*     1.3    69.2    +      -       -      +
    135B  HIS*     4.7     0.4    -      -       +      -
    146B  PHE*     2.7    52.7    +      -       +      -
    194B  MET*     4.7    11.9    -      -       +      -
    195B  LEU*     4.9     7.6    -      -       +      -
    198B  TYR*     4.0    52.9    -      -       +      +
    223B  ILE*     4.8     3.4    -      -       +      -
    321B  ASN*     3.7     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 134 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111B  CYS*     3.3     6.8    -      -       -      +
    112B  ASP      3.3    24.5    +      -       -      -
    133B  ILE*     1.3    74.9    -      -       -      +
    135B  HIS*     1.3    62.8    -      -       -      +
    143B  PHE*     4.1    22.4    -      -       +      -
    144B  TYR      3.1     9.4    -      -       -      +
    145B  VAL*     3.7    19.7    -      -       +      +
    321B  ASN*     2.6    30.6    +      -       -      +
    322B  ILE*     3.8    13.5    +      -       -      +
    325B  VAL*     3.8    30.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 135 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109B  ALA*     3.4    17.3    -      -       +      +
    110B  ASN      3.5     5.8    -      -       -      -
    111B  CYS*     4.1     0.9    -      -       +      +
    133B  ILE*     4.7     0.7    -      -       +      -
    134B  THR*     1.3    78.4    -      -       -      +
    136B  TYR*     1.3    70.0    +      -       -      +
    137B  ASP*     4.3    11.6    +      -       +      +
    144B  TYR*     2.8    43.0    +      +       +      +
    146B  PHE*     5.0     1.1    -      -       +      -
    198B  TYR*     2.6    43.6    +      +       +      +
    201B  LEU*     3.5    22.3    -      -       +      +
    202B  TRP*     3.5    18.4    -      +       -      -
    205B  LYS      5.2     2.2    +      -       -      -
    207B  PRO*     5.2     3.4    -      -       +      -
    210B  PHE*     3.7    19.5    -      +       -      -
----------------------------------------------------------
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Residues in contact with TYR 136 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108B  VAL      4.4     0.9    -      -       -      -
    109B  ALA*     3.2    27.0    -      -       -      +
    110B  ASN*     3.0    19.5    +      -       -      +
    135B  HIS*     1.3    76.1    -      -       -      +
    137B  ASP*     1.3    60.8    +      -       -      +
    138B  SER*     3.3    34.9    +      -       -      -
    141B  ASP*     3.0    40.3    +      -       -      -
    142B  ARG      3.7     5.8    -      -       -      -
    143B  PHE*     3.7    40.2    -      +       +      +
    182B  ARG*     4.2     3.8    +      -       -      -
    325B  VAL*     3.8    17.1    -      -       +      +
    329B  GLN*     3.1    43.5    +      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 137 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107B  ARG*     2.9    45.8    +      -       -      +
    108B  VAL      3.9     2.5    -      -       -      -
    109B  ALA*     4.3     7.8    -      -       -      +
    135B  HIS*     4.4     7.4    +      -       +      -
    136B  TYR*     1.3    78.1    -      -       -      +
    138B  SER*     1.3    62.8    +      -       -      +
    139B  ILE*     3.3    12.8    +      -       -      +
    140B  ASP*     3.2    20.3    +      -       -      +
    141B  ASP*     2.9    18.9    +      -       -      -
    142B  ARG      3.3     6.3    +      -       -      -
    144B  TYR*     3.8    13.9    -      -       +      -
    205B  LYS*     3.9    14.0    -      -       +      +
    207B  PRO*     5.7     0.2    -      -       -      +
----------------------------------------------------------
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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