Contacts of the strand formed by residues 142 - 146 (chain B) in PDB entry 5ANC


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 ILE 142 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89B  LYS*     3.6     1.0    -      -       -      -
     90B  MET*     2.8    52.5    +      -       +      +
     92B  PHE*     3.5    25.1    -      -       +      -
    101B  VAL*     4.6     8.3    -      -       +      -
    103B  VAL*     4.2    25.8    -      -       +      -
    110B  VAL*     4.6    12.3    -      -       +      -
    132B  CYS*     4.4     8.5    -      -       +      -
    133B  TYR      4.1     7.6    -      -       -      +
    134B  ARG*     4.3    16.4    -      -       +      +
    141B  GLU*     1.3    73.9    -      -       -      +
    143B  VAL*     1.3    77.6    +      -       -      +
    144B  LEU*     4.1    14.8    -      -       +      -
    159B  ILE*     6.1     1.3    -      -       +      -
    177B  ILE*     4.9     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 143 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87B  GLU*     4.9     3.6    -      -       +      +
     88B  TYR      3.6     7.6    -      -       -      +
     89B  LYS*     3.5    33.2    -      -       +      -
    132B  CYS*     3.2    27.3    -      -       -      +
    133B  TYR*     3.0    57.9    +      -       +      +
    134B  ARG*     4.5     2.9    -      -       -      -
    135B  ASN      5.1     0.4    -      -       -      +
    141B  GLU*     4.1    18.2    -      -       +      +
    142B  ILE*     1.3    81.7    -      -       -      +
    144B  LEU*     1.3    67.1    +      -       -      +
    145B  THR*     4.1     9.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 144 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88B  TYR      2.8    44.6    +      -       -      +
     90B  MET*     3.6    30.5    -      -       -      -
    110B  VAL*     4.7     2.2    -      -       +      -
    126B  LEU*     3.7    14.6    -      -       +      -
    130B  ILE*     4.0     6.3    -      -       +      -
    131B  THR      3.2     6.5    -      -       -      +
    132B  CYS*     3.5    23.3    -      -       +      -
    142B  ILE*     4.1    15.3    -      -       +      -
    143B  VAL*     1.3    81.0    -      -       -      +
    145B  THR*     1.3    59.1    +      -       -      +
    152B  LEU*     3.4    18.6    -      -       +      +
    155B  SER*     5.4     0.4    -      -       -      -
    156B  CYS*     4.1     9.9    -      -       -      -
    159B  ILE*     3.6    25.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 145 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31B  ARG*     5.2     5.8    -      -       -      +
     85B  GLY*     4.5     2.0    -      -       -      -
     86B  TYR      3.4    12.3    -      -       -      +
     87B  GLU*     4.0    16.5    +      -       +      +
    130B  ILE*     3.3     4.9    -      -       -      +
    131B  THR*     2.8    45.9    +      -       -      +
    132B  CYS*     5.0     0.2    -      -       -      +
    133B  TYR*     3.8    24.4    -      -       -      -
    143B  VAL*     4.1     4.0    -      -       -      +
    144B  LEU*     1.3    75.1    -      -       -      +
    146B  GLY*     1.3    65.2    -      -       -      +
    147B  ASN*     6.0     0.2    -      -       -      +
    152B  LEU*     3.9     2.9    -      -       -      -
    186B  GLU*     4.0    22.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 146 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85B  GLY*     3.4     3.6    -      -       -      -
     86B  TYR*     2.8    34.4    +      -       -      +
    129B  GLY      3.4    15.5    -      -       -      -
    145B  THR*     1.3    77.9    -      -       -      +
    147B  ASN*     1.3    68.2    +      -       -      -
    148B  SER      3.9     0.4    -      -       -      -
    152B  LEU*     3.8    16.0    -      -       -      +
----------------------------------------------------------
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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