Contacts of the strand formed by residues 86 - 93 (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 TYR 86 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77B  ASN*     2.7    49.3    +      -       -      +
     80B  THR*     3.5    13.5    +      -       -      +
     81B  GLY*     3.5    15.0    -      -       -      -
     85B  GLY*     1.3    71.6    -      -       -      -
     87B  GLU*     1.3    60.4    +      -       -      +
     88B  TYR*     4.9     2.2    -      +       +      -
    145B  THR*     3.4     2.1    -      -       -      +
    146B  GLY      2.8    36.2    +      -       -      +
    147B  ASN      3.3    19.7    -      -       -      -
    149B  LEU*     3.3    49.8    -      -       +      -
    152B  LEU*     3.3    17.0    -      -       +      +
    183B  ASN*     5.1    10.8    -      -       -      -
    184B  VAL      3.8     4.3    -      -       -      -
    185B  LEU*     3.6    20.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 87 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85B  GLY      3.7    10.3    -      -       -      +
     86B  TYR*     1.3    77.0    -      -       -      +
     88B  TYR*     1.3    69.1    +      -       -      +
     89B  LYS*     3.9    17.4    +      -       -      -
    133B  TYR*     3.7    20.1    +      -       -      -
    143B  VAL*     4.9     3.6    -      -       +      +
    144B  LEU      3.8     3.4    -      -       -      -
    145B  THR*     4.0    20.1    +      -       +      +
    181B  GLU      3.7     2.8    -      -       -      +
    182B  ARG*     4.1     0.3    -      -       -      -
    184B  VAL*     2.8    52.0    +      -       +      +
    185B  LEU      3.7     2.4    -      -       -      -
    186B  GLU*     3.0    42.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 88 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86B  TYR*     4.9     2.0    -      -       +      -
     87B  GLU*     1.3    78.0    -      -       -      +
     89B  LYS*     1.3    62.0    +      -       -      +
     90B  MET*     3.5     5.2    +      -       +      +
    143B  VAL*     3.6     0.4    -      -       -      -
    144B  LEU*     2.8    43.9    +      -       -      +
    149B  LEU*     4.0    13.2    -      -       +      +
    152B  LEU*     3.4    18.4    -      -       +      -
    153B  SER*     2.7    42.2    +      -       -      -
    156B  CYS*     3.5    36.3    -      -       +      -
    179B  VAL*     4.0    12.1    -      -       +      -
    181B  GLU      3.8     3.4    -      -       -      -
    182B  ARG*     3.3    40.5    -      -       +      +
    183B  ASN*     3.9    13.6    +      -       -      -
   3446N    C      5.5     0.7    -      -       -      -
   3447N    U      3.2    16.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 89 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87B  GLU*     3.9    19.3    +      -       +      -
     88B  TYR*     1.3    70.5    -      -       -      +
     90B  MET*     1.3    63.4    +      -       -      +
    133B  TYR*     5.0     5.6    -      -       -      -
    141B  GLU*     5.0    13.9    -      -       +      +
    142B  ILE      3.7     7.6    -      -       -      +
    143B  VAL*     3.5    26.7    -      -       +      -
    179B  VAL*     4.1     1.1    -      -       -      -
    180B  SER*     3.2     8.2    +      -       -      -
    181B  GLU*     3.2    62.3    +      -       +      +
    184B  VAL*     4.1    23.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 90 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88B  TYR      3.5     4.2    +      -       -      +
     89B  LYS*     1.3    76.4    -      -       -      +
     91B  ARG*     1.3    69.2    +      -       -      +
    141B  GLU*     3.3     4.0    -      -       -      +
    142B  ILE*     2.8    36.3    +      -       +      +
    144B  LEU*     3.6    29.2    -      -       +      -
    156B  CYS*     3.1    35.4    -      -       +      +
    159B  ILE*     4.1    10.1    -      -       +      -
    160B  GLN*     4.1    12.6    -      -       +      +
    177B  ILE*     3.6    34.8    -      -       +      -
    178B  TYR      3.5     7.2    -      -       -      +
    179B  VAL*     3.5    29.8    -      -       +      +
    180B  SER      4.6     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 91 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89B  LYS*     5.5     0.4    -      -       +      -
     90B  MET*     1.3    78.8    -      -       -      +
     92B  PHE*     1.3    66.7    +      -       -      +
    137B  LYS*     5.2    14.3    -      -       -      +
    140B  ASP*     4.4    21.1    +      -       -      +
    141B  GLU*     3.8    34.4    +      -       +      +
    142B  ILE      4.7     0.2    -      -       -      +
    177B  ILE*     4.5     0.2    -      -       -      -
    178B  TYR*     2.8    37.5    +      -       -      +
    180B  SER*     3.5    27.5    +      -       -      +
      1H  ILE*     3.7    35.2    -      -       -      +
      4H  SER*     6.0     2.2    -      -       -      -
      5H  LEU*     3.6    26.8    -      -       +      +
      8H  LEU*     4.9     1.2    -      -       +      +
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Residues in contact with PHE 92 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91B  ARG*     1.3    74.9    -      -       -      +
     93B  VAL*     1.3    66.2    +      -       -      +
     99B  ILE*     3.9    33.0    -      -       +      -
    101B  VAL*     4.3    19.1    -      -       +      -
    134B  ARG*     4.1    13.9    -      -       -      -
    136B  GLU*     3.2    28.7    -      -       -      -
    139B  LYS*     4.0    10.4    -      -       +      +
    140B  ASP*     3.5    28.0    -      -       -      +
    141B  GLU      3.7    10.5    -      -       -      +
    142B  ILE*     3.5    28.7    -      -       +      -
    176B  GLY      3.2    14.8    -      -       -      +
    177B  ILE*     4.0    24.5    -      -       +      -
      5H  LEU*     3.4    15.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 93 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92B  PHE*     1.3    80.5    -      -       -      +
     94B  TYR*     1.3    63.4    +      -       -      +
     99B  ILE*     3.7     4.6    -      -       -      +
    174B  LEU      3.5    20.6    -      -       -      +
    175B  ASP*     2.6    34.0    -      -       -      +
    176B  GLY      3.0     5.9    +      -       -      -
    178B  TYR*     3.6    27.6    -      -       +      -
      2H  GLU*     4.1    22.4    -      -       +      +
      5H  LEU*     3.8    26.5    -      -       +      +
----------------------------------------------------------
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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