Contacts of the strand formed by residues 163 - 171 (chain A) in PDB entry 4A12


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 HIS 163 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134A  HIS*     3.1    29.8    +      +       +      -
    159A  GLN*     3.4     2.1    -      -       -      -
    160A  THR*     2.8    47.0    +      -       -      +
    162A  LYS*     1.4    97.3    -      -       +      +
    164A  TYR*     1.3    58.8    +      -       -      +
    165A  TYR*     4.1    18.0    +      -       +      -
    183A  LYS*     3.6    40.6    -      -       +      -
    184A  MSE      3.3     3.8    -      -       -      +
    185A  PHE*     3.7    24.6    -      +       +      +
    186A  TYR*     3.4     8.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 164 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  ASN*     3.4    42.7    +      -       +      +
    126A  ILE*     3.7    42.4    -      -       +      -
    128A  GLN*     4.0    10.1    +      -       +      -
    156A  VAL*     3.7    26.0    -      -       +      -
    158A  ASN      3.7     1.8    -      -       -      -
    159A  GLN*     3.0    37.9    +      -       +      -
    163A  HIS*     1.3    70.9    -      -       -      +
    165A  TYR*     1.3    62.0    +      -       -      +
    166A  VAL*     3.8     1.9    +      -       +      -
    182A  PHE      3.5     1.9    -      -       -      +
    183A  LYS*     3.8     1.2    -      -       -      -
    184A  MSE      2.7    39.1    +      -       +      +
    186A  TYR*     3.4    46.9    -      +       +      -
----------------------------------------------------------
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Residues in contact with TYR 165 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156A  VAL*     3.5     3.5    -      -       -      -
    157A  VAL*     2.7    35.5    +      -       +      -
    158A  ASN*     2.7    48.0    +      -       +      +
    159A  GLN      4.4     0.7    -      -       -      -
    160A  THR*     3.6    29.0    +      -       +      +
    163A  HIS*     4.1    17.3    +      -       +      +
    164A  TYR*     1.3    73.9    -      -       -      +
    166A  VAL*     1.3    55.3    +      -       -      +
    182A  PHE      3.4     6.7    -      -       -      +
    183A  LYS*     3.6    46.6    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 166 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122A  CYS*     3.7    27.1    -      -       -      -
    125A  LEU*     3.8     7.9    -      -       +      -
    126A  ILE*     3.8    28.5    -      -       +      -
    154A  ALA*     3.8    21.8    -      -       +      -
    155A  ARG      3.4    11.0    -      -       -      +
    156A  VAL*     4.4    11.4    -      -       +      -
    157A  VAL*     4.6     0.4    -      -       -      -
    164A  TYR      4.3     2.9    -      -       -      +
    165A  TYR*     1.3    77.1    -      -       -      +
    167A  GLU*     1.3    65.3    +      -       -      +
    180A  GLY      3.9     0.3    -      -       -      +
    181A  ASN*     3.4     3.8    -      -       -      +
    182A  PHE*     2.7    43.3    +      -       +      +
    184A  MSE      4.0    11.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 167 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153A  GLU      3.7     2.1    -      -       -      +
    154A  ALA*     3.4     1.2    -      -       -      -
    155A  ARG*     2.9    42.2    +      -       +      +
    157A  VAL*     3.6    34.9    -      -       +      +
    166A  VAL*     1.3    71.9    -      -       -      +
    168A  VAL*     1.3    61.4    +      -       -      +
    169A  LYS*     3.5    25.4    +      -       -      +
    179A  LYS*     6.5     0.4    -      -       +      -
    180A  GLY      3.4     3.6    -      -       -      +
    181A  ASN*     3.3    27.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 168 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118A  ALA*     3.9    25.6    -      -       +      +
    121A  LEU*     4.7     2.2    -      -       +      -
    122A  CYS*     3.7    30.1    -      -       -      -
    152A  ALA*     4.5     6.7    -      -       +      -
    153A  GLU      3.4    12.3    -      -       -      +
    154A  ALA*     3.8    11.0    -      -       +      -
    166A  VAL*     4.3     1.1    -      -       +      -
    167A  GLU*     1.3    75.0    -      -       -      +
    169A  LYS*     1.3    66.2    +      -       -      +
    170A  SER*     4.1    14.8    -      -       -      +
    178A  PHE*     4.5     2.7    -      -       +      -
    179A  LYS*     3.4     6.3    -      -       -      +
    180A  GLY      2.7    38.2    +      -       -      +
    182A  PHE*     3.8    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 169 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153A  GLU*     2.9    41.4    +      -       +      +
    155A  ARG*     3.2    30.2    -      -       -      +
    167A  GLU*     3.5    24.7    +      -       -      +
    168A  VAL*     1.3    77.6    -      -       -      +
    170A  SER*     1.3    62.4    +      -       -      +
    171A  TYR*     3.4    32.4    -      -       +      +
    176A  LEU*     3.8    14.6    -      -       +      -
    178A  PHE      3.6     4.0    -      -       -      -
    179A  LYS*     4.3    22.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 170 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114A  LEU*     4.8     3.7    +      -       -      +
    117A  GLN*     4.4     2.1    +      -       -      -
    118A  ALA*     5.3     0.9    -      -       -      +
    150A  VAL*     3.6    22.2    -      -       -      +
    151A  ARG      3.4     4.5    -      -       -      -
    152A  ALA*     3.3    20.1    -      -       -      +
    168A  VAL*     4.1     3.5    -      -       -      +
    169A  LYS*     1.3    72.7    -      -       -      +
    171A  TYR*     1.3    61.0    +      -       -      +
    176A  LEU*     3.6     5.5    -      -       -      +
    177A  VAL*     3.0    24.9    +      -       -      -
    178A  PHE*     2.9    41.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 171 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149A  THR      3.7     0.7    -      -       -      +
    150A  VAL*     3.5     4.7    -      -       -      -
    151A  ARG*     2.8    76.0    +      -       -      +
    153A  GLU*     3.3    25.6    +      -       +      -
    169A  LYS*     3.4    43.9    -      -       +      +
    170A  SER*     1.3    73.8    -      -       -      +
    172A  VAL*     1.3    64.5    +      -       -      +
    173A  LYS      4.0     5.8    -      -       -      +
    174A  HIS*     4.7     3.1    -      -       -      -
    175A  THR      3.3    12.8    -      -       -      +
    176A  LEU*     3.5    40.0    -      -       +      +
    177A  VAL*     4.1     0.7    -      -       -      -
----------------------------------------------------------
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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