Contacts of the strand formed by residues 147 - 154 (chain A) in PDB entry 5A31


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 VAL 147 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130A  ASP*     3.0    36.1    -      -       +      +
    131A  PHE      3.6    15.3    -      -       -      +
    132A  ILE*     4.6    14.6    -      -       +      +
    133A  ILE*     5.6     0.4    -      -       -      -
    146A  GLU*     1.3    83.3    -      -       -      +
    148A  GLU*     1.3    61.0    +      -       -      +
    149A  LYS*     3.5    21.2    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 148 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130A  ASP*     3.4     2.8    -      -       -      -
    131A  PHE*     2.8    47.3    +      -       +      +
    133A  ILE*     4.9    16.0    -      -       +      +
    146A  GLU      4.5     0.2    +      -       -      -
    147A  VAL*     1.3    67.3    -      -       -      +
    149A  LYS*     1.3    60.8    +      -       -      +
    150A  CYS*     3.7     3.3    +      -       -      -
    163A  SER*     4.5    14.1    -      -       -      +
    169A  TYR*     5.2     9.9    -      -       +      +
    215A  HIS*     5.4     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 149 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77A  ARG*     6.0     8.1    -      -       -      +
     80A  VAL*     5.4    14.4    -      -       +      +
    129A  CYS      3.7     7.0    -      -       -      +
    130A  ASP*     3.7    21.1    -      -       +      +
    147A  VAL*     3.5    21.7    +      -       +      +
    148A  GLU*     1.3    70.5    -      -       -      +
    150A  CYS*     1.3    60.7    +      -       -      +
    163A  SER*     3.5     2.3    -      -       -      -
    164A  ILE*     3.0    61.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 150 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  TRP*     3.9     5.0    -      -       -      +
    129A  CYS      2.7    32.2    +      -       -      +
    131A  PHE*     3.4    37.5    -      -       -      -
    148A  GLU*     4.0     2.9    -      -       -      -
    149A  LYS*     1.3    76.9    -      -       -      +
    151A  ILE*     1.3    62.0    +      -       -      +
    152A  CYS*     4.0     3.7    +      -       -      -
    161A  MET*     3.9    16.8    -      -       -      -
    162A  HIS      3.1    31.4    -      -       -      +
    163A  SER*     3.4     9.2    -      -       -      +
    164A  ILE*     4.5     3.1    -      -       -      +
    169A  TYR*     5.2     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 151 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  LEU*     3.8    41.5    -      -       +      -
    100A  VAL*     3.9     4.0    -      -       +      -
    102A  TRP*     3.5    26.6    -      -       +      -
    117A  PHE*     3.8    23.8    -      -       +      -
    126A  ALA*     4.8     1.1    -      -       +      +
    127A  LEU      3.9     4.9    -      -       -      +
    128A  TRP*     3.8    14.9    -      -       +      -
    150A  CYS*     1.3    72.4    -      -       -      +
    152A  CYS*     1.4    61.0    +      -       -      +
    153A  ILE*     3.3    35.4    +      -       +      +
    160A  ASN      3.8     1.0    -      -       -      +
    161A  MET*     3.5     2.4    -      -       -      -
    162A  HIS*     3.2    32.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 152 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126A  ALA*     2.9    23.9    +      -       -      -
    127A  LEU*     2.9    32.7    +      -       +      +
    129A  CYS*     3.8    28.5    -      -       -      -
    131A  PHE*     4.4     0.7    -      -       -      -
    150A  CYS*     4.0     6.5    -      -       -      -
    151A  ILE*     1.4    74.4    -      -       -      +
    153A  ILE*     1.3    61.1    +      -       -      +
    154A  LEU*     3.6     2.5    +      -       -      +
    159A  ILE*     4.6     7.0    -      -       +      -
    160A  ASN      3.2     5.6    -      -       -      +
    161A  MET*     3.3    32.5    -      -       -      -
    187A  LEU*     4.2     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 153 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100A  VAL*     3.4    27.4    -      -       +      -
    117A  PHE*     3.9    20.9    -      -       +      -
    119A  VAL*     3.7    17.0    -      -       +      -
    123A  VAL*     3.4    35.0    -      -       +      -
    126A  ALA*     3.9     5.4    -      -       +      +
    151A  ILE*     3.3    33.0    -      -       +      +
    152A  CYS*     1.3    70.1    -      -       -      +
    154A  LEU*     1.3    59.1    +      -       -      +
    155A  GLN*     3.9     6.4    +      -       -      +
    159A  ILE*     3.7     1.4    -      -       -      -
    160A  ASN*     2.8    43.2    +      -       +      +
    162A  HIS*     6.4     0.4    -      -       +      -
    268O  PHE*     4.5    11.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 154 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123A  VAL*     3.6     5.4    -      -       -      +
    124A  GLN*     2.9    35.8    +      -       +      +
    125A  GLN*     3.5    24.2    +      -       +      -
    126A  ALA      3.8     6.0    -      -       -      +
    152A  CYS      3.6     3.6    +      -       -      +
    153A  ILE*     1.3    72.3    -      -       -      +
    155A  GLN*     1.3    80.8    +      -       -      +
    158A  CYS      3.7     4.9    -      -       -      +
    159A  ILE*     3.3    30.7    -      -       +      -
    173A  LEU*     4.8     6.1    -      -       +      -
    177A  VAL*     3.5    32.1    -      -       +      -
    178A  ALA      5.5     0.2    -      -       -      +
    179A  ASN*     4.9     1.1    -      -       -      -
    180A  VAL*     3.8    31.2    -      -       +      +
----------------------------------------------------------
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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