Contacts of the strand formed by residues 176 - 187 (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 LEU 176 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141A  ILE*     3.3    44.4    -      -       +      +
    142A  GLU*     3.7     8.8    -      -       -      +
    169A  LYS*     3.8    20.4    -      -       +      -
    170A  SER      3.6     8.7    -      -       -      +
    171A  TYR*     3.5    33.6    -      -       +      +
    175A  THR*     1.3    69.9    -      -       -      +
    177A  VAL*     1.3    60.0    +      -       -      +
    178A  PHE      3.4    22.0    -      -       -      +
    179A  LYS*     4.4    15.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 177 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114A  LEU*     4.6     0.4    -      -       +      +
    140A  PHE*     3.5     5.2    -      -       -      +
    141A  ILE*     2.9    25.3    +      -       -      -
    142A  GLU*     3.3    34.2    +      -       +      +
    143A  LYS      5.1     2.9    -      -       -      +
    144A  VAL*     3.7    29.8    -      -       +      +
    150A  VAL*     4.5     3.1    -      -       +      -
    170A  SER*     3.0    26.1    +      -       -      +
    171A  TYR*     4.1     1.1    -      -       -      -
    172A  VAL*     3.9    28.0    -      -       +      -
    175A  THR*     3.5    16.4    -      -       +      +
    176A  LEU*     1.3    72.1    -      -       -      +
    178A  PHE*     1.3    61.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 178 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114A  LEU*     4.1    18.8    -      -       +      -
    115A  PHE*     4.3    12.8    -      -       -      -
    118A  ALA*     3.7    28.7    -      -       +      -
    138A  ILE*     3.5    38.8    -      -       +      -
    139A  GLN      3.3    15.3    -      -       -      -
    140A  PHE*     3.8    32.8    -      +       +      -
    141A  ILE*     3.7     3.6    -      -       -      -
    168A  VAL*     4.5     4.3    -      -       +      -
    170A  SER*     2.9    53.1    +      -       -      -
    176A  LEU*     3.4     9.9    -      -       -      +
    177A  VAL*     1.3    80.1    -      -       -      +
    179A  LYS*     1.3    70.1    +      -       -      +
    180A  GLY*     3.9     7.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 179 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137A  SER      4.7     0.2    -      -       -      -
    138A  ILE*     3.4     2.9    -      -       -      +
    139A  GLN*     2.7    66.8    +      -       +      +
    141A  ILE*     3.6    14.4    -      -       +      -
    167A  GLU*     6.5     0.9    -      -       +      -
    168A  VAL      3.4     9.4    -      -       -      +
    169A  LYS*     4.3    23.8    -      -       +      +
    176A  LEU*     4.4    15.3    -      -       +      -
    178A  PHE*     1.3    77.9    -      -       -      +
    180A  GLY*     1.3    59.1    +      -       -      +
    181A  ASN*     4.7    14.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 180 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137A  SER      3.4     8.1    -      -       -      -
    138A  ILE*     3.9    12.6    -      -       -      -
    167A  GLU*     3.4     4.2    -      -       -      +
    168A  VAL      2.7    39.0    +      -       -      +
    178A  PHE*     3.9     7.4    -      -       -      -
    179A  LYS*     1.3    77.2    -      -       -      +
    181A  ASN*     1.3    66.2    +      -       -      -
    182A  PHE*     4.0     7.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 181 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136A  SER*     3.2     8.3    +      -       -      -
    137A  SER*     2.8    49.1    +      -       -      +
    139A  GLN*     5.3     2.6    +      -       -      -
    166A  VAL      3.4     3.8    -      -       -      +
    167A  GLU*     3.3    28.5    -      -       -      +
    179A  LYS*     4.7    17.6    -      -       -      +
    180A  GLY*     1.3    78.8    -      -       -      +
    182A  PHE*     1.3    60.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 182 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115A  PHE*     3.5    24.5    -      +       -      -
    118A  ALA*     3.7    23.8    -      -       +      -
    119A  ASN*     3.7    22.2    -      -       -      -
    122A  CYS*     3.7    13.9    -      -       -      -
    133A  THR*     4.0    17.9    -      -       +      -
    135A  GLU      3.7     0.9    -      -       -      -
    136A  SER*     3.4    21.1    -      -       -      -
    138A  ILE*     4.3     1.6    -      -       +      -
    164A  TYR      3.5     1.4    -      -       -      +
    165A  TYR*     3.4     8.9    -      -       -      +
    166A  VAL*     2.7    42.2    +      -       +      +
    168A  VAL*     3.8    29.4    -      -       +      -
    180A  GLY*     4.0    17.3    -      -       -      -
    181A  ASN*     1.3    77.3    -      -       -      +
    183A  LYS*     1.3    59.2    +      -       -      +
    184A  MSE      3.8    14.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 183 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133A  THR*     3.8     0.9    -      -       -      -
    134A  HIS*     2.8    37.0    +      -       +      +
    135A  GLU*     2.9    59.4    +      -       +      +
    163A  HIS*     3.6    36.5    -      -       +      +
    164A  TYR      3.8     3.4    -      -       -      -
    165A  TYR*     3.6    38.8    +      -       +      -
    182A  PHE*     1.3    69.7    -      -       -      +
    184A  MSE      1.3    56.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with MSE 184 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119A  ASN      4.6     0.4    -      -       -      +
    122A  CYS*     3.7    25.8    -      -       +      -
    123A  VAL*     3.9    21.8    -      -       +      +
    126A  ILE*     3.7    26.9    -      -       +      -
    131A  VAL*     3.9    20.2    -      -       +      -
    132A  LEU      3.5     2.2    -      -       -      +
    133A  THR*     3.4    44.6    -      -       -      +
    163A  HIS*     3.3     4.4    -      -       -      -
    164A  TYR*     2.7    47.4    +      -       +      +
    166A  VAL*     4.0    11.2    -      -       +      -
    182A  PHE*     3.9    14.1    -      -       +      -
    183A  LYS*     1.3    71.5    -      -       -      +
    185A  PHE*     1.3    63.0    +      -       -      +
    186A  TYR*     6.2     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 185 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130A  THR*     5.1     5.6    -      -       -      -
    131A  VAL*     3.4     7.3    -      -       -      +
    132A  LEU*     2.7    59.6    +      -       +      +
    134A  HIS*     3.4    42.0    -      +       +      +
    162A  LYS*     3.2    47.1    -      -       +      -
    163A  HIS*     3.7     9.4    -      +       +      -
    183A  LYS      3.8     1.0    +      -       -      -
    184A  MSE      1.3    71.5    -      -       -      +
    186A  TYR*     1.3    68.7    +      -       -      +
    187A  ASP*     3.9    29.6    -      -       +      -
    143B  LYS*     5.8     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 186 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126A  ILE*     4.5     4.5    -      -       +      -
    128A  GLN*     3.7    35.7    -      -       +      -
    130A  THR      3.4     6.5    -      -       -      +
    131A  VAL*     5.0     0.2    -      -       +      -
    159A  GLN*     3.2    17.8    +      -       +      -
    160A  THR      2.7    30.5    +      -       -      -
    161A  ALA*     3.1    23.3    +      -       -      +
    162A  LYS*     3.1    26.3    +      -       -      +
    163A  HIS      3.4    17.7    -      -       -      -
    164A  TYR*     3.4    30.5    -      +       +      -
    184A  MSE      6.2     0.2    -      -       +      -
    185A  PHE*     1.3    85.2    -      -       -      +
    187A  ASP*     1.3    63.4    +      -       -      +
    188A  LYS*     4.2    25.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 187 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  GLN*     4.5     3.3    -      -       -      +
    129A  PRO*     3.3    16.8    -      -       -      +
    130A  THR*     3.0    33.4    +      -       -      +
    185A  PHE*     3.9    20.3    -      -       +      -
    186A  TYR*     1.3    77.4    -      -       -      +
    188A  LYS*     1.4    68.4    +      -       -      +
    189A  ARG*     3.4    15.4    +      -       -      +
    190A  GLY      3.3    17.1    +      -       -      -
----------------------------------------------------------
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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