Contacts of the strand formed by residues 176 - 187 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141B  ILE*     3.3    43.4    -      -       +      +
    142B  GLU*     3.6     9.5    -      -       -      +
    169B  LYS*     3.8    23.6    -      -       +      -
    170B  SER      3.6     9.2    -      -       -      +
    171B  TYR*     3.5    29.3    -      -       +      +
    175B  THR*     1.3    70.8    -      -       -      +
    177B  VAL*     1.3    59.5    +      -       -      +
    178B  PHE      3.4    21.8    -      -       -      +
    179B  LYS*     4.0    25.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 177 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114B  LEU*     4.6     0.2    -      -       +      -
    140B  PHE*     3.6     4.5    -      -       -      +
    141B  ILE*     2.9    25.0    +      -       -      -
    142B  GLU*     3.3    33.5    +      -       +      +
    143B  LYS      5.1     2.7    -      -       -      +
    144B  VAL*     3.7    28.5    -      -       +      +
    150B  VAL*     4.5     3.1    -      -       +      -
    170B  SER*     3.0    25.4    +      -       -      +
    171B  TYR*     4.1     1.1    -      -       -      -
    172B  VAL*     3.9    28.5    -      -       +      -
    175B  THR*     3.4    17.5    -      -       +      +
    176B  LEU*     1.3    74.7    -      -       -      +
    178B  PHE*     1.3    63.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 178 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114B  LEU*     4.1    17.7    -      -       +      -
    115B  PHE*     4.3    12.8    -      -       -      -
    118B  ALA*     3.7    28.5    -      -       +      -
    138B  ILE*     3.5    38.8    -      -       +      -
    139B  GLN      3.5    10.8    -      -       -      -
    140B  PHE*     3.8    37.5    -      +       +      -
    141B  ILE*     3.7     3.4    -      -       -      -
    168B  VAL*     4.5     4.7    -      -       +      -
    169B  LYS*     3.6     0.3    -      -       -      -
    170B  SER*     2.9    54.3    +      -       -      -
    176B  LEU*     3.4     9.6    -      -       -      +
    177B  VAL*     1.3    79.8    -      -       -      +
    179B  LYS*     1.3    60.2    +      -       -      +
    180B  GLY*     3.9    16.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 179 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137B  SER      4.1     0.6    -      -       -      +
    138B  ILE*     3.4     2.6    -      -       -      +
    139B  GLN*     2.8    59.4    +      -       +      +
    141B  ILE*     3.6    11.9    -      -       +      -
    168B  VAL      3.4     8.1    -      -       -      +
    169B  LYS*     3.8    35.9    -      -       +      +
    176B  LEU*     4.0    20.9    -      -       +      +
    178B  PHE*     1.3    75.3    -      -       -      +
    180B  GLY*     1.3    59.0    +      -       -      +
    181B  ASN*     5.1     8.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 180 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137B  SER      3.4     7.4    -      -       -      -
    138B  ILE*     3.9    12.8    -      -       -      -
    167B  GLU*     3.5     2.5    -      -       -      +
    168B  VAL*     2.6    44.8    +      -       -      +
    178B  PHE*     3.9     8.8    -      -       -      -
    179B  LYS*     1.3    76.6    -      -       -      +
    181B  ASN*     1.3    64.3    +      -       -      -
    182B  PHE*     3.7     7.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 181 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136B  SER*     3.2     8.5    +      -       -      -
    137B  SER*     2.8    50.2    +      -       -      +
    166B  VAL      3.4     4.3    -      -       -      +
    167B  GLU*     3.3    29.4    -      -       -      +
    179B  LYS*     5.1     7.3    -      -       -      +
    180B  GLY*     1.3    79.6    -      -       -      +
    182B  PHE*     1.3    60.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 182 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115B  PHE*     3.5    25.4    -      +       -      -
    118B  ALA*     3.7    22.4    -      -       +      -
    119B  ASN*     3.7    22.7    -      -       -      -
    122B  CYS*     3.7    18.2    -      -       -      -
    133B  THR*     4.0    17.7    -      -       +      -
    135B  GLU      3.7     1.1    -      -       -      -
    136B  SER*     3.4    21.5    -      -       -      -
    138B  ILE*     4.3     1.8    -      -       +      -
    164B  TYR      3.5     1.0    -      -       -      +
    165B  TYR*     3.4     8.2    -      -       -      +
    166B  VAL*     2.7    42.7    +      -       +      +
    168B  VAL*     3.8    25.6    -      -       +      -
    180B  GLY*     3.7    21.3    -      -       -      -
    181B  ASN*     1.3    77.5    -      -       -      +
    183B  LYS*     1.3    59.2    +      -       -      +
    184B  MSE      3.8     9.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 183 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133B  THR*     3.8     0.9    -      -       -      -
    134B  HIS*     2.8    37.8    +      -       +      +
    135B  GLU*     2.9    58.9    +      -       +      +
    163B  HIS*     3.6    35.5    -      -       +      +
    164B  TYR      3.8     2.7    -      -       -      -
    165B  TYR*     3.6    40.6    +      -       +      -
    182B  PHE*     1.3    70.1    -      -       -      +
    184B  MSE      1.3    56.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with MSE 184 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119B  ASN      4.7     0.2    -      -       -      +
    122B  CYS*     3.8    20.9    -      -       +      -
    123B  VAL*     3.8    20.6    -      -       +      +
    126B  ILE*     3.7    27.6    -      -       +      -
    131B  VAL*     3.7    26.5    -      -       +      -
    132B  LEU*     3.6     2.2    -      -       -      +
    133B  THR*     3.4    45.3    -      -       -      +
    163B  HIS*     3.3     3.4    -      -       -      -
    164B  TYR*     2.7    48.2    +      -       +      +
    166B  VAL*     4.1    10.5    -      -       +      -
    182B  PHE*     4.0    12.6    -      -       +      -
    183B  LYS*     1.3    70.7    -      -       -      +
    185B  PHE*     1.3    62.9    +      -       -      +
    186B  TYR*     3.7     0.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 185 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143A  LYS*     6.1     1.8    -      -       -      -
    130B  THR*     5.1     5.6    -      -       -      -
    131B  VAL*     3.4     7.1    -      -       -      +
    132B  LEU*     2.7    58.7    +      -       +      +
    134B  HIS*     3.4    42.0    -      +       +      +
    162B  LYS*     3.2    40.2    -      -       +      -
    163B  HIS*     3.7     9.0    -      +       +      -
    183B  LYS      3.8     1.0    +      -       -      -
    184B  MSE      1.3    73.3    -      -       -      +
    186B  TYR*     1.3    66.9    +      -       -      +
    187B  ASP*     3.9    30.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 186 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126B  ILE*     4.5     4.7    -      -       +      -
    128B  GLN*     3.7    32.8    -      -       +      -
    130B  THR      3.4     6.5    -      -       -      +
    131B  VAL*     5.0     0.4    -      -       +      -
    159B  GLN*     3.2    17.7    +      -       +      -
    160B  THR      2.7    29.4    +      -       -      -
    161B  ALA*     3.1    24.0    +      -       -      +
    162B  LYS*     3.1    24.8    +      -       -      +
    163B  HIS      3.4    18.4    -      -       -      -
    164B  TYR*     3.4    30.5    -      +       +      -
    184B  MSE      4.7     0.2    -      -       -      +
    185B  PHE*     1.3    83.2    -      -       -      +
    187B  ASP*     1.3    63.6    +      -       -      +
    188B  LYS*     4.2    28.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 187 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128B  GLN*     4.5     1.1    -      -       -      +
    129B  PRO*     3.4    15.8    -      -       -      +
    130B  THR*     3.0    33.8    +      -       -      +
    185B  PHE*     3.9    21.3    -      -       +      -
    186B  TYR*     1.3    75.6    -      -       -      +
    188B  LYS*     1.3    65.4    +      -       -      +
    189B  ARG*     3.0    49.6    +      -       -      +
----------------------------------------------------------
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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