Contacts of the strand formed by residues 164 - 174 (chain H) in PDB entry 2I5N


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 GLU 164 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156H  PRO*     3.6    27.2    -      -       +      +
    157H  VAL      3.5     5.8    -      -       -      +
    158H  VAL*     4.4     7.5    -      -       +      +
    162H  GLY      4.0     1.8    +      -       -      -
    163H  VAL*     1.3    82.6    -      -       -      +
    165H  ALA*     1.3    60.6    +      -       -      +
    166H  GLY*     3.8    23.3    +      -       -      +
    167H  THR*     4.0    10.0    +      -       -      -
    188H  ALA*     4.4     9.4    -      -       +      +
    215H  SER*     4.5     0.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 165 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    157H  VAL*     2.8    13.8    +      -       +      +
    159H  ALA*     4.3     3.1    -      -       +      -
    163H  VAL      3.3     0.8    +      -       -      -
    164H  GLU*     1.3    73.7    -      -       -      +
    166H  GLY*     1.3    57.9    +      -       -      +
    185H  LEU*     4.5     3.0    -      -       +      +
    187H  VAL*     3.6    11.6    -      -       -      +
    188H  ALA*     2.9    24.3    +      -       -      +
    215H  SER*     4.1    18.6    -      -       -      +
    218H  PHE*     3.3    43.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 166 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156H  PRO*     3.5     5.5    -      -       -      +
    157H  VAL*     2.9    28.3    +      -       -      +
    164H  GLU*     3.5    11.0    -      -       -      +
    165H  ALA*     1.3    80.9    -      -       -      +
    167H  THR*     1.3    63.7    +      -       -      -
    185H  LEU*     4.2     4.3    -      -       -      -
    186H  SER      3.1    13.9    -      -       -      -
    188H  ALA*     3.8     9.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 167 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154H  GLY*     3.8    26.0    -      -       -      +
    155H  LEU      3.5     3.6    -      -       -      +
    156H  PRO*     5.1     1.0    -      -       -      +
    157H  VAL*     4.8     0.2    -      -       -      -
    164H  GLU*     4.0     9.9    +      -       -      -
    166H  GLY*     1.3    75.3    +      -       -      -
    168H  VAL*     1.3    74.0    +      -       -      +
    169H  THR*     3.4     6.9    +      -       +      +
    185H  LEU*     3.1     4.3    -      -       -      +
    186H  SER*     2.9    36.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 168 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152H  PRO*     3.2    37.5    -      -       +      +
    153H  ARG*     3.6     4.9    -      -       +      +
    154H  GLY*     2.8    28.6    +      -       -      -
    155H  LEU      2.9    18.6    +      -       -      +
    157H  VAL*     3.7    21.9    -      -       +      +
    167H  THR*     1.3    73.7    -      -       -      +
    169H  THR*     1.3    60.5    +      -       -      +
    170H  ASP      3.9    14.1    -      -       -      +
    183H  LEU*     4.3    15.5    -      -       +      -
    184H  GLU      3.5    13.2    -      -       -      +
    185H  LEU*     4.0     2.9    -      -       +      -
    208H  ILE*     3.9    18.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 169 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138H  ARG*     5.4     1.1    +      -       -      -
    153H  ARG*     3.7    16.6    -      -       -      +
    167H  THR*     3.5    20.2    -      -       +      +
    168H  VAL*     1.3    73.2    -      -       -      +
    170H  ASP*     1.3    63.2    +      -       -      +
    184H  GLU*     2.8    33.4    +      -       -      +
    185H  LEU*     4.1     1.9    -      -       -      -
    186H  SER*     3.7    22.8    +      -       -      +
    193H  THR*     4.7     1.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 170 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136H  PRO*     3.5     3.8    -      -       +      +
    137H  LEU*     3.3    27.7    +      -       -      +
    138H  ARG*     3.1    57.8    +      -       -      +
    153H  ARG*     4.0    14.8    +      -       -      -
    168H  VAL*     3.9     6.6    -      -       -      +
    169H  THR*     1.3    81.6    +      -       -      +
    171H  LEU*     1.3    72.9    +      -       -      +
    183H  LEU*     3.6     3.5    -      -       -      -
    184H  GLU*     2.9    34.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 171 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136H  PRO*     3.3     2.1    -      -       -      +
    137H  LEU*     3.0    39.5    +      -       +      +
    145H  ILE*     4.1     8.1    -      -       +      -
    152H  PRO*     3.8    24.9    -      -       +      -
    153H  ARG*     3.8    33.4    -      -       +      +
    170H  ASP*     1.3    80.5    +      -       -      +
    172H  TRP*     1.3    63.2    +      -       -      +
    180H  PHE*     3.8    44.6    -      -       +      -
    182H  TYR      3.5     7.9    -      -       -      +
    183H  LEU*     3.7    17.7    -      -       +      -
     10M  ILE*     4.2    10.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 172 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134H  ILE*     3.4    40.4    -      -       +      -
    135H  VAL*     3.3     8.3    -      -       -      +
    136H  PRO*     3.7    20.5    -      -       +      +
    171H  LEU*     1.3    77.8    -      -       -      +
    173H  VAL*     1.3    59.0    +      -       -      +
    180H  PHE*     3.6     4.5    -      -       -      -
    181H  ARG*     3.0    26.2    +      -       -      +
    182H  TYR*     2.8    29.3    +      -       +      +
    184H  GLU*     2.9    42.1    +      -       +      +
    195H  LEU*     3.8    28.4    -      -       +      +
    224H  LEU*     3.8    15.0    -      -       +      -
    227H  ARG      3.5    25.6    -      -       -      -
    228H  ASP      3.7     2.2    -      -       -      -
    229H  GLN*     3.6    28.7    -      -       -      -
    230H  ILE*     3.9     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 173 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133H  LYS      3.2     5.7    -      -       -      +
    134H  ILE*     3.4     4.4    -      -       -      -
    135H  VAL      2.8    34.8    +      -       -      +
    137H  LEU*     4.2     6.5    -      -       +      -
    140H  ALA*     3.8    24.5    -      -       +      -
    143H  PHE*     4.0    17.7    -      -       +      -
    171H  LEU      3.9     0.8    +      -       -      -
    172H  TRP*     1.3    72.4    -      -       -      +
    174H  ASP*     1.3    70.3    +      -       -      +
    175H  ARG*     4.1    10.8    -      -       +      -
    179H  TYR      3.7    11.0    -      -       -      +
    180H  PHE*     3.7    24.9    -      -       +      -
     12M  ALA*     3.9    18.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 174 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133H  LYS*     3.4    19.3    +      -       -      +
    134H  ILE*     3.7    14.2    -      -       +      +
    173H  VAL*     1.3    73.7    -      -       -      +
    175H  ARG*     1.3    56.2    +      -       -      +
    176H  SER*     2.9    23.2    +      -       -      -
    177H  GLU*     2.9    20.3    +      -       +      +
    178H  HIS*     2.9    31.0    +      -       -      -
    179H  TYR      2.8    22.3    +      -       -      +
    181H  ARG*     2.9    39.8    +      -       -      +
    231M  ARG*     4.6     2.1    +      -       -      -
----------------------------------------------------------
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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