Contacts of the strand formed by residues 2133 - 2139 (chain B) in PDB entry 2H7C


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 LEU2133 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2124B  PRO*     4.0    17.7    -      -       +      -
   2125B  ALA*     3.7    27.1    -      -       +      +
   2131B  ASN*     4.4    10.3    -      -       +      +
   2132B  ARG*     1.3    80.6    -      -       -      +
   2134B  PRO*     1.3    79.0    -      -       +      +
   2162B  ASN*     3.2    41.7    -      -       -      +
   2164B  VAL*     4.2     7.2    -      -       +      +
   2209B  GLY      2.9    15.8    +      -       -      +
   2210B  GLY*     3.5     2.3    -      -       -      -
   2211B  ASN*     2.8    29.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO2134 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2132B  ARG      4.4     1.6    -      -       -      +
   2133B  LEU*     1.3    92.0    -      -       +      +
   2135B  VAL*     1.3    58.7    +      -       -      +
   2162B  ASN      4.0     6.1    -      -       -      +
   2163B  VAL*     3.6    25.8    -      -       +      +
   2164B  VAL*     2.9    25.3    +      -       -      +
   2214B  SER*     3.8    24.0    -      -       -      +
   2504B  ALA*     4.3    19.3    -      -       +      +
   2505B  ARG*     4.3    26.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL2135 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2133B  LEU      3.7     0.9    -      -       -      +
   2134B  PRO*     1.3    78.2    -      -       -      +
   2136B  MET*     1.3    59.3    +      -       -      +
   2137B  VAL*     3.9    21.5    -      -       +      -
   2164B  VAL*     3.5    11.4    -      -       +      +
   2166B  VAL*     4.0    15.5    -      -       +      -
   2201B  VAL*     4.2     6.3    -      -       +      -
   2205B  ILE*     3.7    26.5    -      -       +      -
   2210B  GLY*     3.9     3.4    -      -       -      -
   2211B  ASN      3.7    31.2    -      -       -      +
   2214B  SER      2.9    10.3    +      -       -      +
   2215B  VAL*     3.4     7.2    -      -       +      -
   2216B  THR*     2.7    35.5    +      -       -      +
   2504B  ALA*     5.2     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET2136 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2135B  VAL*     1.3    75.5    -      -       -      +
   2137B  VAL*     1.3    63.0    +      -       -      +
   2138B  TRP      3.8     0.5    +      -       -      -
   2157B  LEU*     4.3    11.7    -      -       +      -
   2163B  VAL*     4.0    27.6    -      -       +      -
   2164B  VAL      2.8    12.3    +      -       -      +
   2165B  VAL*     3.5     6.6    -      -       +      +
   2166B  VAL      2.9    26.0    +      -       -      +
   2216B  THR*     3.5    14.4    -      -       +      -
   2218B  PHE*     3.6    40.9    -      -       +      -
   2244B  ILE*     4.5     1.1    -      -       +      -
   2500B  TRP*     3.9    30.5    -      -       +      +
   2501B  ALA*     4.4    11.0    -      -       -      -
   2504B  ALA*     3.8    25.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL2137 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2135B  VAL*     3.9    13.0    -      -       +      -
   2136B  MET*     1.3    73.6    -      -       -      +
   2138B  TRP*     1.3    61.4    +      -       -      +
   2139B  ILE*     3.9     3.4    +      -       +      +
   2166B  VAL*     3.3    13.9    -      -       +      +
   2168B  ILE*     3.8    36.6    -      -       +      -
   2197B  ALA*     5.9     0.2    -      -       +      -
   2198B  LEU*     4.1    23.6    -      -       +      -
   2201B  VAL*     4.3    10.8    -      -       +      -
   2215B  VAL*     3.8    24.2    -      -       +      -
   2216B  THR      2.8    11.9    +      -       -      +
   2217B  ILE*     3.4     6.3    -      -       +      +
   2218B  PHE*     3.0    27.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP2138 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2136B  MET      5.2     0.2    -      -       -      +
   2137B  VAL*     1.3    71.9    -      -       -      +
   2139B  ILE*     1.3    67.1    +      -       -      +
   2140B  HIS*     3.6    14.5    +      -       +      +
   2141B  GLY      5.2     0.7    -      -       -      -
   2149B  ALA*     5.7     0.7    -      -       -      -
   2152B  TYR*     3.5    45.1    -      +       -      -
   2165B  VAL*     5.3     1.1    -      -       +      -
   2166B  VAL      2.8    13.9    +      -       -      +
   2167B  THR*     4.2    15.7    -      -       +      -
   2168B  ILE*     3.3    30.2    +      -       -      +
   2218B  PHE*     3.2    62.0    -      +       +      -
   2219B  GLY*     3.5    12.1    -      -       -      -
   2220B  GLU*     3.5    25.4    -      -       +      -
   2246B  GLU*     3.6    11.7    -      -       -      -
   2472B  LEU*     3.4    32.8    -      -       +      -
   2475B  VAL*     5.2     0.4    -      -       +      -
   2476B  PHE*     3.4    22.4    -      +       +      -
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Residues in contact with ILE2139 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2137B  VAL*     4.3     6.7    -      -       +      +
   2138B  TRP*     1.3    78.7    -      -       -      +
   2140B  HIS*     1.3    64.9    +      -       -      +
   2168B  ILE*     3.8    21.5    -      -       +      -
   2170B  TYR*     3.8    13.2    -      -       +      -
   2194B  GLN*     3.5    29.8    -      -       +      +
   2198B  LEU*     5.7     1.8    -      -       +      -
   2217B  ILE*     4.8     8.3    -      -       +      -
   2218B  PHE      2.9    13.8    +      -       -      +
   2219B  GLY*     3.1    20.4    -      -       -      -
   2220B  GLU      3.6     1.4    +      -       -      -
   2223B  GLY*     3.3    13.3    -      -       -      +
   2226B  SER*     4.0    13.7    -      -       -      -
   2227B  VAL*     4.2    16.4    -      -       +      -
   2230B  LEU*     4.0    27.6    -      -       +      -
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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