Contacts of the strand formed by residues 208 - 215 (chain B) in PDB entry 1H1B


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 208 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122B  GLN*     3.4    18.4    -      -       +      +
    123B  LEU      4.4     5.4    -      -       -      +
    124B  PRO*     3.8    31.4    -      -       +      -
    125B  ALA      5.2     0.2    -      -       -      +
    128B  ARG*     4.5    18.4    -      -       -      +
    200B  VAL*     3.7     1.0    -      -       -      -
    201B  CYS      3.0    28.4    +      -       -      +
    204B  ASN      3.7    13.2    -      -       -      +
    205B  GLY*     1.3    85.1    -      -       -      +
    209B  ILE*     1.3    62.0    +      -       -      +
    210B  HIS*     3.2    23.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 209 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29B  PHE*     4.3    13.5    -      -       +      -
     45B  THR*     4.2     5.2    -      -       +      +
     53B  MET*     3.9    21.1    -      -       +      -
    121B  ALA*     3.9    24.0    -      -       +      -
    122B  GLN      3.0    15.8    +      -       -      +
    123B  LEU*     3.8    18.2    -      -       +      -
    124B  PRO*     2.9    21.4    -      -       -      +
    198B  PRO*     4.0    24.5    -      -       +      -
    199B  LEU      3.7     2.0    -      -       -      +
    200B  VAL*     4.6     8.5    -      -       +      -
    205B  GLY      5.6     1.1    -      -       -      +
    208B  LEU*     1.3    71.1    -      -       -      +
    210B  HIS*     1.3    61.0    +      -       -      +
    211B  GLY      3.5    21.8    -      -       -      +
    212B  ILE*     5.1     0.4    -      -       +      -
    231B  VAL*     3.4    12.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 210 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124B  PRO*     3.6    24.9    -      -       +      +
    128B  ARG*     3.6    38.3    +      -       +      -
    130B  LEU*     3.6    32.9    -      -       +      +
    181B  VAL*     4.1    10.9    -      -       -      +
    199B  LEU*     3.0     8.0    +      -       +      -
    201B  CYS*     3.8    41.0    +      -       +      -
    208B  LEU*     3.2    29.2    +      -       +      +
    209B  ILE*     1.3    75.4    -      -       -      +
    211B  GLY*     1.3    57.7    +      -       -      +
    229B  ALA      3.7     1.2    -      -       -      +
    230B  PRO*     3.9     4.2    -      -       -      +
    231B  VAL*     3.1    23.2    +      -       -      -
    232B  ALA*     4.5     4.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 211 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181B  VAL*     5.4     0.4    -      -       -      -
    198B  PRO*     3.1     6.4    -      -       -      +
    199B  LEU*     2.7    43.3    +      -       -      +
    209B  ILE*     3.4     7.4    -      -       -      +
    210B  HIS*     1.3    82.3    -      -       -      +
    212B  ILE*     1.3    62.5    +      -       -      -
    228B  PHE*     3.9     9.9    -      -       -      -
    229B  ALA      3.2    10.3    -      -       -      -
    231B  VAL*     3.8     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 212 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45B  THR*     5.9     1.6    -      -       -      +
     53B  MET*     3.6    23.3    -      -       +      -
     54B  SER*     3.6     3.8    -      -       -      +
     55B  ALA*     3.6    16.6    -      -       +      +
    102B  ASP      5.1     0.2    -      -       -      +
    103B  ILE*     3.4    45.1    -      -       +      -
    196B  GLY*     3.3    41.1    -      -       -      +
    197B  SER      3.2     4.3    -      -       -      -
    198B  PRO*     5.3     1.3    -      -       +      -
    209B  ILE*     5.1     0.2    -      -       +      -
    211B  GLY*     1.3    77.7    -      -       -      +
    213B  ALA*     1.3    63.9    +      -       -      +
    214B  SER*     3.3     0.9    +      -       -      -
    228B  PHE*     3.7     3.1    -      -       -      +
    229B  ALA*     2.8    42.2    +      -       +      +
    231B  VAL*     3.8    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 213 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55B  ALA*     3.8     6.4    -      -       -      +
    190B  VAL*     5.0     9.2    -      -       +      -
    194B  ASP*     3.5    25.1    -      -       +      +
    195B  SER*     3.4     7.6    -      -       -      -
    196B  GLY      2.9    22.9    +      -       -      -
    197B  SER*     2.8    16.2    +      -       -      +
    212B  ILE*     1.3    71.5    -      -       -      +
    214B  SER*     1.3    58.2    +      -       -      +
    227B  ALA      4.1     0.4    -      -       -      -
    228B  PHE*     3.4    26.5    -      -       +      -
    400B  151      4.5     6.5    -      -       +      -
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Residues in contact with SER 214 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55B  ALA*     5.1     0.2    -      -       -      -
     57B  HIS*     5.6     0.5    -      -       -      +
     99B  LEU*     3.6    13.9    -      -       -      +
    102B  ASP*     2.6    40.5    +      -       -      +
    180B  ASN*     5.0     2.7    +      -       -      -
    195B  SER*     3.8     2.2    +      -       -      -
    212B  ILE      3.9     7.2    -      -       -      -
    213B  ALA*     1.3    74.8    -      -       -      +
    215B  PHE*     1.3    76.3    +      -       -      +
    227B  ALA      2.9    15.9    +      -       -      -
    229B  ALA*     4.1     8.1    -      -       -      -
    400B  151      3.4    23.7    -      -       -      +
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Residues in contact with PHE 215 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99B  LEU*     3.5    20.4    -      +       -      +
    177B  ARG*     4.0    33.7    -      -       +      -
    180B  ASN*     3.7    24.7    -      -       -      -
    190B  VAL*     4.9     0.5    -      -       -      +
    214B  SER*     1.3    94.7    -      -       -      +
    216B  VAL*     1.3    70.0    +      -       -      +
    217B  ARG*     3.6    28.7    -      -       +      -
    226B  ASP*     3.9     0.9    -      -       -      +
    227B  ALA*     2.9    49.1    +      -       +      +
    400B  151      3.5    48.6    -      -       +      +
----------------------------------------------------------
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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