Contacts of the helix formed by residues 12 - 25 (chain B) in PDB entry 4HI7


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 SER 12 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  ILE*     3.1    24.8    +      -       -      +
     10B  ASP      3.1     1.2    -      -       -      -
     11B  ALA*     1.3    77.0    -      -       -      +
     13B  PRO*     1.3    68.3    -      -       -      +
     14B  PRO*     3.3    12.0    -      -       -      +
     15B  VAL*     3.5    16.6    -      -       -      +
     16B  ARG*     3.1    21.8    +      -       -      +
     36B  LEU*     5.0     1.3    -      -       -      -
     55B  VAL*     4.2     1.9    -      -       -      +
    301B  GSH      3.3    31.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 13 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  ALA      3.4     8.1    -      -       -      +
     12B  SER*     1.3    82.6    -      -       -      +
     14B  PRO*     1.3    73.0    -      -       +      +
     16B  ARG*     3.0    22.4    +      -       -      +
     17B  ALA      3.1     0.5    +      -       -      -
    103B  GLU*     5.6     0.4    -      -       -      +
    108B  PHE*     4.4     3.1    -      -       +      -
    112B  LEU*     3.8    24.9    -      -       +      -
    166B  SER*     3.1    42.4    -      -       -      +
    167B  SER*     4.1     6.7    -      -       -      +
    170B  SER*     3.4    18.4    -      -       -      +
    208B  PHE*     4.5     9.2    -      -       +      -
    301B  GSH      4.2     8.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 14 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B  SER*     3.3    14.4    -      -       -      +
     13B  PRO*     1.3    97.3    -      -       +      +
     15B  VAL*     1.3    60.1    +      -       -      +
     17B  ALA*     3.3    11.3    +      -       +      +
     18B  VAL*     3.4    10.2    +      -       -      +
     55B  VAL      3.9     5.4    -      -       -      +
     56B  PRO*     3.6    18.6    -      -       +      -
     68B  SER*     3.4    32.0    -      -       -      +
    103B  GLU*     6.1     0.9    -      -       -      +
    108B  PHE*     3.7    15.3    -      -       +      -
    166B  SER*     4.5     1.6    -      -       -      +
    301B  GSH      3.6    29.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 15 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  LEU*     4.4     6.7    -      -       +      +
      8B  GLY*     3.7    24.0    -      -       -      -
      9B  ILE      3.5    21.5    -      -       -      +
     10B  ASP*     4.9     0.2    -      -       -      -
     12B  SER*     3.2    21.5    +      -       -      +
     13B  PRO      3.2     0.6    -      -       -      -
     14B  PRO*     1.3    78.8    -      -       -      +
     16B  ARG*     1.3    57.5    +      -       -      +
     18B  VAL*     3.1     6.1    +      -       -      +
     19B  LYS*     2.9    35.4    +      -       +      +
     31B  TYR*     3.7    21.3    -      -       +      +
     55B  VAL*     3.9     3.1    -      -       +      -
     56B  PRO*     3.7    28.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 16 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  ASP*     2.8    32.0    +      -       +      +
     11B  ALA      2.9    21.2    +      -       -      -
     12B  SER      3.1     5.7    +      -       -      -
     13B  PRO*     3.0    21.1    +      -       -      +
     15B  VAL*     1.3    74.3    -      -       -      +
     17B  ALA*     1.3    64.5    +      -       -      +
     19B  LYS*     3.7     9.1    -      -       +      +
     20B  LEU*     2.9    29.4    +      -       -      +
    166B  SER*     3.1    19.6    +      -       -      -
    169B  SER*     3.5     7.1    +      -       -      -
    170B  SER*     2.8    22.0    +      -       -      -
    200B  GLU      3.5    13.4    -      -       -      +
    201B  ASN*     2.8    60.1    +      -       -      +
    204B  GLY*     3.5     3.6    -      -       -      -
    205B  ALA*     3.4    23.0    -      -       -      +
    208B  PHE*     4.0     3.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 17 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  PRO      3.1     6.4    +      -       -      +
     14B  PRO*     3.6    11.9    -      -       +      +
     15B  VAL      3.3     0.4    -      -       -      -
     16B  ARG*     1.3    76.1    -      -       -      +
     18B  VAL*     1.3    60.2    +      -       -      +
     20B  LEU*     3.4     4.4    +      -       -      +
     21B  THR*     2.9    26.2    +      -       -      -
     68B  SER*     4.7     2.2    -      -       -      +
     72B  MET*     3.5    23.2    -      -       +      +
    162B  PHE*     3.7    20.3    -      -       -      +
    163B  SER*     3.9     7.6    -      -       -      +
    166B  SER*     3.6    19.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 18 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  LEU*     3.8    26.0    -      -       +      -
     14B  PRO      3.4    12.5    +      -       -      +
     15B  VAL*     3.1     8.4    +      -       -      +
     17B  ALA*     1.3    75.4    -      -       -      +
     19B  LYS*     1.3    59.0    +      -       -      +
     21B  THR*     3.1     2.1    +      -       -      -
     22B  LEU*     2.9    41.7    +      -       +      +
     56B  PRO*     4.0     8.5    -      -       +      -
     58B  LEU*     5.1     0.4    -      -       +      -
     68B  SER*     3.9    23.8    -      -       -      +
     71B  ILE*     3.9    31.0    -      -       +      -
     72B  MET*     4.2     8.1    -      -       +      -
     75B  LEU*     4.2     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 19 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  LEU*     3.9    17.0    -      -       +      -
     10B  ASP*     2.7    38.0    +      -       -      +
     15B  VAL*     2.9    23.1    +      -       +      +
     16B  ARG*     3.2    11.4    +      -       +      +
     18B  VAL*     1.3    74.7    -      -       -      +
     20B  LEU*     1.3    62.9    +      -       -      +
     22B  LEU*     3.4     4.5    +      -       -      +
     23B  ALA*     3.0    24.3    +      -       -      +
     29B  TYR*     3.9    13.0    +      -       -      +
     31B  TYR*     3.6    22.8    -      -       +      +
    200B  GLU*     3.2    52.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 20 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16B  ARG      2.9    18.9    +      -       -      +
     17B  ALA*     3.6     6.7    -      -       -      +
     19B  LYS*     1.3    76.5    -      -       -      +
     21B  THR*     1.3    58.3    +      -       -      +
     23B  ALA*     3.3     5.7    +      -       -      +
     24B  ALA*     2.9    29.1    +      -       -      +
    162B  PHE*     3.8    32.3    -      -       +      +
    165B  ILE*     3.7    30.3    -      -       +      -
    166B  SER      5.3     0.2    -      -       -      +
    195B  LEU*     5.5     1.8    -      -       +      -
    197B  TYR*     3.7    36.8    -      -       +      +
    198B  TYR*     4.4    10.5    -      -       +      -
    200B  GLU*     4.2     1.1    -      -       +      -
    201B  ASN*     3.9    31.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 21 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  ALA      2.9    12.7    +      -       -      -
     18B  VAL*     3.1     9.2    +      -       -      -
     20B  LEU*     1.3    74.8    -      -       -      +
     22B  LEU*     1.3    65.4    +      -       -      +
     24B  ALA*     3.2     1.9    +      -       -      +
     25B  LEU*     3.0    46.2    +      -       +      +
     72B  MET*     3.1    33.8    -      -       +      +
     75B  LEU*     4.4     7.6    -      -       +      -
     76B  VAL*     4.1    18.6    -      -       +      -
     85B  LEU*     5.2     0.7    -      -       +      -
    159B  ILE*     4.0     7.8    -      -       +      +
    162B  PHE*     3.3    18.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 22 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4B  PRO*     4.8     2.7    -      -       +      -
      6B  LEU*     4.1     9.2    -      -       +      -
     18B  VAL*     2.9    35.4    +      -       +      +
     19B  LYS      3.8     2.2    -      -       -      +
     21B  THR*     1.3    75.2    -      -       -      +
     23B  ALA*     1.3    57.4    +      -       -      +
     25B  LEU*     3.4     4.6    +      -       +      +
     26B  GLN*     3.0    21.7    +      -       -      -
     27B  LEU*     3.1    41.7    +      -       +      +
     29B  TYR*     3.5    59.7    -      -       +      -
     58B  LEU*     5.0     3.6    -      -       +      -
     75B  LEU*     3.8    26.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 23 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  LYS      3.0    17.1    +      -       -      +
     20B  LEU      3.5     4.7    -      -       -      +
     22B  LEU*     1.3    75.1    -      -       -      +
     24B  ALA*     1.3    67.4    +      -       -      +
     26B  GLN*     3.1    19.7    +      -       -      +
     29B  TYR*     5.3     0.9    -      -       -      -
    197B  TYR*     3.6    36.3    -      -       +      -
    200B  GLU*     4.2    11.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 24 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20B  LEU      2.9    15.7    +      -       -      +
     21B  THR      3.2     4.9    +      -       -      +
     23B  ALA*     1.3    76.7    -      -       -      +
     25B  LEU*     1.3    62.2    +      -       -      +
     26B  GLN*     3.2     9.2    +      -       -      +
     85B  LEU*     3.9    16.0    -      -       +      +
    162B  PHE*     3.8    15.3    -      -       +      -
    197B  TYR*     3.4    32.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 25 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21B  THR*     3.0    28.0    +      -       +      +
     22B  LEU*     3.8     7.6    -      -       -      +
     23B  ALA      3.2     0.2    -      -       -      -
     24B  ALA*     1.3    76.6    -      -       -      +
     26B  GLN*     1.3    68.4    +      -       -      +
     27B  LEU*     3.1    16.5    +      -       +      +
     75B  LEU*     3.8    39.0    -      -       +      +
     76B  VAL*     4.2     6.3    -      -       +      +
     79B  TYR*     4.6    11.1    -      -       +      +
     80B  GLY*     3.7    28.9    -      -       -      +
     81B  LYS      5.0     1.1    -      -       -      +
     85B  LEU*     4.0    21.5    -      -       +      -
----------------------------------------------------------
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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