Contacts of the helix formed by residues 197 - 207 (chain L) in PDB entry 1H2I


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 197 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    192L  LYS*     2.7    29.8    +      -       -      +
    195L  ASP      3.4     8.7    +      -       -      +
    196L  LEU*     1.3    82.1    -      -       -      +
    198L  PRO*     1.3    60.3    -      -       -      +
    199L  SER*     3.3     6.7    +      -       -      -
    200L  VAL*     3.0    19.1    +      -       +      +
    201L  GLU*     2.7    33.4    +      -       -      +
     42M  ALA*     3.6    19.8    -      -       -      +
     45M  GLN*     3.4    19.5    +      -       -      +
     77M  GLU*     4.6    13.3    +      -       -      +
     78M  MET*     4.0    22.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 198 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194L  GLN*     6.0     0.9    -      -       -      +
    196L  LEU*     3.3    22.4    -      -       +      +
    197L  GLU*     1.3    90.5    -      -       -      +
    199L  SER*     1.3    60.8    +      -       -      +
    201L  GLU*     3.3     7.5    +      -       +      +
    202L  GLU*     2.9    32.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 199 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197L  GLU*     3.3     4.4    +      -       -      -
    198L  PRO*     1.3    78.2    -      -       -      +
    200L  VAL*     1.3    65.5    +      -       -      +
    202L  GLU*     3.4    16.7    +      -       -      +
    203L  ALA*     3.1    23.9    +      -       -      +
     34M  GLU*     5.1     0.5    -      -       -      +
     38M  ALA*     3.9    11.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 200 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197L  GLU*     3.0    17.8    +      -       +      +
    199L  SER*     1.3    79.0    +      -       -      +
    201L  GLU*     1.3    58.5    +      -       -      +
    203L  ALA*     3.7     1.4    -      -       -      +
    204L  ARG*     2.8    58.0    +      -       -      +
     35M  GLU*     4.6     1.7    -      -       +      +
     38M  ALA*     3.4    40.8    -      -       +      +
     39M  ILE*     3.6    16.2    -      -       +      +
     42M  ALA*     4.0    13.5    -      -       +      -
     77M  GLU      4.5     1.3    -      -       -      +
     78M  MET*     3.4    15.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 201 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    196L  LEU*     5.1     8.3    -      -       +      -
    197L  GLU      2.7    15.2    +      -       -      +
    198L  PRO*     3.7     9.0    -      -       +      +
    199L  SER      3.2     0.2    -      -       -      -
    200L  VAL*     1.3    77.9    -      -       -      +
    202L  GLU*     1.3    59.5    -      -       -      +
    204L  ARG*     3.6    11.5    +      -       -      +
    205L  TYR*     2.8    32.5    +      -       +      +
     77M  GLU*     5.8     0.6    -      -       -      +
     36N  TYR*     2.7    38.7    +      -       -      -
     37N  GLN*     4.4    15.1    -      -       -      +
     40N  GLN*     4.4    10.4    -      -       -      +
     41N  LYS*     5.4     2.6    -      -       -      +
     44N  ARG*     4.9    14.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 202 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198L  PRO      2.9    21.6    +      -       -      +
    199L  SER*     3.5    16.2    -      -       -      +
    200L  VAL      3.2     0.2    -      -       -      -
    201L  GLU*     1.3    74.9    -      -       -      +
    203L  ALA*     1.3    66.8    +      -       -      +
    205L  TYR*     3.0     9.0    +      -       -      +
    206L  ASN*     2.9    36.8    +      -       -      +
     34M  GLU*     4.7     8.3    -      -       -      +
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Residues in contact with ALA 203 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199L  SER      3.1    13.7    +      -       -      +
    200L  VAL      3.8     2.7    -      -       -      +
    202L  GLU*     1.3    81.3    -      -       -      +
    204L  ARG*     1.3    62.5    +      -       -      +
    206L  ASN*     3.2    12.2    +      -       -      +
    207L  SER*     3.4    12.3    +      -       -      -
     32M  THR*     4.8     2.1    +      -       -      -
     34M  GLU*     3.7    31.2    -      -       +      +
     35M  GLU*     3.6    34.3    -      -       -      +
     38M  ALA*     4.5     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 204 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200L  VAL*     2.8    32.4    +      -       -      +
    201L  GLU*     3.6    14.3    +      -       -      +
    203L  ALA*     1.3    73.1    -      -       -      +
    205L  TYR*     1.3    62.2    +      -       -      +
    207L  SER*     2.5    23.6    +      -       -      -
    208L  CYS*     4.0     6.6    -      -       -      -
     35M  GLU*     2.7    49.4    +      -       -      +
     39M  ILE*     4.1     0.8    -      -       -      +
     77M  GLU      2.8    29.3    +      -       -      -
     78M  MET      3.2    19.0    +      -       -      -
     79M  PHE*     3.5    21.8    -      -       -      +
     80M  GLY*     3.6     6.3    -      -       -      +
     82M  ASN*     4.8     1.6    -      -       -      +
    116M  LYS*     4.2    10.3    -      -       -      +
     36N  TYR*     2.7    43.3    +      -       +      +
     40N  GLN*     4.6     1.0    +      -       -      -
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Residues in contact with TYR 205 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201L  GLU*     2.8    25.0    +      -       +      +
    202L  GLU*     3.3     6.3    -      -       -      +
    204L  ARG*     1.3    79.0    -      -       -      +
    206L  ASN*     1.3    72.0    +      -       -      +
    207L  SER      3.2     1.2    +      -       -      -
    208L  CYS*     3.6    12.5    +      -       -      -
    209L  ARG*     3.1    34.8    +      -       -      -
     33N  ALA*     3.5    40.7    -      -       +      +
     34N  GLU*     4.5     7.3    +      -       -      +
     36N  TYR*     4.6    10.3    -      +       -      -
     37N  GLN*     3.1    40.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 206 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202L  GLU*     2.9    27.7    +      -       -      +
    203L  ALA      3.2     5.3    +      -       -      +
    205L  TYR*     1.3    84.5    -      -       -      +
    207L  SER*     1.3    59.7    +      -       -      +
    208L  CYS      3.3     1.2    +      -       -      -
    209L  ARG*     3.7    40.2    +      -       -      +
     34M  GLU*     3.8    24.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 207 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    203L  ALA      3.4     8.1    +      -       -      -
    204L  ARG*     2.5    24.9    +      -       -      +
    205L  TYR      3.2     0.2    -      -       -      -
    206L  ASN*     1.3    75.1    -      -       -      +
    208L  CYS*     1.3    61.5    +      -       -      +
    209L  ARG      3.3    11.2    +      -       -      +
     32M  THR*     3.8    30.6    -      -       -      +
     35M  GLU*     3.9    13.2    +      -       -      -
    116M  LYS*     4.7     5.3    +      -       -      -
     30N  GLN*     5.3     2.9    -      -       -      +
----------------------------------------------------------
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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