Contacts of the helix formed by residues 299 - 310 (chain I) in PDB entry 5G04


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 299 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    290I  PHE*     5.6     0.2    -      -       -      -
    291I  VAL*     5.4    11.7    -      -       -      -
    297I  THR      4.3     0.2    +      -       -      -
    298I  THR*     1.3    74.0    -      -       -      +
    300I  VAL*     1.3    62.8    +      -       -      +
    301I  GLN*     3.3     3.8    -      -       -      -
    302I  ASP*     3.3    21.4    +      -       -      +
    303I  GLU*     3.0    33.0    +      -       -      +
    456I  PHE      5.8     1.3    -      -       -      -
     58O  ARG*     4.1     7.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 300 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    287I  LEU*     3.8    31.9    -      -       +      +
    290I  PHE*     3.5    34.1    -      -       +      -
    291I  VAL*     4.0    20.7    -      -       +      +
    299I  SER*     1.3    70.6    -      -       -      +
    301I  GLN*     1.3    67.6    +      -       -      +
    303I  GLU*     4.9     2.7    -      -       -      -
    304I  PHE*     2.9    38.1    +      -       +      +
    456I  PHE*     3.9    32.0    -      -       +      +
    470I  PHE*     4.6     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 301 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    299I  SER*     3.3     1.9    -      -       -      -
    300I  VAL*     1.3    80.6    -      -       -      +
    302I  ASP*     1.3    75.8    +      -       -      +
    304I  PHE*     3.8     2.1    -      -       -      +
    305I  MET*     3.0    33.4    +      -       +      +
    452I  LEU*     3.6    20.9    -      -       -      +
    453I  THR*     3.8    29.4    +      -       -      +
    456I  PHE*     3.6    26.0    +      -       +      +
    457I  ASN*     3.4    29.8    +      -       -      +
     62O  GLN*     3.5    21.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 302 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    298I  THR*     6.0     0.2    -      -       -      -
    299I  SER*     3.3    28.2    +      -       -      +
    301I  GLN*     1.3    92.6    -      -       -      +
    303I  GLU*     1.3    62.5    +      -       +      +
    305I  MET*     3.6     7.2    +      -       -      +
    306I  HIS*     3.3    21.1    +      -       -      +
     55O  MET*     5.7     1.1    -      -       -      +
     58O  ARG*     3.5    48.4    +      -       +      +
     61O  ASN*     5.2     1.7    +      -       -      -
     62O  GLN*     3.5    20.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 303 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    290I  PHE*     3.3    33.7    -      -       -      -
    295I  ASN*     5.7     0.5    -      -       -      +
    298I  THR*     3.5    38.7    -      -       -      +
    299I  SER      3.0    13.4    +      -       -      +
    300I  VAL*     4.5     2.0    -      -       -      +
    302I  ASP*     1.3    73.9    -      -       -      +
    304I  PHE*     1.3    66.1    +      -       -      +
    306I  HIS*     3.6     8.1    +      -       -      +
    307I  LEU      3.3    13.0    +      -       -      -
    313I  ALA      4.7     2.1    -      -       -      +
    314I  SER*     4.7    10.8    +      -       -      +
    316I  GLU*     3.6    20.6    -      -       -      +
    317I  LEU*     3.4    32.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 304 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    287I  LEU*     4.6    10.1    -      -       +      -
    290I  PHE*     5.8     1.3    -      +       -      -
    300I  VAL*     2.9    36.4    +      -       +      +
    301I  GLN      3.8     0.4    -      -       -      +
    303I  GLU*     1.3    78.4    -      -       -      +
    305I  MET*     1.3    51.7    +      -       -      +
    307I  LEU*     2.7    42.4    +      -       +      +
    308I  LEU*     2.7    16.5    +      -       -      +
    317I  LEU*     4.4    19.1    -      -       +      -
    320I  LEU*     6.0     3.6    -      -       +      -
    321I  LEU*     5.1    13.7    -      -       +      -
    417I  PHE*     4.8    10.5    -      +       -      -
    420I  TRP*     3.8    30.0    -      +       -      -
    421I  LEU*     4.6    11.9    -      -       +      -
    452I  LEU*     3.7    19.1    -      -       +      -
    456I  PHE*     3.9    22.4    -      +       -      -
----------------------------------------------------------
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Residues in contact with MET 305 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301I  GLN*     3.0    22.1    +      -       +      +
    302I  ASP*     3.8     6.1    -      -       -      +
    303I  GLU      3.3     0.4    -      -       -      -
    304I  PHE*     1.3    74.7    -      -       -      +
    306I  HIS*     1.3    57.6    +      -       -      +
    308I  LEU*     3.2    17.8    +      -       -      +
    309I  LEU*     3.0    56.5    +      -       +      +
    449I  ALA*     4.8    12.6    -      -       -      +
    452I  LEU*     3.8    18.4    -      -       +      +
    453I  THR*     5.4     2.7    -      -       -      +
     61O  ASN*     3.4    27.8    -      -       +      +
     62O  GLN*     3.2    47.3    -      -       +      +
     65O  LEU*     4.9     6.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 306 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    302I  ASP      3.3    11.9    +      -       -      +
    303I  GLU*     3.6    11.4    -      -       -      +
    305I  MET*     1.3    77.7    -      -       -      +
    307I  LEU*     1.3    49.1    +      -       -      +
    309I  LEU      4.7     0.2    -      -       -      +
    310I  TRP*     2.8    54.5    +      +       +      +
    312I  LYS*     3.6    37.4    +      -       +      +
    313I  ALA*     3.8    12.9    +      -       -      -
    314I  SER*     4.1    12.0    +      -       -      -
     57O  ARG*     3.9    27.2    +      -       +      -
     61O  ASN*     3.5    26.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 307 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    303I  GLU      3.3     7.4    +      -       -      +
    304I  PHE*     2.7    42.0    +      -       +      +
    306I  HIS*     1.3    73.2    +      -       -      +
    308I  LEU*     1.3    59.6    +      -       -      +
    310I  TRP      3.0    19.0    -      -       -      +
    311I  GLY*     4.8     5.5    -      -       -      +
    313I  ALA*     3.6    31.2    -      -       +      +
    317I  LEU*     4.3    10.3    -      -       +      -
    321I  LEU*     4.7    16.2    -      -       +      -
    420I  TRP*     3.7    17.4    +      -       +      -
    421I  LEU*     5.1     2.0    -      -       +      -
    424I  ALA*     4.1    24.7    -      -       +      -
    427I  ARG*     5.9     1.1    +      -       -      +
    428I  MET*     5.8     6.3    -      -       +      -
    130O  SER*     5.2     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 308 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    304I  PHE      2.7    12.4    +      -       -      +
    305I  MET*     3.2    14.8    +      -       -      +
    307I  LEU*     1.3    75.0    -      -       -      +
    309I  LEU*     1.3    74.0    +      -       +      +
    420I  TRP*     3.6    31.3    +      -       +      +
    445I  ILE*     4.1    33.8    -      -       +      +
    448I  VAL*     3.9    14.4    -      -       +      -
    449I  ALA*     3.8    27.1    -      -       -      +
    452I  LEU*     3.8    23.6    -      -       +      -
     65O  LEU*     5.0     1.3    -      -       +      -
    130O  SER*     4.2     9.9    -      -       -      -
    131O  VAL*     4.6     6.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 309 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    305I  MET*     3.0    37.0    +      -       +      +
    308I  LEU*     1.3    96.2    -      -       +      +
    310I  TRP*     1.3    71.7    +      -       +      +
     61O  ASN*     3.1    41.5    -      -       +      +
     64O  LEU*     3.8    23.1    -      -       +      -
     65O  LEU*     4.2    21.8    -      -       +      -
    130O  SER*     3.1    17.5    -      -       -      -
    131O  VAL*     4.8     8.1    -      -       +      -
    132O  VAL*     3.6    21.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 310 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    306I  HIS*     2.8    44.3    +      +       +      +
    307I  LEU*     3.0    17.2    -      -       -      +
    309I  LEU*     1.3    88.6    -      -       +      +
    311I  GLY*     1.3    58.8    +      -       -      +
    312I  LYS*     3.0    32.6    +      -       +      +
    313I  ALA      3.7     0.3    +      -       -      -
     41O  LEU*     4.9     3.8    -      -       +      -
     44O  MET*     3.6    31.0    -      -       +      -
     45O  SER*     4.2    18.5    -      -       -      -
     61O  ASN*     3.4    32.1    -      -       -      -
     64O  LEU*     3.7    17.3    -      -       +      -
    126O  VAL*     4.0    30.4    -      -       +      +
    127O  HIS*     4.5     4.7    -      -       -      -
    130O  SER*     3.5     3.4    -      -       -      -
    132O  VAL*     3.5    33.3    -      -       +      +
----------------------------------------------------------
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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