Contacts of the strand formed by residues 374 - 378 (chain G) in PDB entry 1G9N


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 HIS 374 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    256G  SER*     4.4     0.9    -      -       -      -
    257G  THR      2.8    26.5    +      -       -      +
    258G  GLN*     3.6    14.8    +      -       +      +
    259G  LEU*     3.4    46.9    -      -       +      +
    261G  LEU*     4.2    17.5    -      -       +      +
    294G  ILE*     4.3    16.2    -      -       +      +
    296G  CYS*     5.3     0.6    -      -       -      -
    373G  THR*     1.3    72.5    -      -       -      +
    375G  SER*     1.3    60.7    +      -       -      +
    376G  PHE*     3.4    34.3    -      +       -      -
    385G  CYS*     2.8    39.1    +      -       +      +
    387G  SER*     3.9     9.8    +      -       -      -
    416G  LEU*     5.3     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 375 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    256G  SER*     3.3     1.9    -      -       -      -
    257G  THR*     3.0    40.2    +      -       -      +
    370G  GLU*     3.7    25.2    -      -       -      +
    373G  THR*     3.3     1.7    +      -       -      -
    374G  HIS*     1.3    73.9    +      -       -      +
    376G  PHE*     1.3    74.6    +      -       -      +
    382G  PHE*     5.0     2.6    -      -       -      +
    383G  PHE      2.9    19.1    +      -       -      -
    384G  TYR*     3.5    24.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 376 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    254G  VAL*     5.7     0.7    -      -       +      -
    255G  VAL      3.7    10.3    -      -       -      +
    256G  SER*     3.4    17.7    -      -       -      +
    261G  LEU*     4.3    17.3    -      -       +      -
    296G  CYS*     3.4    29.4    -      -       +      -
    374G  HIS*     3.4    31.9    -      +       -      -
    375G  SER*     1.3    85.8    +      -       -      +
    377G  ASN*     1.3    70.3    +      -       -      +
    378G  CYS*     4.0    13.0    -      -       +      -
    382G  PHE*     3.6     5.4    -      -       -      -
    383G  PHE*     2.8    58.3    +      +       +      -
    385G  CYS*     3.5    20.0    -      -       -      -
    445G  CYS*     5.1     4.3    -      -       +      -
    762G  NAG      5.4     2.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 377 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112G  TRP*     4.1    21.5    -      -       +      -
    116G  LEU*     3.6    11.9    -      -       -      +
    210G  PHE*     4.2    14.3    -      -       +      +
    212G  PRO*     5.8     2.4    -      -       -      +
    255G  VAL      3.9     7.4    +      -       -      +
    376G  PHE*     1.3    77.5    -      -       -      +
    378G  CYS*     1.3    62.7    +      -       -      +
    379G  GLY      3.9     0.3    +      -       -      -
    380G  GLY*     2.8    52.7    +      -       -      -
    381G  GLU      3.4     8.3    -      -       -      +
    382G  PHE*     3.6    23.6    -      -       +      +
    762G  NAG      3.6    19.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 378 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    376G  PHE*     4.0     9.7    +      -       +      -
    377G  ASN*     1.3    73.5    +      -       -      +
    379G  GLY*     1.3    60.4    +      -       -      +
    380G  GLY      3.0     3.6    -      -       -      -
    381G  GLU*     2.8    37.7    +      -       -      +
    383G  PHE*     3.6    20.4    -      -       +      -
    443G  ILE*     3.6    14.3    -      -       -      +
    444G  ARG      3.3    15.9    -      -       -      -
    445G  CYS*     2.0    50.0    -      -       +      -
    762G  NAG      5.2     0.2    -      -       -      -
----------------------------------------------------------
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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