Contacts of the strand formed by residues 347 - 351 (chain C) in PDB entry 1G88


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 ILE 347 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    345C  CYS      3.0     4.7    -      -       -      +
    346C  PRO*     1.3    86.8    -      -       +      +
    348C  VAL*     1.3    61.0    +      -       -      +
    349C  THR*     4.9     2.6    +      -       -      +
    360C  ASP*     3.7    20.8    -      -       -      +
    388C  GLN*     3.2    46.9    -      -       +      +
    389C  LEU      3.4     5.6    -      -       -      +
    390C  GLU*     3.4    39.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 348 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    323C  TRP*     4.3     6.0    -      -       +      -
    326C  ILE*     4.1    20.0    -      -       +      -
    339C  PHE*     4.0    12.8    -      -       +      -
    341C  VAL*     3.9    34.3    -      -       +      -
    346C  PRO      4.2     0.6    -      -       -      -
    347C  ILE*     1.3    76.0    -      -       -      +
    349C  THR*     1.3    71.8    +      -       -      +
    350C  VAL*     4.2     3.3    +      -       +      -
    360C  ASP*     3.4    18.6    -      -       -      +
    361C  ARG      4.0     0.4    -      -       -      +
    362C  PHE*     4.3     2.2    -      -       +      +
    388C  GLN*     3.5     4.9    -      -       -      +
    389C  LEU*     3.0    56.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 349 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    347C  ILE*     4.9     1.9    +      -       -      +
    348C  VAL*     1.3    74.8    -      -       -      +
    350C  VAL*     1.3    63.1    +      -       -      +
    351C  ASP*     3.8    24.9    -      -       +      +
    360C  ASP      3.0     9.7    +      -       -      -
    361C  ARG*     3.2    16.5    -      -       +      +
    362C  PHE      2.6    34.7    +      -       -      +
    385C  LYS      4.4     5.4    -      -       -      +
    387C  VAL      3.6     9.9    -      -       -      +
    388C  GLN*     4.1    16.1    +      -       -      +
    402C  LEU*     5.1     6.0    -      -       +      +
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Residues in contact with VAL 350 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    326C  ILE*     4.1    21.3    -      -       +      -
    348C  VAL*     4.6     7.2    -      -       +      -
    349C  THR*     1.3    78.8    -      -       -      +
    351C  ASP*     1.3    60.0    +      -       -      +
    362C  PHE*     3.0    19.7    -      -       +      +
    364C  LEU*     3.8    29.8    -      -       +      -
    386C  GLY*     3.3     3.1    -      -       -      -
    387C  VAL*     3.1    35.2    +      -       +      +
    389C  LEU*     4.6    10.5    -      -       +      -
    505C  PHE*     3.7    27.8    -      -       +      -
    525C  ILE*     4.6     9.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 351 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    541A  HIS*     5.4     0.2    +      -       -      -
    349C  THR*     3.8    10.8    -      -       +      +
    350C  VAL*     1.3    74.7    -      -       -      +
    352C  GLY*     1.3    58.6    +      -       -      +
    353C  TYR*     2.7    32.5    +      -       +      +
    361C  ARG*     2.7    33.5    +      -       -      -
    362C  PHE      3.0     4.0    +      -       -      +
    363C  CYS*     3.3    11.7    -      -       -      -
    364C  LEU*     3.1    26.3    +      -       -      +
    383C  ILE*     4.0     5.8    -      -       -      -
    384C  GLY      3.1    16.2    -      -       -      +
    385C  LYS*     3.7    13.9    -      -       -      +
    386C  GLY*     4.1     1.6    -      -       -      +
----------------------------------------------------------
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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