Contacts of the strand formed by residues 97 - 101 (chain C) in PDB entry 3GTL


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 VAL 97 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44C  LEU*     3.5    28.5    -      -       +      -
     80C  LEU*     4.7     1.8    -      -       +      -
     96C  SER*     1.3    76.8    -      -       -      +
     98C  VAL*     1.3    64.6    +      -       -      +
     99C  LEU*     3.4     6.5    +      -       +      +
    120C  ILE*     3.9    13.9    -      -       +      -
    122C  SER*     3.5     4.9    -      -       -      +
    124C  LEU*     3.6    31.6    -      -       +      -
    129C  ILE*     3.4    33.0    -      -       +      +
    130C  GLY*     4.6     6.3    -      -       -      -
    157C  CYS      3.3    10.4    -      -       -      +
    158C  VAL*     4.6     0.7    -      -       -      -
    159C  ALA*     3.3    20.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 98 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50C  GLU*     5.6     1.6    -      -       -      +
     91C  HIS*     4.3    28.9    -      -       +      +
     93C  ASP      6.3     0.2    -      -       -      +
     96C  SER*     4.3     6.5    -      -       -      +
     97C  VAL*     1.3    71.9    -      -       -      +
     99C  LEU*     1.3    63.9    +      -       -      +
    120C  ILE*     3.9     0.7    -      -       -      +
    121C  VAL*     3.1    32.6    +      -       +      +
    122C  SER*     3.5    24.4    +      -       -      +
    156C  THR*     3.6    28.3    -      -       +      +
    157C  CYS      3.5    10.1    -      -       -      +
    158C  VAL*     4.3     8.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 99 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46C  ILE*     3.6    25.6    -      -       +      -
     72C  LEU*     3.8    21.1    -      -       +      -
     97C  VAL*     3.9     9.6    -      -       +      +
     98C  VAL*     1.3    78.6    -      -       -      +
    100C  THR*     1.3    64.0    +      -       -      +
    118C  LEU*     4.4    21.8    -      -       +      -
    119C  VAL      3.2     6.7    -      -       -      +
    120C  ILE*     3.2    47.6    -      -       +      +
    121C  VAL*     4.0     0.9    -      -       -      -
    130C  GLY*     4.1     6.3    -      -       -      +
    132C  PRO*     5.0     1.1    -      -       +      -
    156C  THR*     3.1    10.0    -      -       -      +
    157C  CYS*     2.6    44.6    +      -       +      +
    159C  ALA*     5.2     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 100 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99C  LEU*     1.3    76.1    +      -       -      +
    101C  LEU*     1.3    79.9    -      -       -      +
    102C  GLN*     4.2    21.1    -      -       +      +
    117C  ASP      4.1     0.2    -      -       -      +
    118C  LEU*     3.6     7.5    -      -       -      +
    119C  VAL*     2.6    58.2    +      -       +      +
    121C  VAL*     3.3    16.5    -      -       -      +
    154C  LYS*     5.5     2.9    -      -       +      -
    155C  LEU      3.5    12.8    +      -       -      +
    156C  THR*     4.2     9.4    -      -       +      +
    157C  CYS*     5.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 101 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67C  LEU*     5.3     4.5    -      -       +      -
    100C  THR*     1.3    75.8    -      -       -      +
    102C  GLN*     1.3    75.8    +      -       -      +
    103C  ALA*     4.9     0.4    -      -       +      -
    113C  VAL*     3.8    31.4    -      -       +      -
    114C  TYR      4.1     2.9    -      -       -      +
    115C  SER*     5.5     0.2    -      -       -      -
    117C  ASP*     3.3    33.7    -      -       +      +
    118C  LEU*     3.8    22.4    -      -       +      -
    144C  ILE*     4.8     5.8    -      -       +      -
    153C  LEU*     3.6    28.9    -      -       +      +
    155C  LEU*     3.1    48.0    +      -       +      +
    157C  CYS*     5.7     0.9    -      -       -      -
----------------------------------------------------------
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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