Contacts of the strand formed by residues 365 - 370 (chain D) in PDB entry 6T8G


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 365 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    360D  HIS      5.4     0.4    -      -       -      +
    362D  GLY*     3.1    20.7    +      -       -      +
    364D  VAL*     1.3    85.8    -      -       +      +
    366D  THR*     1.3    72.6    +      -       -      +
    367D  ARG*     3.7    17.7    -      -       +      +
    412D  GLU*     4.0    19.3    -      -       +      +
    413D  ILE      3.3    17.9    -      -       -      +
    414D  PRO*     4.2     9.0    -      -       +      -
    415D  ASN*     3.1     7.5    -      -       -      +
    447D  ILE*     3.7    42.4    -      -       +      +
    673D  LEU*     4.5     2.5    -      -       +      -
    690D  ARG*     3.4    38.1    -      -       -      +
    692D  HIS*     4.8     2.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 366 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    331D  TYR*     5.0     0.5    -      -       -      -
    336D  LEU*     4.1    10.1    -      -       +      +
    359D  VAL*     3.8    12.1    -      -       +      -
    360D  HIS      4.0     3.6    -      -       -      -
    361D  PRO*     3.7    24.2    -      -       +      +
    365D  ILE*     1.3    75.2    +      -       -      +
    367D  ARG*     1.3    62.9    +      -       -      +
    368D  PHE*     3.4    31.9    +      -       +      -
    411D  ILE      3.8     0.5    -      -       -      +
    413D  ILE*     2.7    32.1    +      -       -      +
    415D  ASN*     2.5    33.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 367 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    359D  VAL*     3.7     0.5    -      -       -      -
    360D  HIS*     3.0    49.8    +      -       +      +
    365D  ILE*     3.7    13.0    -      -       +      +
    366D  THR*     1.3    70.6    -      -       -      +
    368D  PHE*     1.3    74.7    +      -       -      +
    369D  GLU*     4.0    13.2    +      -       +      +
    398D  ARG*     5.2     0.4    -      -       -      +
    400D  VAL*     4.0    18.8    -      -       -      +
    403D  ILE*     3.4    31.6    -      -       -      +
    410D  GLY*     4.3     4.8    -      -       -      -
    411D  ILE      3.6     7.4    -      -       -      +
    412D  GLU*     2.4    32.8    +      -       +      +
    447D  ILE*     3.5    31.8    -      -       +      +
    690D  ARG*     5.9     1.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 368 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    336D  LEU*     5.0     2.2    -      -       +      -
    339D  MET*     3.9    40.8    -      -       +      -
    340D  SER*     4.6     2.9    -      -       -      -
    343D  LEU*     3.9    18.8    -      -       +      -
    356D  VAL*     5.0     7.9    -      -       +      -
    358D  SER      4.0     3.4    -      -       -      +
    359D  VAL*     3.6    25.6    -      -       +      -
    366D  THR*     3.6    29.2    -      -       +      -
    367D  ARG*     1.3    81.3    -      -       -      +
    369D  GLU*     1.3    67.1    +      -       -      +
    370D  ILE*     4.1     8.2    -      -       +      +
    409D  VAL      3.7     2.6    -      -       -      +
    410D  GLY*     3.7     0.7    -      -       -      -
    411D  ILE*     2.7    41.4    +      -       +      +
    413D  ILE*     3.6    33.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 369 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    356D  VAL*     4.1     4.0    -      -       -      +
    357D  ASP*     3.2    25.3    +      -       -      +
    358D  SER*     2.9    32.7    +      -       -      +
    360D  HIS*     3.8    18.9    +      -       +      -
    367D  ARG*     3.9     9.6    -      -       -      -
    368D  PHE*     1.3    76.9    -      -       -      +
    370D  ILE*     1.3    63.3    +      -       -      +
    403D  ILE*     4.7    18.8    -      -       +      +
    406D  LYS*     2.8    43.8    +      -       -      +
    408D  THR*     3.8    19.8    +      -       +      +
    409D  VAL      4.4     2.2    -      -       -      -
    410D  GLY*     4.9     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 370 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    343D  LEU*     3.8    12.8    -      -       +      -
    347D  LEU*     4.7     0.4    -      -       +      -
    354D  VAL*     3.6    33.9    -      -       +      -
    355D  SER      3.7     8.3    -      -       -      +
    356D  VAL*     4.5     9.0    -      -       +      -
    357D  ASP*     4.3     0.4    -      -       -      -
    368D  PHE*     4.1     4.5    -      -       +      +
    369D  GLU*     1.3    81.2    -      -       -      +
    371D  GLN*     1.3    63.7    +      -       -      +
    372D  PRO*     3.2    29.2    -      -       +      +
    381D  ILE*     6.5     0.9    -      -       +      -
    408D  THR*     3.3    12.0    -      -       -      -
    409D  VAL*     3.2    39.5    +      -       +      +
    411D  ILE*     3.7    32.8    -      -       +      -
----------------------------------------------------------
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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