Contacts of the strand formed by residues 409 - 414 (chain A) 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 VAL 409 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    368A  PHE      3.6     0.2    -      -       -      +
    369A  GLU*     4.2     1.2    -      -       -      -
    370A  ILE*     3.1    50.6    +      -       +      +
    372A  PRO*     4.2    14.3    -      -       +      +
    378A  VAL*     3.7    33.7    -      -       +      -
    381A  ILE*     5.4    11.0    -      -       +      -
    399A  VAL*     5.3     4.3    -      -       +      -
    400A  VAL*     3.7    11.0    -      -       -      +
    401A  GLU      3.9    16.6    -      -       -      +
    403A  ILE*     5.0     1.6    -      -       -      -
    408A  THR*     1.3    80.2    -      -       -      +
    410A  GLY*     1.3    60.9    +      -       -      +
    411A  ILE*     6.2     0.2    -      -       +      -
    390B  ARG*     4.1    17.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 410 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    367A  ARG*     4.2    11.0    -      -       -      -
    368A  PHE      3.5     8.7    -      -       -      -
    369A  GLU*     5.1     0.9    -      -       -      -
    399A  VAL*     3.5     6.1    -      -       -      +
    400A  VAL*     2.6    52.7    +      -       -      +
    403A  ILE*     5.3     0.4    -      -       -      -
    408A  THR      4.3     0.2    +      -       -      -
    409A  VAL*     1.3    78.1    -      -       -      +
    411A  ILE*     1.3    64.3    +      -       -      -
    412A  GLU*     3.9     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 411 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    343A  LEU*     3.8    18.6    -      -       +      -
    347A  LEU*     4.3     4.0    -      -       +      -
    366A  THR      3.4     1.9    -      -       -      +
    367A  ARG      3.3     3.1    -      -       -      -
    368A  PHE*     2.9    41.4    +      -       +      -
    370A  ILE*     3.7    28.3    -      -       +      -
    381A  ILE*     4.8    14.1    -      -       +      -
    388A  LEU*     3.8    26.2    -      -       +      -
    397A  VAL*     3.7    22.7    -      -       +      -
    398A  ARG      4.2     2.0    -      -       -      -
    399A  VAL*     4.9     3.4    -      -       +      +
    409A  VAL*     4.2     0.4    +      -       +      -
    410A  GLY*     1.3    74.1    -      -       -      +
    412A  GLU*     1.3    62.0    +      -       -      +
    413A  ILE*     3.7    24.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 412 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    365A  ILE*     4.2    20.8    -      -       +      +
    366A  THR      3.4     4.0    -      -       -      +
    367A  ARG*     3.3    24.8    +      -       +      +
    397A  VAL*     3.6    20.3    -      -       -      +
    398A  ARG*     2.8    65.3    +      -       +      +
    400A  VAL*     3.3    24.7    -      -       +      +
    411A  ILE*     1.3    73.4    -      -       -      +
    413A  ILE*     1.3    60.8    +      -       -      +
    414A  PRO*     4.1     3.0    -      -       -      +
    447A  ILE*     3.7    11.0    -      -       -      +
    690A  ARG*     3.6    14.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 413 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    339A  MET*     3.9    11.2    -      -       +      -
    343A  LEU*     4.5     2.0    -      -       +      -
    365A  ILE*     4.2     0.7    -      -       -      -
    366A  THR*     2.8    38.7    +      -       -      +
    368A  PHE*     3.6    29.2    -      -       +      -
    392A  LEU*     3.8    28.0    -      -       +      -
    394A  VAL*     3.7    29.8    -      -       +      -
    397A  VAL*     3.7    18.8    -      -       +      -
    411A  ILE*     3.7    15.5    -      -       +      -
    412A  GLU*     1.3    76.5    -      -       -      +
    414A  PRO*     1.3    70.7    -      -       +      +
    415A  ASN      3.6     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 414 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    364A  VAL*     3.4     8.3    -      -       +      +
    365A  ILE*     3.7    21.3    -      -       +      -
    394A  VAL*     3.6    18.5    -      -       +      +
    395A  ILE*     3.7    28.2    -      -       +      +
    396A  SER*     3.3    22.2    -      -       -      +
    412A  GLU      4.1     3.1    -      -       -      +
    413A  ILE*     1.3    90.9    -      -       +      +
    415A  ASN*     1.3    69.4    +      -       -      +
    416A  GLU*     3.7     1.2    +      -       -      +
    673A  LEU*     4.7    17.9    -      -       +      -
----------------------------------------------------------
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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