Contacts of the strand formed by residues 407 - 412 (chain A) in PDB entry 3SUP


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 407 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    404A  TYR*     3.8    31.9    -      -       +      +
    405A  LYS      5.0     0.4    -      -       -      +
    406A  TYR*     1.3    79.7    -      -       -      +
    408A  MET*     1.3    70.4    +      -       -      +
    409A  SER*     4.6     0.9    -      -       -      +
    618A  LEU*     4.3     9.0    -      -       +      -
    626A  TYR*     4.0    32.8    -      -       +      -
    627A  VAL      3.4     8.1    -      -       -      +
    628A  SER*     5.2     0.2    -      -       -      -
    629A  ALA*     4.5     0.4    -      -       -      +
    651A  LEU*     5.7     0.8    -      -       -      +
    687A  ALA      3.7     1.2    -      -       -      +
    688A  ILE*     3.6     2.1    -      -       -      +
    689A  ALA*     2.7    41.9    +      -       +      +
    702A  TRP*     4.3     2.7    -      -       +      -
    710A  LEU*     3.9    31.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 408 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    407A  VAL*     1.3    77.8    -      -       -      +
    409A  SER*     1.3    61.9    +      -       -      +
    410A  PHE*     4.0    10.5    -      -       +      -
    627A  VAL*     2.8    44.1    +      -       +      +
    629A  ALA*     3.9    18.8    -      -       +      -
    632A  ILE*     6.4     0.7    -      -       -      -
    651A  LEU*     3.2    39.7    -      -       +      +
    654A  PHE*     5.0     3.8    -      -       -      -
    655A  ALA*     3.2    35.0    -      -       +      -
    659A  MET*     4.5    15.0    -      -       -      +
    685A  ARG*     4.0     3.8    -      -       +      -
    687A  ALA      3.2     5.2    -      -       -      +
    688A  ILE*     3.7    24.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 409 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    407A  VAL*     4.2     1.5    -      -       -      +
    408A  MET*     1.3    73.8    -      -       -      +
    410A  PHE*     1.3    61.7    +      -       -      +
    624A  SER*     5.9     0.4    -      -       -      -
    625A  ILE      3.3     6.5    -      -       -      -
    626A  TYR*     3.5    36.4    -      -       -      -
    685A  ARG*     3.5     8.5    -      -       -      +
    686A  GLU*     2.8    38.1    +      -       -      +
    687A  ALA*     2.9    44.1    +      -       -      +
    710A  LEU*     5.8     0.2    -      -       -      -
    726A  LYS*     6.1     0.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 410 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    408A  MET*     4.0    23.6    -      -       +      -
    409A  SER*     1.3    75.9    -      -       -      +
    411A  ASP*     1.3    60.9    +      -       -      +
    624A  SER*     3.1     8.3    -      -       -      -
    625A  ILE*     3.0    37.7    +      -       +      -
    627A  VAL*     4.2    10.8    -      -       +      -
    655A  ALA*     3.8    19.7    -      -       +      -
    659A  MET*     3.7    40.6    -      -       +      -
    660A  GLU*     4.0    16.6    -      -       +      -
    663A  ILE*     3.7    19.5    -      -       +      -
    683A  MET*     3.6    22.7    -      -       +      -
    684A  ASP      3.3     7.0    -      -       -      -
    685A  ARG*     3.5    33.9    -      -       +      -
    686A  GLU*     4.2     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 411 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    410A  PHE*     1.3    76.2    -      -       -      +
    412A  LEU*     1.3    65.9    +      -       -      +
    413A  THR*     3.8     1.4    +      -       -      -
    623A  ASP*     3.0    10.4    -      -       -      +
    624A  SER*     3.9     2.9    -      -       -      -
    682A  PHE      3.6     0.7    -      -       -      +
    683A  MET*     3.3     5.9    -      -       -      +
    684A  ASP*     2.8    32.1    +      -       -      +
    686A  GLU*     3.6    35.7    -      -       +      +
    904A  DCP      3.0    10.2    +      -       -      -
    905A   CA      2.5    31.1    -      -       -      -
    906A   CA      2.7    21.2    -      -       -      -
    908A   CA      3.9     8.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 412 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    411A  ASP*     1.3    74.0    -      -       -      +
    413A  THR*     1.3    63.2    +      -       -      +
    415A  LEU*     3.8    28.2    +      -       +      -
    593A  ALA*     5.1     6.7    -      -       +      -
    594A  LEU*     5.5     2.7    -      -       -      +
    623A  ASP*     3.1    31.9    +      -       +      +
    667A  PHE*     4.0    19.1    -      -       +      -
    681A  MET*     3.6    25.1    -      -       +      -
    682A  PHE      3.4    32.3    -      -       -      +
    683A  MET*     3.8    20.2    -      -       +      +
    904A  DCP      3.2     2.8    +      -       -      -
    905A   CA      2.3    30.1    -      -       -      -
----------------------------------------------------------
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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