Contacts of the strand formed by residues 351 - 356 (chain A) in PDB entry 6S1M


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 LEU 351 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  ARG*     4.0    20.6    -      -       +      -
     79A  TRP*     3.8    32.3    -      -       +      +
    339A  SER      4.7     0.2    -      -       -      -
    340A  LEU*     3.4    11.1    -      -       -      +
    341A  GLY*     3.0    38.8    +      -       -      +
    349A  PRO*     3.8     1.8    -      -       -      +
    350A  PHE*     1.3    93.8    -      -       +      +
    352A  ARG*     1.3    67.1    +      -       -      +
    353A  LEU*     4.3     5.4    -      -       +      -
    384A  PHE*     3.6    35.9    -      -       +      -
    388A  MET*     4.6    12.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 352 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    339A  SER      3.7     3.8    -      -       -      -
    340A  LEU*     3.6    30.8    -      -       +      +
    349A  PRO*     3.4    28.1    -      -       -      +
    351A  LEU*     1.3    79.1    -      -       -      +
    353A  LEU*     1.3    60.7    +      -       -      +
    365A  GLY*     3.5    26.9    +      -       -      +
    366A  ALA*     3.4    12.2    -      -       +      +
    367A  LYS*     3.3    22.9    +      -       -      +
    513A  LEU*     4.1    13.9    -      -       +      +
    517A  TYR*     5.2    17.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 353 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  ARG*     4.0    22.7    -      -       +      +
    337A  ILE      5.0     0.4    -      -       -      -
    338A  CYS*     3.6     1.7    -      -       -      +
    339A  SER*     2.9    42.0    +      -       -      +
    351A  LEU*     4.3     7.6    -      -       +      -
    352A  ARG*     1.3    77.9    -      -       -      +
    354A  ALA*     1.3    68.2    +      -       -      +
    355A  LEU*     4.3    22.7    -      -       +      -
    366A  ALA*     5.4     0.7    -      -       -      -
    367A  LYS*     4.0    22.0    -      -       +      +
    369A  GLN*     3.8    27.6    -      -       -      +
    381A  TRP*     5.9     0.2    -      -       +      -
    384A  PHE*     4.1    36.3    -      -       +      -
    513A  LEU*     4.4     3.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 354 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    337A  ILE      3.7     5.4    -      -       -      -
    338A  CYS*     3.7    20.0    -      -       -      -
    353A  LEU*     1.3    78.3    -      -       -      +
    355A  LEU*     1.3    63.9    +      -       -      +
    356A  THR*     4.1     6.0    +      -       +      +
    363A  ILE*     5.7     0.7    -      -       +      -
    366A  ALA*     5.6     0.7    -      -       +      -
    367A  LYS      3.3    12.5    +      -       -      +
    368A  VAL*     3.6    15.4    -      -       +      +
    369A  GLN      3.5    20.6    +      -       -      +
    509A  ALA*     5.1     9.0    -      -       +      -
    513A  LEU*     4.3    15.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 355 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  ARG*     5.4     2.2    -      -       -      +
    336A  GLN*     3.4     4.0    -      -       -      +
    337A  ILE*     2.9    44.3    +      -       +      +
    338A  CYS*     4.9     0.2    -      -       -      -
    339A  SER*     5.9     0.9    -      -       -      +
    353A  LEU*     4.3    21.3    -      -       +      -
    354A  ALA*     1.3    75.0    -      -       -      +
    356A  THR*     1.3    61.6    +      -       -      +
    369A  GLN*     3.7    25.6    -      -       +      +
    371A  TYR*     3.6    33.4    -      -       +      +
    377A  LEU*     3.7    18.3    -      -       +      +
    380A  ALA*     4.5     6.7    -      -       +      +
    381A  TRP*     4.1    40.6    -      -       +      +
    384A  PHE*     5.7     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 356 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    335A  ILE      3.7     7.6    -      -       -      -
    336A  GLN*     3.7    30.1    -      -       +      +
    338A  CYS*     6.1     0.4    -      -       -      -
    354A  ALA*     4.5     7.6    -      -       +      +
    355A  LEU*     1.3    80.9    -      -       -      +
    357A  LEU*     1.3    60.4    +      -       -      +
    358A  ARG      3.0    20.4    +      -       -      -
    360A  CYS*     4.1    19.3    -      -       +      +
    368A  VAL*     5.0     4.5    -      -       +      -
    369A  GLN      3.3     7.6    +      -       -      +
    370A  SER*     3.4    12.3    +      -       -      -
    371A  TYR*     3.6    17.5    +      -       -      -
    377A  LEU*     3.4    13.9    -      -       -      +
    505A  ARG*     6.2     3.1    -      -       -      -
    509A  ALA*     4.9     7.0    -      -       +      -
----------------------------------------------------------
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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