Contacts of the strand formed by residues 336 - 342 (chain v) in PDB entry 6FF7


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 ALA 336 (chain v).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    288v  VAL*     3.9    19.4    -      -       -      +
    289v  CYS*     5.0     3.7    -      -       -      +
    304v  GLN*     5.4     8.6    -      -       +      +
    334v  PRO      3.4     5.0    +      -       -      +
    335v  VAL*     1.3    75.7    -      -       -      +
    337v  ALA*     1.3    61.9    +      -       -      +
    338v  ALA      4.3     7.2    -      -       -      +
    339v  MET*     5.8     1.6    -      -       +      -
    349v  VAL*     4.0    15.5    -      -       +      -
    350v  ALA      3.4    29.8    -      -       -      +
    351v  SER*     3.7     1.8    -      -       -      +
    352v  GLU*     4.5     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 337 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14v  ILE      4.3    16.4    -      -       -      +
     15v  SER*     4.5    13.1    -      -       -      +
    288v  VAL*     3.3    22.0    -      -       -      +
    289v  CYS*     4.8     1.0    -      -       -      -
    336v  ALA*     1.3    74.5    -      -       -      +
    338v  ALA*     1.3    60.6    +      -       +      +
    350v  ALA      2.9    10.8    +      -       -      +
    352v  GLU*     4.1    18.8    -      -       +      +
     61x  LYS*     5.2    11.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 338 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15v  SER      5.0     2.0    -      -       -      +
     16v  PHE*     4.8     5.8    -      -       -      -
     17v  ALA*     4.1    35.3    -      -       +      +
    289v  CYS*     4.9     5.4    -      -       -      -
    336v  ALA*     3.5     4.7    -      -       -      +
    337v  ALA*     1.3    81.3    -      -       +      +
    339v  MET*     1.3    61.2    +      -       -      +
    348v  PHE      4.2     0.9    -      -       -      +
    349v  VAL*     4.3     0.3    -      -       -      -
    350v  ALA*     3.3    32.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with MET 339 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17v  ALA*     4.6     8.8    -      -       -      +
     18v  ILE*     5.9     0.2    -      -       -      -
    289v  CYS*     4.6    13.3    -      -       +      +
    291v  ALA*     3.7    33.6    -      -       +      +
    302v  LEU      5.2     1.3    -      -       -      +
    336v  ALA*     6.0     1.8    -      -       +      -
    338v  ALA*     1.3    76.2    -      -       -      +
    340v  CYS*     1.3    64.4    +      -       -      +
    341v  VAL*     4.0     0.9    -      -       +      +
    348v  PHE      3.5     9.2    -      -       -      +
    349v  VAL*     4.8     5.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 340 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17v  ALA*     5.3     8.7    -      -       +      -
     18v  ILE*     4.8     5.8    -      -       -      +
     19v  HIS*     4.0    28.7    -      -       +      +
     30v  ILE*     5.6     6.7    -      -       +      -
    339v  MET*     1.3    75.7    -      -       -      +
    341v  VAL*     1.3    65.6    +      -       -      +
    342v  LEU*     3.8     5.4    +      -       -      +
    347v  LEU*     4.0     0.7    -      -       -      -
    348v  PHE*     3.0    40.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 341 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19v  HIS*     4.6     9.9    -      -       -      +
    291v  ALA*     5.0    14.5    -      -       +      +
    292v  THR      4.8    15.4    +      -       -      +
    293v  HIS*     4.8    12.1    -      -       +      -
    302v  LEU*     5.6     5.8    -      -       +      -
    339v  MET*     4.0     3.0    -      -       +      +
    340v  CYS*     1.3    74.8    -      -       -      +
    342v  LEU*     1.3    60.0    +      -       -      +
    346v  PHE      3.6     8.7    -      -       -      +
    347v  LEU*     4.4     8.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 342 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28v  GLN*     5.4     9.9    -      -       +      -
    340v  CYS      4.5     4.0    -      -       -      +
    341v  VAL*     1.3    76.2    -      -       -      +
    343v  LYS*     1.3    67.3    +      -       -      +
    345v  GLY*     3.8     7.4    +      -       -      -
    346v  PHE*     2.9    36.2    +      -       +      +
----------------------------------------------------------
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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