Contacts of the strand formed by residues 490 - 495 (chain B) 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 PHE 490 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    481B  MET*     5.5     7.0    -      -       +      -
    482B  TYR      3.5    11.2    -      -       -      +
    483B  SER*     4.6     1.6    -      -       -      +
    484B  THR*     5.3     1.1    -      -       -      -
    487B  GLY      6.0     0.2    -      -       -      +
    488B  VAL      3.9     2.3    +      -       -      +
    489B  GLN*     1.3    74.9    -      -       -      +
    491B  HIS*     1.3    63.0    +      -       -      +
    492B  ALA      4.0     1.5    +      -       -      -
    553B  GLU*     4.9     0.9    -      -       -      -
    554B  GLY*     4.0    19.8    +      -       -      -
    556B  ASP*     5.2    16.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 491 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    481B  MET*     4.4     1.1    -      -       -      -
    482B  TYR*     2.9    46.5    +      -       +      +
    483B  SER*     5.0     2.4    -      -       -      +
    484B  THR*     5.2     3.7    -      -       -      +
    490B  PHE*     1.3    71.7    -      -       -      +
    492B  ALA*     1.3    66.1    -      -       -      +
    493B  PHE*     3.9     1.9    +      -       -      +
    551B  LEU*     4.6     9.4    -      -       +      -
    552B  ILE      3.3    21.8    -      -       -      +
    553B  GLU*     5.2     1.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 492 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    478B  THR*     4.9    11.2    -      -       -      -
    480B  LYS      3.4    10.3    -      -       -      +
    481B  MET*     4.2     4.7    -      -       +      +
    490B  PHE      4.0     2.8    +      -       -      -
    491B  HIS*     1.3    75.4    -      -       -      +
    493B  PHE*     1.3    58.5    +      -       -      +
    551B  LEU*     3.2     3.3    -      -       -      -
    552B  ILE*     2.9    37.1    +      -       +      +
    554B  GLY      5.6     1.4    -      -       -      +
    555B  VAL*     6.1     1.8    -      -       +      +
    556B  ASP*     3.7    29.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 493 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    478B  THR*     3.7     5.2    -      -       -      -
    479B  THR      3.2     4.7    +      -       -      -
    480B  LYS*     2.8    51.5    +      -       +      +
    482B  TYR*     5.3     4.9    -      -       +      +
    491B  HIS      4.4     3.6    -      -       -      +
    492B  ALA*     1.3    77.2    -      -       -      +
    494B  GLY*     1.3    59.0    +      -       -      +
    550B  VAL      3.4     9.6    -      -       -      +
    551B  LEU*     4.2    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 494 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221B  ILE*     6.2     1.3    -      -       -      -
    477B  HIS      3.3    16.4    +      -       -      -
    478B  THR*     3.7     5.1    -      -       -      +
    479B  THR*     4.2     2.7    -      -       -      -
    493B  PHE*     1.3    75.6    -      -       -      +
    495B  ARG*     1.3    61.5    +      -       -      -
    496B  VAL      3.9     0.3    +      -       -      -
    549B  TRP*     3.8     7.9    -      -       -      +
    550B  VAL*     2.9    32.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 495 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221B  ILE*     4.6    30.2    -      -       +      +
    476B  CYS*     4.6     0.4    -      -       -      -
    477B  HIS*     2.9    39.2    +      -       +      +
    494B  GLY*     1.3    72.9    -      -       -      -
    496B  VAL*     1.3    64.6    +      -       -      +
    497B  LEU*     4.1     0.5    +      -       -      +
    547B  GLY      5.4     2.2    -      -       -      +
    548B  ASN      3.4    11.9    -      -       -      +
    549B  TRP*     3.8     7.6    -      -       +      +
----------------------------------------------------------
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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