Contacts of the strand formed by residues 62 - 69 (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 ILE 62 (chain v).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15v  SER*     5.4     7.8    -      -       -      -
     16v  PHE*     5.6     5.1    -      -       +      +
     33v  SER*     4.1    24.7    -      -       -      -
     35v  GLY*     3.1    20.8    +      -       -      +
     60v  GLY      5.5     0.2    -      -       -      +
     61v  VAL*     1.3    70.5    -      -       -      +
     63v  ARG*     1.3    62.1    +      -       -      +
     64v  SER      3.4     6.9    -      -       -      +
     65v  LEU*     5.4     5.2    -      -       +      +
     80v  VAL*     6.0     4.7    -      -       +      -
     81v  GLY      4.4     3.8    -      -       -      +
     82v  SER*     4.9     1.8    -      -       -      -
   1156v  CYS*     6.5     0.2    -      -       -      -
     47x  PHE*     6.0     1.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 63 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61v  VAL*     3.4     5.4    +      -       +      +
     62v  ILE*     1.3    74.4    -      -       -      +
     64v  SER*     1.3    59.4    +      -       -      +
     81v  GLY      3.3     7.5    +      -       -      +
     82v  SER*     4.5    10.8    -      -       -      -
     83v  ASP*     5.0     0.9    -      -       -      +
    118v  GLY      3.3    20.4    -      -       -      +
    119v  GLN*     3.2    21.2    -      -       -      +
     45x  GLY*     4.5    20.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 64 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62v  ILE*     3.4     3.6    -      -       -      +
     63v  ARG*     1.3    81.2    -      -       -      +
     65v  LEU*     1.3    61.7    +      -       -      +
     79v  VAL      4.3     1.1    -      -       -      -
     80v  VAL*     3.3     7.4    -      -       -      +
     81v  GLY*     2.9    37.3    +      -       -      +
    118v  GLY*     3.3    17.9    -      -       -      -
    119v  GLN      4.3     4.7    -      -       -      -
    120v  PHE*     4.5     1.1    -      -       -      -
    121v  LEU*     3.7    27.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 65 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16v  PHE*     4.1    28.0    -      -       +      +
     17v  ALA      5.6     1.9    -      -       -      +
     18v  ILE*     5.0     9.2    -      -       +      +
     33v  SER*     4.9    11.7    -      -       -      -
     62v  ILE*     5.4     5.4    -      -       +      +
     64v  SER*     1.3    75.6    -      -       -      +
     66v  MET*     1.3    64.8    +      -       -      +
     79v  VAL      3.6     4.0    -      -       -      -
     80v  VAL*     4.8     3.4    -      -       +      +
    121v  LEU*     5.2     0.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 66 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18v  ILE*     5.1     4.3    -      -       -      -
     65v  LEU*     1.3    76.2    -      -       -      +
     67v  ALA*     1.3    63.8    +      -       -      +
     68v  PHE*     5.5     0.2    -      -       -      +
     78v  ILE*     4.7     2.0    -      -       -      +
     79v  VAL*     2.9    41.3    +      -       +      +
    121v  LEU*     4.9    18.6    -      -       +      +
    122v  ALA*     5.9     2.2    -      -       -      +
    123v  VAL*     5.7     7.9    -      -       +      -
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Residues in contact with ALA 67 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18v  ILE*     4.6    19.0    -      -       +      +
     19v  HIS      4.7    12.1    -      -       -      +
     20v  GLY*     5.9     0.4    -      -       -      -
     66v  MET*     1.3    78.7    -      -       -      +
     68v  PHE*     1.3    61.8    +      -       -      +
     76v  ASP*     4.7    12.6    -      -       +      -
     77v  TYR      3.2    14.1    -      -       -      +
     78v  ILE*     4.4     4.5    -      -       +      +
    123v  VAL*     5.2     3.9    -      -       -      +
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Residues in contact with PHE 68 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66v  MET      4.3     0.4    +      -       -      -
     67v  ALA*     1.3    75.9    -      -       -      +
     69v  ARG*     1.3    65.1    +      -       -      +
     70v  LEU      4.1     1.0    +      -       -      -
     76v  ASP*     3.3     6.6    -      -       -      -
     77v  TYR*     2.9    37.0    +      -       +      +
     79v  VAL*     6.5     0.7    -      -       +      -
    123v  VAL*     4.5    19.7    -      -       +      -
    124v  ASP      4.7     8.1    -      -       -      +
    125v  PRO*     6.2     0.4    -      -       +      -
    127v  GLY*     5.1     5.8    -      -       -      -
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Residues in contact with ARG 69 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68v  PHE*     1.3    72.7    -      -       -      +
     70v  LEU*     1.3    63.9    +      -       -      +
     73v  GLY      5.5     4.7    -      -       -      +
     74v  THR      5.9     2.9    -      -       -      +
     75v  LYS      4.8     0.7    -      -       -      +
     76v  ASP*     4.7    10.1    -      -       +      +
    125v  PRO*     3.9    12.3    +      -       -      +
    126v  LYS      3.1    19.2    -      -       -      +
    127v  GLY*     3.3    10.9    +      -       -      -
----------------------------------------------------------
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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