Contacts of the strand formed by residues 903 - 911 (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 TRP 903 (chain v).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184X  PRO      4.5     0.7    -      -       -      +
    185X  GLY      1.3    38.9    -      -       -      +
    186X  ARG*     1.8     0.8    -      -       -      +
    187X  HIS*     0.9    95.1    +      -       +      +
    893v  VAL*     5.8     4.7    -      -       +      -
    894v  CYS      4.0     5.2    -      -       -      +
    901v  GLU      3.5     1.4    +      -       -      -
    902v  ASP*     1.3    62.4    -      -       -      +
    904v  TYR      1.3    47.8    -      -       -      +
    929v  LYS      2.9     8.6    +      -       -      +
    930v  LEU*     4.5    19.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 904 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183X  VAL      3.0    22.4    -      -       -      +
    185X  GLY      2.7     2.6    +      -       -      -
    186X  ARG      4.0     0.2    -      -       -      +
    187X  HIS*     1.2    80.2    -      -       +      +
    188X  ASP*     2.6    14.1    -      -       -      +
    189X  ILE      4.5     1.6    -      -       -      +
    892v  ALA      3.8     1.2    -      -       -      +
    893v  VAL*     3.5     5.2    -      -       -      +
    894v  CYS*     3.1    29.3    +      -       +      +
    903v  TRP*     1.3    64.0    -      -       -      +
    905v  VAL*     1.3    58.2    +      -       -      +
    927v  THR*     6.2     1.1    -      -       -      -
    930v  LEU*     5.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 905 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187X  HIS*     2.9     3.8    -      -       +      +
    892v  ALA      3.7     8.7    -      -       -      +
    893v  VAL*     5.3     3.8    -      -       +      -
    904v  TYR*     1.3    74.3    -      -       -      +
    906v  LEU*     1.3    60.1    +      -       -      +
    907v  VAL*     4.0     1.9    +      -       +      +
    926v  TYR      3.5     1.4    -      -       -      +
    927v  THR*     3.3     7.1    -      -       -      -
    928v  TYR*     2.9    45.4    +      -       +      +
    930v  LEU*     5.6     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 906 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    890v  SER      3.7     1.7    -      -       -      +
    891v  VAL*     3.4    22.5    -      -       -      +
    892v  ALA*     3.3    13.7    +      -       +      +
    904v  TYR      4.2     0.6    -      -       -      -
    905v  VAL*     1.3    72.7    -      -       -      +
    907v  VAL*     1.3    60.4    +      -       -      +
    925v  VAL*     6.2     2.5    -      -       +      -
    926v  TYR      3.4     5.8    -      -       -      +
    927v  THR*     4.9     1.8    -      -       -      +
    952v  ILE*     4.4    15.5    -      -       +      +
    959v  VAL*     5.6     9.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 907 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    888v  ALA*     5.6     7.4    -      -       +      -
    890v  SER      3.4     7.0    -      -       -      +
    891v  VAL*     4.7     6.5    -      -       +      +
    905v  VAL*     5.4     2.0    -      -       +      +
    906v  LEU*     1.3    73.1    -      -       -      +
    908v  GLY*     1.3    63.5    +      -       -      +
    909v  VAL*     3.7     3.1    +      -       +      +
    925v  VAL*     3.3     7.0    -      -       -      +
    926v  TYR*     2.9    48.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 908 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    888v  ALA*     3.3     5.2    -      -       -      +
    889v  PHE*     2.9    30.9    +      -       -      +
    890v  SER*     2.9    14.8    +      -       -      -
    906v  LEU      4.2     0.2    -      -       -      -
    907v  VAL*     1.3    71.2    -      -       -      +
    909v  VAL*     1.3    60.3    +      -       -      -
    924v  PHE      3.9     4.3    -      -       -      -
    925v  VAL*     4.8     1.8    -      -       -      -
    949v  PRO*     3.6    31.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 909 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    886v  GLU*     5.2     8.3    -      -       +      -
    887v  ALA      3.1    13.9    -      -       -      +
    888v  ALA*     5.0     2.0    -      -       +      -
    907v  VAL*     3.7     4.5    +      -       +      +
    908v  GLY*     1.3    74.2    -      -       -      +
    910v  ALA*     1.3    62.0    +      -       -      +
    923v  GLY*     3.4     2.6    -      -       -      -
    924v  PHE*     2.8    47.3    +      -       +      +
    926v  TYR*     5.7     4.3    -      -       +      +
    949v  PRO*     5.1     6.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 910 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    862v  TRP*     5.4     0.2    -      -       -      +
    885v  ASN      3.2     4.6    -      -       -      +
    886v  GLU*     3.3     3.6    -      -       -      -
    887v  ALA*     2.8    38.9    +      -       +      +
    889v  PHE*     6.2     3.3    -      -       +      +
    909v  VAL*     1.3    74.1    -      -       -      +
    911v  LYS*     1.3    61.4    +      -       -      +
    913v  LEU*     4.7    17.5    -      -       +      -
    922v  GLY      5.3     0.7    -      -       -      +
    923v  GLY*     4.3     5.4    -      -       -      -
    948v  VAL*     3.8    26.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 911 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    885v  ASN*     3.3    13.5    -      -       +      +
    886v  GLU*     5.1     3.8    -      -       +      -
    910v  ALA*     1.3    75.3    -      -       -      +
    912v  ASP*     1.3    72.9    +      -       +      +
    913v  LEU*     3.6     2.3    -      -       -      -
    920v  VAL*     5.1     1.0    -      -       -      +
    921v  ALA      3.6    10.6    +      -       -      +
    922v  GLY      3.1    25.3    +      -       -      +
    923v  GLY*     4.4     2.4    -      -       -      -
----------------------------------------------------------
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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