Contacts of the strand formed by residues 37 - 43 (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 37 (chain v).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10v  ARG*     5.3     7.2    -      -       +      -
     11v  ALA*     4.7    14.8    -      -       +      +
     32v  VAL      4.1     0.2    -      -       -      +
     33v  SER*     3.4     3.6    -      -       -      -
     34v  ARG*     2.6    49.0    +      -       +      +
     35v  GLY      4.1     0.5    +      -       -      -
     36v  LYS*     1.3    79.6    -      -       +      +
     38v  LEU*     1.3    60.1    -      -       -      +
     39v  GLU*     4.1     3.5    +      -       +      -
     55v  THR*     6.1     3.4    -      -       -      -
     56v  VAL      3.5    10.8    -      -       -      +
     57v  GLU*     4.9     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 38 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32v  VAL      3.7     6.1    -      -       -      +
     33v  SER*     4.6     3.8    -      -       -      +
     36v  LYS      4.1     0.8    +      -       -      -
     37v  ILE*     1.3    73.2    -      -       -      +
     39v  GLU*     1.3    60.3    +      -       -      +
     54v  LEU      4.2     0.3    -      -       -      +
     55v  THR*     3.6     1.4    -      -       -      -
     56v  VAL*     2.9    41.7    +      -       +      +
     58v  VAL*     5.2    12.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 39 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31v  VAL*     3.4     5.4    -      -       -      +
     32v  VAL*     2.9    42.2    +      -       +      +
     34v  ARG*     6.3     1.3    -      -       +      +
     37v  ILE*     4.1     4.4    -      -       +      +
     38v  LEU*     1.3    75.0    -      -       -      +
     40v  LEU*     1.3    63.5    +      -       -      +
     41v  LEU*     4.2     1.7    +      -       +      -
     52v  THR*     6.1     3.8    -      -       -      -
     54v  LEU      3.5     8.1    -      -       -      +
     55v  THR*     4.6     9.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 40 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29v  GLU*     6.2     2.5    -      -       +      -
     30v  ILE      3.4     8.5    -      -       -      +
     31v  VAL*     4.6     3.8    -      -       +      +
     39v  GLU*     1.3    75.4    -      -       -      +
     41v  LEU*     1.3    60.3    +      -       -      +
     52v  THR*     3.8     5.4    -      -       -      -
     53v  LEU*     3.3    27.1    +      -       +      -
     54v  LEU*     2.9    25.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 41 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29v  GLU*     3.6     6.8    -      -       -      +
     30v  ILE*     2.9    47.0    +      -       +      +
     32v  VAL*     6.3     2.5    -      -       +      +
     39v  GLU*     4.2     2.0    -      -       +      -
     40v  LEU*     1.3    73.9    -      -       -      +
     42v  ARG*     1.3    60.6    +      -       -      +
     43v  PRO      4.2     0.6    -      -       -      -
     50v  VAL*     5.7     7.4    -      -       +      -
     51v  HIS      4.0     6.7    -      -       -      +
     52v  THR*     4.7     4.5    -      -       -      +
     53v  LEU*     5.6     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 42 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28v  GLN      5.3     1.1    -      -       -      -
     29v  GLU*     5.1     8.1    -      -       +      +
     41v  LEU*     1.3    76.4    -      -       -      +
     43v  PRO*     1.3    59.6    -      -       -      +
     44v  ASP*     3.1    11.1    +      -       +      +
     50v  VAL*     3.9     3.0    -      -       -      -
     51v  HIS*     3.2    36.7    +      -       +      +
     53v  LEU*     5.5     7.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 43 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28v  GLN      4.9    11.0    -      -       -      +
     29v  GLU*     5.6     0.4    -      -       -      -
     30v  ILE*     5.8     0.4    -      -       -      -
     41v  LEU*     4.2     1.8    -      -       -      -
     42v  ARG*     1.3    68.2    -      -       -      +
     44v  ASP*     1.3    62.9    +      -       -      +
     45v  PRO*     3.1     8.8    -      -       -      +
     48v  GLY      5.8     0.4    -      -       -      +
     49v  LYS      4.0     7.0    -      -       -      +
     50v  VAL*     5.0     4.5    -      -       +      -
    346v  PHE*     5.5    12.1    -      -       +      -
----------------------------------------------------------
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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