Contacts of the strand formed by residues 31 - 35 (chain e) 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 LYS 31 (chain e).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15e  GLY*     3.8    22.7    -      -       -      +
     16e  HIS      3.4     7.4    -      -       -      +
     17e  ILE*     4.4     1.8    -      -       +      +
     30e  GLY*     1.3    72.3    -      -       -      -
     32e  LEU*     1.3    64.4    +      -       -      +
     33e  ILE*     3.3     2.8    +      -       -      +
     43e  MET*     3.4     4.7    -      -       -      -
     44e  SER*     3.3    36.8    +      -       -      +
     45e  ASN*     5.4     2.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 32 (chain e). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10e  LEU      5.8     0.7    -      -       -      +
     13e  ALA*     3.8    21.3    -      -       +      +
     14e  GLU*     2.9     7.8    -      -       -      -
     15e  GLY*     2.2    37.5    +      -       -      -
     16e  HIS      2.9    12.7    +      -       -      +
     18e  VAL*     5.1     9.4    -      -       +      +
     30e  GLY      3.8     1.6    +      -       -      -
     31e  LYS*     1.3    69.6    -      -       -      +
     33e  ILE*     1.3    57.0    +      -       -      +
     34e  GLU      3.5     5.6    -      -       -      +
     35e  ALA*     5.8     5.2    -      -       +      -
     41e  CYS*     6.2     4.3    -      -       +      -
     42e  GLN      3.8     6.1    -      -       -      +
     43e  MET*     4.8     2.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 33 (chain e). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14e  GLU*     3.7    13.3    -      -       -      +
     15e  GLY*     4.4     3.2    +      -       -      +
     31e  LYS      3.3     5.3    +      -       -      +
     32e  LEU*     1.3    73.7    -      -       -      +
     34e  GLU*     1.3    64.1    +      -       +      +
     42e  GLN*     2.8    25.7    +      -       +      +
     43e  MET*     4.7     2.7    -      -       -      +
     44e  SER*     5.1     7.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 34 (chain e). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14e  GLU*     4.6     7.0    -      -       -      -
     32e  LEU*     3.5     3.5    -      -       -      +
     33e  ILE*     1.3    84.1    -      -       +      +
     35e  ALA*     1.3    59.4    +      -       -      +
     36e  GLU      4.0     1.8    +      -       -      +
     41e  CYS*     3.5     3.3    -      -       -      +
     42e  GLN*     3.1    33.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 35 (chain e). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7e  ILE*     5.2     4.7    -      -       -      +
     10e  LEU*     4.0    38.5    +      -       +      +
     11e  HIS*     5.2     6.1    +      -       -      +
     14e  GLU*     5.4     2.4    -      -       +      +
     32e  LEU*     5.8     6.3    -      -       +      -
     34e  GLU*     1.3    71.3    -      -       -      +
     36e  GLU*     1.3    66.8    +      -       -      +
     39e  MET*     5.4     2.2    -      -       -      +
     40e  ASN      3.6     4.5    -      -       -      -
     41e  CYS*     4.5     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