Contacts of the strand formed by residues 45 - 50 (chain z) 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 45 (chain z).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36N  TYR*     5.9     1.1    -      -       -      +
     40N  GLY*     5.1     1.6    -      -       -      -
     43N  GLY      4.4     0.2    -      -       -      +
     44N  PRO*     0.9    74.7    -      -       -      +
     45N  ILE*     0.5   410.9    +      -       +      +
     46N  ARG*     1.5     0.4    -      -       -      -
     63N  VAL      3.8     6.7    -      -       -      +
     65N  GLU      4.7     0.2    -      -       -      -
     39z  PHE*     4.1    21.3    -      -       +      +
     40z  GLY*     5.4     0.4    -      -       -      -
     43z  GLY      4.7     0.7    -      -       -      +
     44z  PRO*     1.3     5.8    -      -       -      +
     46z  ARG      1.3    17.7    -      -       -      +
     47z  GLN      5.5     0.4    -      -       -      +
     64z  TYR*     4.3     1.6    -      -       -      +
     65z  GLU*     4.6     2.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 46 (chain z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45N  ILE*     1.4    14.3    -      -       -      +
     46N  ARG*     0.6   357.3    -      -       +      +
     47N  GLN*     1.0    35.5    +      -       +      +
     63N  VAL      2.9     1.2    +      -       -      -
     45z  ILE*     1.3    35.6    -      -       -      +
     47z  GLN*     1.3    11.3    +      -       -      +
     63z  VAL*     2.9    25.1    +      -       +      +
     64z  TYR*     3.4     9.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 47 (chain z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45N  ILE*     3.6     6.3    -      -       -      +
     46N  ARG      2.9     1.4    -      -       -      +
     47N  GLN*     0.6   395.0    +      -       +      +
     48N  ILE*     1.2    43.0    -      -       -      +
     63N  VAL      3.2     1.9    +      -       -      +
    414u  VAL*     5.6     3.8    -      -       +      -
    415u  LEU      6.3     0.2    -      -       -      +
     45z  ILE*     3.9     0.4    -      -       -      +
     46z  ARG*     1.3    27.8    -      -       -      +
     48z  ILE*     1.3    13.0    +      -       -      +
     62z  VAL*     4.0     0.7    -      -       -      +
     63z  VAL      2.9    14.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 48 (chain z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47N  GLN*     4.5     0.5    -      -       -      +
     48N  ILE*     0.2   427.3    +      -       +      +
     49N  ARG*     1.3    34.0    +      -       -      +
     50N  VAL*     5.8     1.8    -      -       +      -
     60N  ALA*     5.9     1.1    -      -       +      -
     61N  TYR      3.4     0.2    -      -       -      -
    414u  VAL*     3.8    10.0    -      -       -      +
    415u  LEU*     6.1     3.4    -      -       +      -
     35z  MET*     5.6     9.6    -      -       +      -
     47z  GLN*     1.3    18.0    -      -       -      +
     49z  ARG      1.3    17.0    -      -       -      +
     61z  TYR      3.8     2.9    -      -       -      +
     62z  VAL*     4.7     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 49 (chain z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48N  ILE      2.8     0.4    -      -       -      -
     49N  ARG*     0.3   418.1    +      -       +      +
     50N  VAL*     1.0    45.9    -      -       -      +
    412u  TYR*     4.6     0.2    -      -       -      -
     48z  ILE*     1.3    31.1    -      -       -      +
     50z  VAL      1.3     5.0    +      -       -      -
     59z  THR      4.4     0.2    -      -       -      +
     60z  ALA*     3.4     4.5    -      -       -      -
     61z  TYR*     2.9    27.2    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 50 (chain z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49N  ARG      1.7     0.6    -      -       -      -
     50N  VAL*     0.5   443.0    +      -       +      +
     51N  GLY      2.1    12.1    -      -       -      +
     52N  ASN*     4.4     0.2    -      -       -      +
     60N  ALA*     5.0     0.2    -      -       -      -
    413u  LYS*     2.6    34.0    +      -       +      +
    415u  LEU*     6.1     0.7    -      -       +      -
     49z  ARG      1.3     0.4    -      -       -      -
     51z  GLY*     1.3    28.4    +      -       -      +
----------------------------------------------------------
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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