Contacts of the strand formed by residues 1471 - 1475 (chain A) in PDB entry 5FLM


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 PHE1471 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    875A  TYR*     3.2    21.3    -      -       +      +
   1468A  THR*     3.6    21.3    -      -       -      -
   1469A  GLY      3.7     5.4    -      -       -      +
   1470A  CYS*     1.3    81.2    -      -       +      +
   1472A  ASP*     1.3    65.7    +      -       -      +
   1473A  LEU*     3.6    21.5    -      -       +      -
     60F  TYR*     4.0     2.5    -      -       +      -
     61F  GLU*     3.5    37.7    -      -       +      +
     64F  ARG*     3.4    62.3    +      -       +      -
    106F  ILE*     3.7    23.6    -      -       +      -
    107F  ARG      3.5    13.9    -      -       -      +
    108F  ARG*     4.4     1.3    -      -       -      +
    109F  TYR*     4.7     5.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP1472 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1471A  PHE*     1.3    78.6    -      -       -      +
   1473A  LEU*     1.3    88.1    +      -       -      +
   1474A  LEU*     4.4     7.6    -      -       -      +
     64F  ARG*     4.8     7.5    +      -       -      +
    106F  ILE*     3.5     1.7    -      -       -      -
    107F  ARG*     2.5    49.3    +      -       +      +
    109F  TYR*     3.2    33.8    +      -       +      +
     58G  VAL*     3.7    23.6    -      -       -      +
     59G  ILE      4.3     4.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU1473 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1471A  PHE*     3.6    20.4    -      -       +      -
   1472A  ASP*     1.3    89.7    +      -       -      +
   1474A  LEU*     1.3    65.2    +      -       -      +
     64F  ARG*     3.7    31.6    -      -       +      +
     65F  VAL*     3.7    13.9    -      -       +      -
     68F  THR*     3.3    36.3    -      -       +      +
    104F  ILE*     3.8    10.8    -      -       +      -
    105F  ILE      4.0     0.9    -      -       -      -
    106F  ILE*     3.6    29.6    -      -       +      -
     59G  ILE*     3.3    36.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU1474 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1472A  ASP*     4.4     4.7    -      -       -      +
   1473A  LEU*     1.3    80.9    -      -       -      +
   1475A  LEU*     1.3    60.5    +      -       -      +
    104F  ILE*     3.3     6.8    -      -       -      +
    105F  ILE*     2.8    63.7    +      -       +      +
    107F  ARG*     3.3    54.5    -      -       +      +
    117F  ASP*     4.2     6.3    -      -       -      +
     56G  ALA*     4.6     9.4    -      -       +      +
     57G  GLY      3.2     9.2    -      -       -      +
     58G  VAL*     3.4    34.1    -      -       +      -
     59G  ILE*     3.2     6.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU1475 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1474A  LEU*     1.3    72.0    -      -       -      +
   1476A  ASP*     1.3    80.0    +      -       -      +
   1477A  ALA*     3.5     3.8    +      -       -      +
   1480A  CYS*     3.7     8.3    -      -       -      -
     72F  GLN*     4.3    11.4    -      -       -      +
    103F  PRO*     4.0    12.3    -      -       +      +
    104F  ILE*     5.3     1.1    -      -       +      -
    105F  ILE*     4.8     4.0    -      -       -      +
     18G  PHE*     3.8    43.3    -      -       +      -
     22G  LEU*     3.5    16.2    -      -       +      -
     56G  ALA*     5.5     1.7    -      -       -      +
     57G  GLY      2.9    26.1    +      -       -      +
     59G  ILE*     3.3    10.2    -      -       +      +
     66G  VAL*     4.3    13.7    -      -       +      -
     68G  TYR*     3.5    21.7    +      -       -      +
----------------------------------------------------------
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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