Contacts of the strand formed by residues 96 - 101 (chain B) in PDB entry 3FN3


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 ASN 96 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39B  GLU*     3.5    32.4    +      -       -      +
     40B  CYS      3.7     1.5    -      -       -      +
     41B  LYS*     3.3    34.4    -      -       +      +
     42B  PHE*     3.4     4.9    -      -       -      -
     91B  GLN*     3.0    51.5    +      -       +      +
     92B  LEU*     3.5     5.7    -      -       -      +
     94B  LEU*     5.1     3.4    -      -       +      -
     95B  GLY*     1.3    76.4    -      -       -      +
     97B  ALA*     1.3    61.5    +      -       -      +
     98B  ALA*     3.1    34.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 97 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39B  GLU*     4.6     0.2    -      -       -      -
     40B  CYS*     2.7    29.8    +      -       +      +
     42B  PHE*     3.7     6.1    -      -       +      -
     55B  VAL*     4.0    20.9    -      -       +      -
     57B  TRP*     3.0    35.1    -      -       +      +
     87B  LEU*     4.2     5.6    -      -       -      -
     92B  LEU*     4.5     3.6    -      -       -      -
     96B  ASN*     1.3    69.2    -      -       -      +
     98B  ALA*     1.3    57.2    +      -       -      +
     99B  LEU      3.9     0.2    -      -       -      -
    116B  ILE*     3.8    21.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 98 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  THR*     4.4     5.4    -      -       +      -
     38B  ILE      3.6     4.9    -      -       -      -
     39B  GLU*     4.1     8.7    -      -       +      +
     87B  LEU*     3.6     7.6    -      -       -      +
     88B  LEU*     3.0    55.4    +      -       +      +
     91B  GLN*     4.4     1.8    -      -       +      +
     92B  LEU*     4.9     1.4    -      -       -      +
     96B  ASN*     3.1    31.9    +      -       -      +
     97B  ALA*     1.3    70.1    -      -       -      +
     99B  LEU*     1.3    61.9    +      -       -      +
    100B  GLN      3.8     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 99 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36B  MET      3.7     0.3    -      -       -      +
     37B  THR*     3.3     3.9    -      -       -      -
     38B  ILE*     2.8    51.4    +      -       +      +
     57B  TRP*     3.6    43.7    -      -       +      +
     64B  ILE*     3.8    37.9    -      -       +      -
     65B  ILE*     4.0    10.8    -      -       +      -
     86B  ARG      3.3    18.6    -      -       -      +
     87B  LEU*     4.6     0.4    -      -       -      -
     97B  ALA      3.7     2.2    +      -       -      -
     98B  ALA*     1.3    73.4    -      -       -      +
    100B  GLN*     1.3    67.2    +      -       -      +
    101B  ILE*     3.6    26.1    +      -       +      +
    112B  TYR*     4.5     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 100 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35B  ASN*     5.1     9.4    -      -       +      +
     36B  MET      3.1    10.5    -      -       -      +
     37B  THR*     3.6    17.8    +      -       -      +
     84B  ARG      3.6     1.6    -      -       -      +
     85B  ALA*     3.5     2.3    -      -       -      -
     86B  ARG*     2.9    62.9    +      -       +      +
     88B  LEU*     3.8    28.7    -      -       +      +
     98B  ALA      3.8     0.2    +      -       -      -
     99B  LEU*     1.3    74.8    -      -       -      +
    101B  ILE*     1.3    77.1    +      -       -      +
    102B  THR*     4.4    15.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 101 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35B  ASN*     3.3     4.9    -      -       -      +
     36B  MET*     2.7    60.0    +      -       +      +
     38B  ILE*     6.0     0.2    -      -       +      -
     64B  ILE*     4.2     7.6    -      -       +      -
     81B  TYR*     4.5     7.4    -      -       +      -
     84B  ARG*     3.4    36.3    -      -       -      +
     85B  ALA*     3.7    16.8    -      -       +      -
     99B  LEU*     3.6    27.1    -      -       +      -
    100B  GLN*     1.3    86.5    -      -       -      +
    102B  THR*     1.3    64.6    +      -       -      +
    104B  VAL*     4.1    12.6    -      -       +      +
    108B  ASP*     3.5    11.4    -      -       -      +
    112B  TYR*     5.1     8.1    -      -       +      +
----------------------------------------------------------
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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