Contacts of the strand formed by residues 94 - 99 (chain A) in PDB entry 5FN4


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 TYR 94 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  VAL*     3.3    35.4    -      -       +      +
     73A  ILE      4.6     0.4    -      -       -      -
     74A  HIS*     4.1    30.9    +      -       +      -
     84A  TRP*     3.5    22.8    +      -       -      -
     85A  VAL*     3.8    37.2    -      -       +      -
     89A  GLY*     4.6     4.0    -      -       -      -
     90A  PRO*     3.9     9.4    -      -       -      +
     91A  ASN*     2.9    50.5    +      -       -      -
     92A  PRO      2.7    10.6    +      -       -      +
     93A  PRO*     1.3    70.9    -      -       -      +
     95A  MET*     1.3    56.8    +      -       -      +
     96A  VAL      3.9     0.2    +      -       -      -
    117A  ARG*     4.2     9.4    -      -       -      -
    118A  ILE*     3.3    10.6    -      -       +      +
    119A  ALA      2.8    38.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 95 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  ASP*     3.2    31.2    -      -       +      +
     70A  THR      4.4     1.3    -      -       -      +
     71A  GLY*     3.7    11.3    -      -       -      +
     72A  VAL      2.8    14.7    +      -       -      +
     73A  ILE*     4.0    13.5    -      -       +      -
     74A  HIS*     2.8    34.6    +      -       -      +
     94A  TYR*     1.3    72.2    -      -       -      +
     96A  VAL*     1.3    54.8    +      -       -      +
    119A  ALA      3.3    22.7    -      -       -      +
    120A  GLY*     3.5    22.7    -      -       -      +
    179A  PRO*     4.9     0.2    -      -       +      -
    215A  MET*     3.2    45.8    -      -       +      +
    217A  LEU*     3.6    24.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 96 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  HIS      3.3     3.1    -      -       -      +
     76A  VAL*     3.6    26.5    -      -       +      -
     82A  LEU*     5.8     0.7    -      -       +      -
     85A  VAL*     3.9    15.9    -      -       +      -
     94A  TYR*     4.3     0.4    -      -       +      +
     95A  MET*     1.3    79.2    -      -       -      +
     97A  LEU*     1.3    60.4    +      -       -      +
     98A  LEU*     3.7     6.7    -      -       +      -
    111A  LEU*     4.1     7.2    -      -       +      -
    118A  ILE*     3.5    23.8    -      -       +      -
    120A  GLY      3.2     5.2    +      -       -      +
    121A  LEU*     3.3    42.4    -      -       +      -
    122A  ALA*     2.8    31.5    +      -       -      +
    215A  MET*     5.5     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 97 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73A  ILE*     6.0     2.0    -      -       +      -
     74A  HIS      2.8    13.9    +      -       -      +
     75A  VAL*     3.4    16.6    -      -       +      +
     76A  VAL      2.8    28.3    +      -       -      +
     77A  GLU*     6.0     0.2    -      -       -      +
     95A  MET      4.2     0.6    -      -       -      -
     96A  VAL*     1.3    71.8    -      -       -      +
     98A  LEU*     1.3    64.6    +      -       -      +
     99A  GLU*     3.4    24.1    -      -       -      +
    122A  ALA*     3.4    20.0    -      -       +      -
    124A  SER*     4.5    10.5    -      -       -      +
    183A  LEU*     4.6     5.4    -      -       +      -
    189A  THR*     4.5    10.3    -      -       -      +
    192A  ILE*     3.3    50.3    -      -       +      -
    193A  LYS*     4.7    11.7    -      -       -      +
    215A  MET*     5.3     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 98 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76A  VAL*     3.7    37.0    -      -       +      +
     96A  VAL*     3.7    19.3    -      -       +      -
     97A  LEU*     1.3    80.6    -      -       -      +
     99A  GLU*     1.3    72.5    -      -       -      +
    102A  HIS*     5.3     3.4    -      -       +      -
    103A  PHE*     4.0    29.8    -      -       +      +
    107A  LEU*     4.1    25.4    -      -       +      -
    108A  MET*     5.0     0.2    -      -       -      -
    111A  LEU*     5.2     0.9    -      -       +      -
    121A  LEU*     3.4    22.4    -      -       +      -
    122A  ALA      2.8    15.3    +      -       -      +
    123A  VAL*     3.4     5.2    -      -       +      -
    124A  SER      2.8    24.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 99 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  VAL*     5.9     0.5    -      -       -      +
     76A  VAL      4.4     1.8    +      -       -      +
     77A  GLU*     5.4     9.4    -      -       +      +
     97A  LEU*     3.4    23.4    -      -       -      +
     98A  LEU*     1.3    88.9    -      -       -      +
    100A  SER*     1.3    67.1    +      -       -      +
    101A  LYS*     3.2     8.5    -      -       +      +
    102A  HIS*     3.7    30.5    +      -       +      +
    103A  PHE*     3.5     9.7    +      -       -      +
    123A  VAL*     4.4     1.3    -      -       -      -
    124A  SER*     3.5    21.9    +      -       -      -
    126A  THR*     3.6    16.1    +      -       +      +
    186A  GLU*     4.7     8.3    -      -       -      +
    189A  THR*     5.3     1.4    +      -       -      -
    193A  LYS*     3.7    28.1    +      -       -      +
----------------------------------------------------------
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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