Contacts of the strand formed by residues 113 - 118 (chain B) in PDB entry 1FTA


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 113 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29B  GLU*     3.4    26.2    -      -       -      -
     30B  LEU*     4.0    21.7    -      -       +      +
     33B  LEU*     3.9    24.2    -      -       +      -
     90B  ALA*     3.1    16.5    +      -       +      +
     91B  THR*     3.3     8.6    -      -       +      -
     92B  CYS*     2.9    25.3    +      -       -      -
     93B  VAL      3.6     1.2    +      -       -      -
    111B  GLY      3.4     1.4    +      -       -      -
    112B  LYS*     1.3    90.4    -      -       +      +
    114B  VAL*     1.3    64.0    +      -       -      +
    115B  VAL      4.1     0.2    -      -       -      -
    138B  ILE*     3.7    19.3    -      -       +      -
    139B  TYR      3.7     9.6    -      -       -      +
    140B  ARG*     4.0    17.3    -      -       +      -
    160B  VAL*     4.2     9.9    -      -       +      -
    338B  AMP      2.8    58.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 114 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92B  CYS*     3.8    18.2    -      -       -      -
     93B  VAL*     3.2    27.6    -      -       +      +
     95B  VAL*     5.4     0.4    -      -       +      -
    113B  TYR*     1.3    76.9    -      -       -      +
    115B  VAL*     1.3    60.0    +      -       -      +
    116B  CYS*     4.6     5.6    -      -       -      -
    137B  GLY      3.7     0.7    -      -       -      +
    138B  ILE*     3.2     4.3    -      -       -      -
    139B  TYR*     2.8    54.8    +      -       +      +
    141B  LYS*     3.8    18.6    -      -       +      -
    151B  ASP*     4.1    22.7    -      -       +      +
    152B  ALA*     4.1    16.2    -      -       +      -
    154B  GLN*     4.4     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 115 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  LEU*     4.1    16.4    -      -       +      -
     37B  LEU*     4.8     7.0    -      -       +      -
     85B  LEU*     3.9    11.7    -      -       +      -
     91B  THR*     3.9    23.3    -      -       +      -
     93B  VAL      3.1     5.9    +      -       -      +
     94B  LEU*     3.4    15.3    -      -       +      -
     95B  VAL      3.0    23.2    +      -       -      +
    114B  VAL*     1.3    77.0    -      -       -      +
    116B  CYS*     1.3    67.1    +      -       -      +
    117B  PHE*     3.7    22.9    -      -       +      -
    136B  PHE*     4.7     7.2    -      -       +      -
    137B  GLY      3.2     8.7    -      -       -      +
    138B  ILE*     4.0    20.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 116 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95B  VAL*     3.2    28.9    -      -       +      +
    114B  VAL*     4.6     7.4    -      -       -      -
    115B  VAL*     1.3    75.7    -      -       -      +
    117B  PHE*     1.3    59.6    +      -       -      +
    136B  PHE*     3.3     2.3    -      -       -      +
    137B  GLY      2.8    33.5    +      -       -      +
    139B  TYR*     3.8    28.5    -      -       +      -
    152B  ALA*     4.6     1.3    -      -       -      -
    278B  LEU*     3.7    36.6    -      -       +      +
    279B  TYR*     3.9    11.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 117 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  LEU*     6.2     0.7    -      -       +      -
     78B  ASN*     3.7    19.5    -      -       -      -
     81B  VAL*     3.8    28.7    -      -       +      -
     82B  MET*     3.7    25.6    -      -       +      -
     85B  LEU*     4.0    15.9    -      -       +      -
     94B  LEU*     4.4     9.0    -      -       +      -
     95B  VAL      3.0    15.3    +      -       -      +
     96B  SER*     3.6    12.2    -      -       -      -
     97B  GLU      3.5    19.1    +      -       -      -
    115B  VAL*     3.7    25.4    -      -       +      -
    116B  CYS*     1.3    74.2    -      -       -      +
    118B  ASP*     1.3    60.0    +      -       -      +
    119B  PRO*     3.7    19.0    -      -       +      +
    134B  THR*     5.4     3.1    -      -       +      -
    135B  ILE      3.1    14.6    -      -       -      +
    136B  PHE*     4.0    10.5    -      -       +      -
    279B  TYR*     3.7     9.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 118 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97B  GLU*     3.7    25.6    -      -       -      +
    117B  PHE*     1.3    73.1    -      -       -      +
    119B  PRO*     1.3    69.7    -      -       -      +
    120B  LEU      3.3     3.8    +      -       -      +
    121B  ASP*     3.2    27.6    +      -       -      +
    133B  GLY      4.0     1.6    -      -       -      +
    134B  THR*     3.5     1.9    -      -       -      +
    135B  ILE*     3.0    33.8    +      -       +      +
    276B  ARG*     4.0     3.1    +      -       -      -
    279B  TYR*     3.8    21.2    -      -       +      +
    280B  GLU*     3.0    30.8    -      -       -      +
----------------------------------------------------------
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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