Contacts of the strand formed by residues 72 - 77 (chain D) in PDB entry 1FYT


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 SER 72 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22D  CYS      3.3     5.2    -      -       -      -
     23D  ASN*     3.4    15.7    -      -       -      +
     24D  TYR*     3.9     2.9    -      -       -      -
     65D  GLU      4.1     1.1    +      -       -      -
     66D  PHE*     3.6     5.5    -      -       -      -
     67D  LYS*     3.0    50.4    +      -       -      +
     70D  GLU*     3.6    12.3    -      -       -      +
     71D  THR*     1.3    78.1    -      -       -      +
     73D  PHE*     1.3    65.6    +      -       -      +
     74D  HIS*     3.5    25.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 73 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22D  CYS*     2.8    20.9    +      -       +      +
     24D  TYR*     5.0     0.7    -      -       +      -
     32D  LEU*     3.5    48.2    -      -       +      -
     33D  PHE      4.5     0.4    -      -       -      -
     34D  TRP*     2.8    52.9    +      +       -      -
     47D  LEU*     3.8    20.4    -      -       +      -
     48D  LYS      4.4     0.7    -      -       -      -
     49D  TYR*     3.5    29.6    -      -       +      -
     56D  VAL*     4.3     7.2    -      -       +      -
     64D  ALA*     3.7    20.2    -      -       +      -
     65D  GLU      3.5     5.6    -      -       -      -
     66D  PHE*     3.7    26.0    -      +       +      -
     72D  SER*     1.3    74.2    -      -       -      +
     74D  HIS*     1.3    57.8    +      -       -      +
     90D  CYS*     4.7     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 74 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19D  LEU*     3.9    21.8    -      -       +      -
     20D  LEU      3.4     8.3    -      -       -      +
     21D  ARG*     3.3    38.0    +      -       +      -
     22D  CYS      3.0    26.1    +      -       -      +
     23D  ASN*     4.0    10.5    +      -       -      -
     63D  GLU      3.8     0.2    -      -       -      +
     64D  ALA*     3.2    24.6    -      -       -      +
     65D  GLU      3.7     7.6    +      -       -      -
     67D  LYS*     5.9     5.2    -      -       +      -
     72D  SER*     3.5    30.5    +      -       -      -
     73D  PHE*     1.3    75.7    -      -       -      +
     75D  LEU*     1.3    59.7    +      -       -      +
     76D  THR*     4.1     2.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 75 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18D  VAL*     3.5     1.3    -      -       -      +
     19D  LEU*     3.2     5.2    -      -       -      +
     20D  LEU*     2.7    52.1    +      -       +      +
     34D  TRP*     3.7    38.1    -      -       +      -
     46D  LEU*     3.5    26.0    -      -       +      -
     47D  LEU*     3.9    17.7    -      -       +      -
     62D  PHE*     3.6    30.7    -      -       +      -
     63D  GLU      3.4    13.7    -      -       -      +
     64D  ALA*     4.2     0.9    -      -       +      -
     73D  PHE      3.9     0.8    +      -       -      -
     74D  HIS*     1.3    73.5    -      -       -      +
     76D  THR*     1.3    59.0    +      -       -      +
     88D  TYR*     3.7    19.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 76 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17D  LEU*     4.5    16.4    -      -       +      -
     18D  VAL      2.9    17.0    -      -       -      +
     19D  LEU*     3.3    29.8    -      -       +      -
     61D  GLY      4.3     0.2    -      -       -      +
     62D  PHE*     3.4     7.2    -      -       -      -
     63D  GLU*     2.8    55.8    +      -       -      +
     64D  ALA*     5.0     0.7    -      -       -      -
     65D  GLU      5.7     0.3    +      -       -      -
     74D  HIS*     4.5     3.3    +      -       -      +
     75D  LEU*     1.3    71.2    -      -       -      +
     77D  LYS*     1.3    64.0    +      -       -      +
     78D  PRO*     4.8     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 77 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16D  ALA      4.0     0.5    -      -       -      +
     17D  LEU*     3.7     4.0    -      -       -      +
     18D  VAL*     2.8    36.6    +      -       +      +
     60D  ASN      2.5    31.7    +      -       -      -
     61D  GLY*     3.4    23.6    +      -       -      +
     62D  PHE*     3.7    24.9    -      -       +      -
     76D  THR*     1.3    77.9    -      -       -      +
     78D  PRO*     1.3    73.7    -      -       +      +
     79D  SER      3.5    21.3    -      -       -      +
     80D  ALA*     4.6     2.0    -      -       -      -
     81D  HIS*     4.6     5.6    -      -       -      +
     84D  ASP*     3.0    30.7    +      -       -      +
----------------------------------------------------------
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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