Contacts of the strand formed by residues 1444 - 1448 (chain A) in PDB entry 6A5T


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 PHE1444 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    853A  TYR*     4.3     7.9    -      -       -      -
   1062A  PRO      6.2     0.2    -      -       -      -
   1440A  GLY      4.4    11.0    -      -       -      -
   1441A  THR*     4.7     4.7    -      -       -      -
   1442A  GLY      3.2     4.4    +      -       -      -
   1443A  ALA*     1.3    91.8    -      -       +      +
   1445A  ASP*     1.3    72.9    +      -       -      +
   1446A  VAL*     4.7     2.0    -      -       +      -
     88F  TYR*     3.8    10.5    -      -       +      -
     89F  GLU*     3.2    47.8    -      -       +      -
     92F  ARG*     3.4    37.6    +      -       +      -
     93F  ILE*     5.5     0.2    -      -       +      -
    134F  ILE*     3.5    29.6    -      -       +      -
    135F  ARG      3.1    24.0    -      -       -      +
    136F  ARG*     4.3     4.7    -      -       +      -
    137F  TYR*     4.6     6.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP1445 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1444A  PHE*     1.3    88.8    -      -       -      +
   1446A  VAL*     1.3    68.0    +      -       -      +
   1447A  MET*     4.2     9.2    -      -       +      -
     92F  ARG*     5.2     4.0    +      -       -      +
    134F  ILE*     4.3     1.6    -      -       -      +
    135F  ARG*     3.5    23.7    +      -       +      -
    137F  TYR*     2.2    42.0    +      -       -      +
     60G  ARG*     3.2    42.6    +      -       +      +
     63G  PRO*     5.0     4.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL1446 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1444A  PHE*     4.2     6.3    -      -       +      +
   1445A  ASP*     1.3    83.5    -      -       -      +
   1447A  MET*     1.3    66.9    +      -       -      +
     92F  ARG*     3.8    39.6    -      -       +      +
     93F  ILE*     4.8     7.6    -      -       +      -
     96F  THR*     5.0    10.8    -      -       +      +
    132F  LEU*     4.1    26.9    -      -       +      -
    133F  VAL      3.8     6.5    -      -       -      +
    134F  ILE*     5.1     2.9    -      -       +      -
     60G  ARG*     3.6     4.0    -      -       -      +
     61G  ILE*     2.7    46.6    +      -       +      +
     63G  PRO*     6.1     0.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET1447 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1445A  ASP*     4.2     6.3    -      -       +      -
   1446A  VAL*     1.3    73.7    -      -       -      +
   1448A  ILE*     1.3    65.0    +      -       -      +
   1449A  ASP      4.2     0.2    -      -       -      -
    132F  LEU*     3.3    15.6    -      -       -      +
    133F  VAL*     2.9    45.0    +      -       +      +
    135F  ARG*     3.2    54.7    -      -       +      +
    145F  ASP*     5.7     0.7    -      -       -      +
     58G  LYS*     3.6    22.4    -      -       +      +
     59G  GLY      3.1    21.5    -      -       -      +
     60G  ARG*     3.5    35.7    -      -       +      -
     61G  ILE*     3.0    16.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE1448 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1447A  MET*     1.3    79.4    -      -       -      +
   1449A  ASP*     1.3    70.0    +      -       -      +
   1450A  GLU*     3.2    14.2    +      -       -      +
   1453A  LEU*     4.6     9.6    -      -       +      -
    100F  GLN*     5.5     1.1    -      -       -      +
    131F  PRO*     3.9    18.4    -      -       +      +
    132F  LEU*     4.6     3.8    -      -       +      -
     18G  PHE*     4.3    28.5    -      -       +      -
     22G  MET*     4.2    22.6    -      -       +      +
     58G  LYS*     5.0     0.5    -      -       -      +
     59G  GLY*     2.6    33.5    +      -       -      +
     61G  ILE*     3.5    17.9    -      -       +      +
     68G  ALA*     4.6     4.3    -      -       +      -
     70G  PHE*     3.9    25.1    -      -       +      -
----------------------------------------------------------
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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