Contacts of the strand formed by residues 1400 - 1405 (chain F) in PDB entry 6BAA


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 GLU1400 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1349F  ASN      3.2     7.1    -      -       -      +
   1350F  LEU*     3.3     1.0    -      -       -      -
   1351F  SER*     3.0    36.4    +      -       -      +
   1398F  MET*     3.3     9.2    -      -       -      +
   1399F  PHE*     1.3    79.4    -      -       +      +
   1401F  GLY*     1.3    68.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY1401 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1348F  GLN      3.2    16.8    -      -       -      -
   1349F  ASN*     3.3     8.9    +      -       -      +
   1398F  MET*     4.3     6.7    -      -       -      +
   1400F  GLU*     1.3    80.5    -      -       -      +
   1402F  ARG*     1.3    62.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG1402 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1346F  GLN      4.3     1.8    -      -       -      +
   1347F  ILE*     4.0     6.8    -      -       -      +
   1348F  GLN*     3.2    32.9    +      -       +      +
   1350F  LEU*     4.7     5.1    -      -       -      +
   1398F  MET*     5.2     5.2    -      -       -      -
   1401F  GLY*     1.3    76.6    -      -       -      +
   1403F  ILE*     1.3    62.9    +      -       -      +
   1404F  ILE*     6.4     0.4    -      -       +      -
   1409F  ASP*     4.9    12.8    -      -       +      -
   1411F  ALA*     5.8     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE1403 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1347F  ILE*     3.8    20.2    -      -       +      -
   1350F  LEU*     5.8     3.4    -      -       +      -
   1391F  ALA*     4.9    23.8    -      -       +      +
   1392F  PHE*     5.7     1.6    -      -       -      +
   1398F  MET*     5.7     3.7    -      -       +      +
   1402F  ARG*     1.3    74.1    -      -       -      +
   1404F  ILE*     1.3    62.1    +      -       -      +
   1409F  ASP*     3.3    19.2    -      -       -      +
   1410F  ILE*     3.3    11.6    +      -       +      +
   1411F  ALA*     4.6     5.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE1404 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1344F  LYS      5.0     0.4    -      -       -      +
   1345F  ILE*     3.9    19.1    -      -       -      +
   1346F  GLN*     3.7    24.6    +      -       +      +
   1347F  ILE*     4.5     4.4    -      -       -      +
   1392F  PHE*     5.5     4.0    -      -       -      -
   1402F  ARG*     4.2     0.6    -      -       +      -
   1403F  ILE*     1.3    73.2    -      -       -      +
   1405F  ILE*     1.3    59.5    +      -       -      +
   1406F  ASP      4.2     0.4    -      -       -      -
   1407F  GLY*     4.0    16.6    -      -       -      +
   1408F  ILE      3.4    17.0    -      -       -      -
   1409F  ASP*     3.7     5.8    -      -       +      +
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Residues in contact with ILE1405 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1345F  ILE*     5.3     1.8    -      -       -      -
   1392F  PHE*     4.6    22.2    -      -       +      +
   1403F  ILE      4.2     0.6    +      -       -      -
   1404F  ILE*     1.3    72.7    -      -       -      +
   1406F  ASP*     1.3    68.0    +      -       +      +
   1407F  GLY      3.1     0.4    -      -       -      -
   1408F  ILE*     2.7    33.2    +      -       -      +
   1410F  ILE*     4.8    10.7    -      -       +      +
   1502F  ILE*     5.7     3.8    -      -       +      -
----------------------------------------------------------
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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