Contacts of the strand formed by residues 1399 - 1404 (chain H) in PDB entry 6C3P


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 GLU1399 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1348H  ASN      4.4     1.6    -      -       -      +
   1350H  SER*     3.0    41.2    +      -       -      +
   1397H  THR*     3.4     9.0    +      -       -      +
   1398H  PHE*     1.3   104.7    -      -       +      +
   1400H  GLY*     1.3    71.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY1400 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1347H  GLN      3.8     5.4    -      -       -      -
   1348H  ASN*     3.2    24.1    +      -       -      +
   1349H  LEU*     4.1     3.6    -      -       -      -
   1397H  THR*     4.0     7.1    +      -       -      +
   1398H  PHE      5.1     0.3    -      -       -      +
   1399H  GLU*     1.3    84.8    +      -       -      +
   1401H  HIS*     1.3    69.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS1401 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1345H  GLN      5.5     0.2    -      -       -      -
   1346H  ILE*     4.0     1.4    -      -       -      -
   1347H  GLN*     2.9    67.5    +      -       +      +
   1349H  LEU*     4.2    13.8    -      -       -      +
   1397H  THR*     5.2     1.3    -      -       -      -
   1400H  GLY*     1.3    78.8    -      -       -      +
   1402H  ILE*     1.3    60.7    +      -       -      +
   1403H  ILE*     3.8    31.2    -      -       +      +
   1408H  ASP*     3.4    23.3    -      -       -      +
   1409H  ILE*     5.5     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE1402 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1344H  ILE*     3.7    16.8    -      -       +      -
   1345H  GLN      4.0     2.7    -      -       -      -
   1346H  ILE*     3.6    25.6    -      -       +      +
   1349H  LEU*     4.5    11.8    -      -       +      +
   1390H  ALA      4.8     9.6    -      -       -      +
   1391H  PHE*     3.6    39.9    -      -       +      +
   1401H  HIS*     1.3    75.4    -      -       -      +
   1403H  ILE*     1.3    70.1    +      -       -      +
   1404H  ILE*     4.1     8.5    +      -       +      -
   1408H  ASP*     2.9    19.9    +      -       -      +
   1409H  ILE*     3.1    47.5    +      -       +      +
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Residues in contact with ILE1403 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1343H  LYS      3.7     0.9    -      -       -      +
   1344H  ILE*     3.5     8.7    -      -       -      +
   1345H  GLN*     3.1    42.3    +      -       +      +
   1401H  HIS*     3.8    26.9    -      -       +      +
   1402H  ILE*     1.3    74.7    -      -       -      +
   1404H  ILE*     1.3    70.5    +      -       -      +
   1405H  ASP*     4.8     0.9    -      -       -      -
   1406H  GLY      4.2     7.2    -      -       -      +
   1407H  ILE*     2.9    19.3    -      -       -      +
   1408H  ASP*     3.4    29.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE1404 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1338H  TRP*     3.3    33.2    -      -       +      -
   1339H  PRO*     5.0     6.1    -      -       +      -
   1342H  GLY*     5.2     5.2    -      -       -      -
   1343H  LYS      3.9     5.4    -      -       -      +
   1344H  ILE*     4.9    15.9    -      -       +      -
   1391H  PHE*     6.4     1.1    -      -       +      -
   1402H  ILE*     4.4    16.6    -      -       +      -
   1403H  ILE*     1.3    77.9    -      -       -      +
   1405H  ASP*     1.3    66.2    +      -       -      +
   1406H  GLY      2.9     0.7    +      -       -      -
   1407H  ILE*     2.6    38.8    +      -       -      +
   1408H  ASP      4.2    10.1    -      -       -      +
   1409H  ILE*     3.5    32.1    -      -       +      -
   1412H  LEU*     5.4     2.7    -      -       +      -
   1421H  LEU*     5.7    10.8    -      -       +      -
   1501H  ILE*     5.4     7.9    -      -       +      -
----------------------------------------------------------
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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