Contacts of the strand formed by residues 1345 - 1352 (chain H) 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 ILE1345 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1343H  GLY      3.8     3.3    +      -       -      +
   1344H  LYS*     1.3    74.8    -      -       -      +
   1346H  GLN*     1.3    57.9    +      -       -      +
   1347H  ILE*     6.2     2.2    -      -       +      -
   1368H  LEU*     3.3     2.3    -      -       -      +
   1369H  ILE*     2.4    59.6    +      -       +      +
   1392H  PHE*     6.0     4.9    -      -       +      -
   1404H  ILE*     3.9    15.5    -      -       -      +
   1405H  ILE*     5.3     0.9    -      -       -      -
   1406H  ASP      5.2     2.9    -      -       -      +
   1532H  THR*     5.8     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN1346 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1345H  ILE*     1.3    76.0    -      -       -      +
   1347H  ILE*     1.3    67.4    +      -       -      +
   1348H  GLN*     4.1     2.4    +      -       +      +
   1367H  THR      3.3     9.4    -      -       -      +
   1368H  LEU*     4.3    10.3    -      -       +      -
   1402H  ARG      4.3     1.4    -      -       -      +
   1404H  ILE*     3.7    29.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE1347 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1345H  ILE*     6.1     2.0    -      -       +      -
   1346H  GLN*     1.3    81.2    -      -       -      +
   1348H  GLN*     1.3    61.6    +      -       -      +
   1350H  LEU*     3.7    22.7    -      -       +      -
   1362H  LEU*     6.4     0.2    -      -       +      -
   1365H  VAL*     3.4    33.4    -      -       +      +
   1366H  ASN*     3.3     6.4    -      -       -      +
   1367H  THR*     2.6    40.0    +      -       -      +
   1402H  ARG      4.0     1.8    -      -       -      +
   1403H  ILE*     3.8    28.7    -      -       +      -
   1404H  ILE      4.5     5.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN1348 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1346H  GLN*     4.1     2.4    +      -       +      +
   1347H  ILE*     1.3    75.2    -      -       -      +
   1349H  ASN*     1.3    69.4    +      -       +      +
   1350H  LEU      3.4     1.6    -      -       -      -
   1366H  ASN*     4.9     2.2    -      -       -      +
   1401H  GLY*     3.2    19.2    -      -       -      -
   1402H  ARG*     3.2    16.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN1349 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1348H  GLN*     1.3    73.0    -      -       +      +
   1350H  LEU*     1.3    61.6    +      -       -      +
   1351H  SER*     3.4     4.9    +      -       -      -
   1364H  HIS*     4.2    17.0    -      -       +      +
   1365H  VAL      2.9    16.7    +      -       -      -
   1366H  ASN*     4.6     4.4    -      -       -      +
   1400H  GLU*     3.2    15.3    -      -       +      +
   1401H  GLY*     3.3     8.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU1350 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1347H  ILE*     3.7    23.8    -      -       +      -
   1348H  GLN      4.1     1.3    -      -       -      -
   1349H  ASN*     1.3    75.1    -      -       -      +
   1351H  SER*     1.3    58.2    +      -       -      +
   1362H  LEU*     3.6    23.6    -      -       +      +
   1364H  HIS      3.5     4.9    +      -       -      -
   1365H  VAL*     3.2    25.9    +      -       +      +
   1398H  MET*     4.8     8.7    -      -       +      -
   1400H  GLU      3.3     8.5    -      -       -      +
   1401H  GLY*     4.4     0.2    -      -       -      -
   1402H  ARG      4.7     9.4    -      -       -      +
   1403H  ILE*     5.8     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER1351 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1349H  ASN      3.4     4.2    +      -       -      -
   1350H  LEU*     1.3    76.3    +      -       -      +
   1352H  VAL*     1.3    55.6    +      -       -      +
   1360H  PRO*     5.8     2.9    -      -       -      -
   1362H  LEU      3.3     9.3    +      -       -      -
   1363H  LYS*     4.3     1.9    -      -       -      -
   1364H  HIS*     3.8    13.3    +      -       -      -
   1398H  MET*     3.2     5.6    -      -       -      -
   1399H  PHE*     2.4    40.3    +      -       -      -
   1400H  GLU*     3.0    24.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL1352 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1351H  SER*     1.3    74.5    -      -       -      +
   1353H  ARG*     1.3    64.2    +      -       -      +
   1354H  TYR*     5.1     3.4    -      -       +      +
   1360H  PRO*     3.4     4.6    -      -       -      +
   1361H  VAL*     2.4    41.2    +      -       +      -
   1362H  LEU*     3.2    41.0    +      -       +      +
   1387H  SER*     4.6     6.5    -      -       -      +
   1391H  ALA*     5.6     5.4    -      -       +      -
   1396H  VAL*     3.7    22.0    -      -       +      +
   1397H  ASP      3.3    26.0    -      -       -      +
   1398H  MET*     4.3     4.0    -      -       +      -
   1399H  PHE*     4.1     6.5    -      -       -      +
----------------------------------------------------------
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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