Contacts of the strand formed by residues 1344 - 1350 (chain G) 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 ILE1344 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1342G  GLY      3.3    18.4    -      -       -      +
   1343G  LYS*     1.3    76.5    -      -       -      +
   1345G  GLN*     1.3    59.4    +      -       -      +
   1346G  ILE*     4.0     9.4    -      -       +      -
   1366G  ALA      3.2     2.6    -      -       -      +
   1367G  LEU*     4.3     0.2    -      -       -      -
   1368G  ILE*     2.3    69.0    +      -       +      +
   1391G  PHE*     4.8    22.2    -      -       +      -
   1402G  ILE*     3.7    32.5    -      -       +      -
   1403G  ILE      3.5     5.2    -      -       -      +
   1404G  ILE*     4.9    13.9    -      -       +      -
   1501G  ILE*     5.5    13.2    -      -       +      -
   1531G  THR*     5.6     3.4    -      -       +      -
   1533G  VAL*     5.3     7.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN1345 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1343G  LYS*     4.3     4.5    -      -       -      -
   1344G  ILE*     1.3    73.2    -      -       -      +
   1346G  ILE*     1.3    62.5    +      -       -      +
   1347G  GLN*     5.5     1.7    -      -       -      +
   1366G  ALA      3.0     6.7    -      -       -      +
   1367G  LEU*     4.1    22.0    -      -       +      -
   1401G  HIS*     4.5     1.4    +      -       -      +
   1402G  ILE*     4.0     0.3    -      -       -      -
   1403G  ILE*     3.1    42.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE1346 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1344G  ILE*     4.0     8.7    -      -       +      -
   1345G  GLN*     1.3    76.6    -      -       -      +
   1347G  GLN*     1.3    65.1    +      -       -      +
   1349G  LEU*     4.1    12.8    -      -       +      -
   1364G  VAL*     3.5    37.7    -      -       +      +
   1365G  ASN*     3.1     4.2    -      -       -      +
   1366G  ALA*     2.7    55.2    +      -       +      +
   1368G  ILE*     5.8     1.6    -      -       +      -
   1387G  PHE*     3.5    31.2    -      -       +      -
   1401G  HIS      3.9     7.0    -      -       -      +
   1402G  ILE*     3.6    32.3    -      -       +      +
   1556G  ILE*     5.4     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN1347 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1345G  GLN      5.5     0.9    -      -       -      +
   1346G  ILE*     1.3    79.1    -      -       -      +
   1348G  ASN*     1.3    73.7    +      -       +      +
   1349G  LEU      2.9     5.8    +      -       -      +
   1364G  VAL      3.2     5.1    +      -       -      -
   1365G  ASN*     3.6    11.4    -      -       +      -
   1400G  GLY*     3.8     0.9    -      -       -      -
   1401G  HIS*     2.9    58.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN1348 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1347G  GLN*     1.3    76.9    -      -       +      +
   1349G  LEU*     1.3    64.0    +      -       -      +
   1350G  SER*     3.0    14.7    +      -       -      +
   1363G  HIS*     3.9    27.0    -      -       +      +
   1364G  VAL      2.9    17.6    +      -       -      +
   1365G  ASN*     4.3     2.0    -      -       -      +
   1399G  GLU*     4.4     1.7    -      -       +      +
   1400G  GLY*     3.2    16.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU1349 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1346G  ILE*     4.1    18.4    -      -       +      -
   1347G  GLN      2.9     6.3    +      -       -      +
   1348G  ASN*     1.3    73.2    -      -       -      +
   1350G  SER*     1.3    57.4    +      -       -      +
   1351G  VAL*     4.1    12.1    -      -       +      -
   1361G  LEU*     3.3    10.8    -      -       +      +
   1362G  LYS*     3.4     6.1    -      -       -      -
   1364G  VAL*     3.1    33.0    +      -       +      +
   1387G  PHE*     3.6    35.7    -      -       +      -
   1390G  ALA*     4.2    14.4    -      -       +      +
   1397G  THR*     3.8    23.6    -      -       -      +
   1400G  GLY*     4.1     2.7    -      -       -      -
   1401G  HIS*     4.2    22.9    -      -       -      +
   1402G  ILE*     4.5    11.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER1350 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1348G  ASN      3.0    12.1    +      -       -      -
   1349G  LEU*     1.3    69.6    -      -       -      +
   1351G  VAL*     1.3    60.8    +      -       -      +
   1361G  LEU      3.1     4.5    -      -       -      -
   1362G  LYS*     3.3    21.6    -      -       -      +
   1363G  HIS*     3.4    12.6    +      -       -      -
   1397G  THR      3.2     0.9    -      -       -      -
   1398G  PHE*     3.0    39.2    +      -       -      -
   1399G  GLU*     3.0    34.8    +      -       -      +
----------------------------------------------------------
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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