Contacts of the helix formed by residues 1306 - 1316 (chain A) in PDB entry 1Y8Z


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 GLU1306 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1116A  HIS*     4.7     7.3    +      -       -      +
   1176A  PRO*     4.9     3.4    -      -       -      -
   1208A  TRP*     3.1    21.3    -      -       -      -
   1209A  LYS*     2.9    23.3    +      -       -      -
   1292A  GLN*     2.8    12.1    +      -       -      +
   1294A  SER*     2.4    35.1    +      -       -      -
   1296A  LEU*     5.3     5.2    -      -       +      -
   1304A  SER      5.1     3.1    -      -       -      +
   1305A  LEU*     1.3    76.8    -      -       -      +
   1307A  TYR*     1.3    67.1    +      -       -      +
   1308A  THR      3.2     0.2    -      -       -      -
   1309A  HIS*     2.8    32.6    +      -       +      +
   1310A  LEU*     3.2     8.7    +      -       -      +
   1385A  GLN*     5.0     1.3    -      -       -      -
   3006A  UDP      3.5    22.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR1307 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1015A  GLY      3.6    10.3    -      -       -      -
   1018A  LYS*     3.4    28.0    -      -       +      -
   1019A  PHE*     3.2    41.5    -      -       -      -
   1022A  GLU*     4.0     3.8    -      -       +      +
   1176A  PRO*     3.3    36.0    -      -       +      +
   1177A  PRO      2.7    36.1    +      -       -      -
   1178A  MET*     3.7    19.1    -      -       +      -
   1306A  GLU*     1.3    72.5    -      -       -      +
   1308A  THR*     1.3    57.3    +      -       -      +
   1310A  LEU*     3.2     6.9    +      -       +      +
   1311A  GLU*     2.8    36.3    +      -       -      +
   3006A  UDP      3.3    38.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR1308 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1202A  ILE*     3.5    32.8    +      -       +      +
   1203A  GLY*     5.0     5.6    -      -       -      +
   1209A  LYS*     4.9     2.0    +      -       -      +
   1275A  TYR*     3.9     6.7    -      -       -      +
   1292A  GLN*     2.6    36.2    +      -       -      +
   1307A  TYR*     1.3    76.4    -      -       -      +
   1309A  HIS*     1.3    61.1    +      -       -      +
   1311A  GLU*     3.5     6.1    -      -       -      +
   1312A  LEU*     3.2    26.5    +      -       -      +
   3006A  UDP      2.9    48.7    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS1309 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1292A  GLN*     3.0    38.1    +      -       -      -
   1294A  SER*     4.1     7.9    -      -       -      -
   1305A  LEU*     3.6    32.5    -      -       +      +
   1306A  GLU*     2.8    46.7    +      -       +      +
   1308A  THR*     1.3    83.1    +      -       -      +
   1310A  LEU*     1.3    64.4    +      -       -      +
   1312A  LEU*     3.3     8.1    +      -       -      +
   1313A  GLY      3.5     5.2    +      -       -      -
   1321A  PHE*     3.4    49.1    -      +       +      -
   1322A  TRP      5.4     0.2    -      -       -      -
   1325A  THR*     4.4    15.6    -      -       +      +
   1381A  LEU*     4.2     1.9    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU1310 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1176A  PRO      3.9     7.2    -      -       -      +
   1178A  MET*     3.7    36.3    -      -       +      -
   1180A  ILE*     4.3    15.3    -      -       +      +
   1305A  LEU*     4.0    24.5    -      -       +      -
   1306A  GLU      3.6    10.8    -      -       -      +
   1307A  TYR*     3.2     9.6    +      -       +      +
   1309A  HIS*     1.3    81.1    -      -       -      +
   1311A  GLU*     1.3    56.6    +      -       -      +
   1313A  GLY*     3.4     1.4    +      -       -      -
   1314A  ALA*     2.9    31.4    +      -       -      +
   1381A  LEU*     4.4    14.6    -      -       +      +
   1385A  GLN*     3.7    48.7    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU1311 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1018A  LYS*     4.1     8.7    +      -       -      -
   1178A  MET*     3.8    20.6    -      -       +      -
   1183A  VAL*     5.3     0.2    -      -       -      -
   1202A  ILE*     4.9     1.1    -      -       +      -
   1277A  ASN*     2.9    19.1    +      -       -      +
   1280A  MET*     3.3    14.7    -      -       +      +
   1281A  LEU*     3.8    22.7    -      -       +      +
   1284A  MET*     5.6     0.2    -      -       -      -
   1307A  TYR*     2.8    17.4    +      -       -      +
   1308A  THR*     3.5    14.4    -      -       -      +
   1309A  HIS      3.3     0.4    -      -       -      -
   1310A  LEU*     1.3    76.2    -      -       -      +
   1312A  LEU*     1.3    63.5    +      -       +      +
   1314A  ALA*     4.2     0.8    -      -       -      +
   1315A  CYS*     3.1    28.6    +      -       -      +
   3006A  UDP      2.6    46.9    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU1312 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1202A  ILE*     3.6    13.9    -      -       +      -
   1280A  MET*     5.6     0.4    -      -       -      -
   1284A  MET*     3.5    42.4    -      -       +      -
   1290A  GLY*     3.5    29.8    -      -       -      +
   1291A  TYR      3.7    13.2    -      -       -      +
   1292A  GLN*     3.9     5.2    -      -       +      -
   1308A  THR      3.2    11.7    -      -       -      +
   1309A  HIS      3.3     5.4    +      -       -      +
   1310A  LEU      3.2     0.4    -      -       -      -
   1311A  GLU*     1.3    82.0    -      -       -      +
   1313A  GLY*     1.3    63.6    +      -       -      +
   1315A  CYS*     3.5     1.6    -      -       -      -
   1316A  GLY      3.5     3.5    +      -       -      -
   1317A  THR*     3.4    33.4    +      -       +      +
   1319A  PRO*     4.3     9.4    -      -       +      -
   1321A  PHE*     3.8    20.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY1313 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1180A  ILE*     5.5     0.2    -      -       -      -
   1188A  TRP*     3.5    19.8    -      -       -      -
   1309A  HIS      3.5     4.6    +      -       -      -
   1310A  LEU      3.4     2.8    +      -       -      -
   1312A  LEU*     1.3    82.3    -      -       -      +
   1314A  ALA*     1.3    59.6    +      -       -      +
   1316A  GLY*     3.6     1.7    +      -       -      -
   1317A  THR      4.8     2.0    -      -       -      +
   1319A  PRO*     3.9    12.2    -      -       -      +
   1374A  ARG*     5.1     0.7    -      -       -      +
   1377A  ALA*     5.1     0.7    -      -       -      -
   1378A  TYR*     3.9    15.1    +      -       -      +
   1381A  LEU*     3.4    26.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA1314 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1178A  MET*     3.9     7.0    -      -       +      -
   1180A  ILE*     3.6    23.7    -      -       +      +
   1183A  VAL*     3.6    26.2    -      -       +      -
   1184A  ARG*     3.1    30.1    -      -       -      +
   1188A  TRP*     3.5     3.5    -      -       -      -
   1310A  LEU      2.9    18.4    +      -       -      +
   1311A  GLU      4.2     0.9    -      -       -      +
   1313A  GLY*     1.3    77.5    -      -       -      +
   1315A  CYS*     1.3    59.6    +      -       -      +
   1316A  GLY      3.3     0.2    -      -       -      -
   1378A  TYR*     4.1     9.4    -      -       -      -
   1381A  LEU*     4.8     0.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS1315 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1183A  VAL*     4.1     9.2    -      -       +      +
   1187A  TYR*     4.4    11.7    -      -       +      -
   1188A  TRP*     3.7    13.7    -      -       -      +
   1189A  LYS      4.4     0.9    +      -       -      -
   1281A  LEU*     4.0    19.1    -      -       +      +
   1284A  MET*     3.3    41.7    -      -       -      -
   1285A  SER*     3.3    27.6    -      -       -      -
   1311A  GLU      3.1    22.3    +      -       -      +
   1312A  LEU      3.5     8.5    -      -       -      -
   1314A  ALA*     1.3    76.6    -      -       -      +
   1316A  GLY*     1.3    57.1    +      -       -      +
   1317A  THR      4.2     2.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY1316 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1188A  TRP*     3.4    28.0    -      -       -      -
   1194A  ILE*     3.6     9.1    -      -       -      +
   1285A  SER      5.1     2.7    -      -       -      -
   1312A  LEU      3.5     2.4    +      -       -      -
   1313A  GLY      3.6     1.9    +      -       -      -
   1314A  ALA      3.3     4.4    -      -       -      -
   1315A  CYS*     1.3    79.2    -      -       -      +
   1317A  THR*     1.3    61.5    +      -       -      +
   1374A  ARG*     2.7    36.6    +      -       -      -
----------------------------------------------------------
 Back to top of page


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