Contacts of the helix formed by residues 1197 - 1216 (chain B) in PDB entry 1CJY
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.
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 GLY1197 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1196B GLY* 1.3 73.6 - - - -
1198B GLY* 1.3 63.2 + - - +
1200B ARG* 3.1 32.6 + - - +
1201B ALA* 2.7 26.0 + - - +
1228B SER* 4.0 4.8 + - - -
1229B GLY 4.1 0.2 - - - +
1555B ASN* 4.4 3.4 - - - +
1680B THR* 4.2 12.6 - - - +
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Residues in contact with GLY1198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1197B GLY* 1.3 78.7 - - - +
1199B PHE* 1.3 58.4 + - - -
1201B ALA* 3.1 2.3 + - - +
1202B MET* 3.0 21.7 + - - +
1229B GLY* 3.6 9.1 - - - -
1232B TRP* 3.9 17.7 - - - -
1397B PHE* 3.4 36.0 - - - -
1680B THR 4.5 3.4 - - - -
1683B PHE* 5.4 0.2 - - - -
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Residues in contact with PHE1199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1198B GLY* 1.3 68.9 - - - -
1200B ARG* 1.3 66.8 + - - +
1202B MET* 3.6 26.2 - - + -
1203B VAL* 2.9 30.1 + - + +
1232B TRP* 3.8 19.7 - + - -
1259B VAL* 3.6 32.8 - - + -
1263B PRO* 4.4 8.5 - - + -
1299B ILE* 4.5 8.1 - - + -
1302B THR* 4.2 17.3 - - + -
1303B LEU* 4.6 5.2 - - + -
1680B THR 4.8 2.2 + - - -
1682B ASN 3.8 8.4 + - - +
1683B PHE* 3.4 60.2 - + + -
1685B TYR* 3.5 20.4 - + + -
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Residues in contact with ARG1200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1197B GLY* 3.1 23.0 + - - +
1199B PHE* 1.3 76.8 - - - +
1201B ALA* 1.3 57.1 + - - +
1204B GLY* 2.9 25.8 + - - -
1418B GLU* 4.2 2.4 + - - -
1576B PHE* 2.7 29.4 + - + +
1577B SER* 4.0 1.4 - - - +
1578B ALA* 3.3 25.0 - - - +
1642B LEU* 3.6 22.7 - - + -
1671B PHE* 3.9 12.5 - - - -
1678B PHE* 3.1 32.0 + - + +
1679B SER 5.1 1.9 + - - +
1680B THR* 2.7 39.4 + - - +
1682B ASN 5.3 0.2 + - - -
1685B TYR* 3.2 21.1 + - - +
1693B LEU* 3.5 21.2 - - + +
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Residues in contact with ALA1201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1195B SER 3.7 11.4 - - - +
1196B GLY 3.4 30.7 - - - +
1197B GLY* 2.7 13.4 + - - +
1198B GLY 3.4 9.0 - - - +
1200B ARG* 1.3 75.6 - - - +
1202B MET* 1.3 58.7 + - - +
1204B GLY 3.8 0.2 - - - -
1205B PHE* 2.9 33.3 + - - +
1229B GLY* 3.9 7.9 - - - -
1230B SER* 4.4 0.2 + - - -
1576B PHE* 3.9 17.7 - - + -
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Residues in contact with MET1202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1198B GLY 3.0 13.6 + - - +
1199B PHE* 3.3 46.0 + - + +
1201B ALA* 1.3 77.1 - - - +
1203B VAL* 1.3 61.7 + - + +
1205B PHE* 4.7 0.2 - - - -
1206B SER* 3.1 26.3 + - - -
1229B GLY* 3.4 16.8 + - - +
1232B TRP* 3.9 11.0 - - + +
1233B TYR* 3.8 30.9 - - + +
1255B LEU* 4.1 15.0 - - + -
1259B VAL* 4.0 10.1 - - + -
1303B LEU* 3.6 38.8 - - + -
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Residues in contact with VAL1203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199B PHE* 2.9 23.3 + - + +
1200B ARG 4.2 1.3 - - - +
1202B MET* 1.3 77.0 - - + +
1204B GLY* 1.3 67.0 + - - +
1206B SER* 2.7 24.2 + - - -
1207B GLY 3.3 3.1 + - - -
1255B LEU* 4.4 8.3 - - + -
1259B VAL* 5.3 1.1 - - + -
1685B TYR* 4.1 16.8 - - + -
1690B PHE* 3.4 46.4 - - + +
1693B LEU* 3.8 27.4 - - + -
1694B HIS* 3.9 12.0 - - - +
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Residues in contact with GLY1204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1200B ARG 2.9 16.0 + - - -
1203B VAL* 1.3 77.6 - - - +
1205B PHE* 1.3 61.8 + - - +
1207B GLY 3.1 10.4 + - - -
1208B VAL* 3.2 10.4 + - - +
1576B PHE* 3.5 22.4 - - - -
1693B LEU* 3.9 16.3 - - - +
1697B MET* 3.5 15.1 - - - +
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Residues in contact with PHE1205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1192B ILE* 4.1 23.3 - - + -
1194B GLY* 3.8 21.1 - - - -
1201B ALA 2.9 19.0 + - - +
1202B MET 3.9 3.8 - - - +
1204B GLY* 1.3 73.7 - - - +
1206B SER* 1.3 66.2 + - - +
1208B VAL* 3.2 19.6 + - + +
1209B MET* 2.8 45.8 + - + +
1224B VAL* 4.2 9.9 - - + -
1225B ALA 4.9 0.2 - - - -
1230B SER* 3.7 33.9 - - - +
1233B TYR* 4.1 15.0 - + + -
1234B MET* 4.1 20.6 - - + -
1574B PHE* 4.2 4.9 - + + -
1576B PHE* 3.3 19.7 - + + -
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Residues in contact with SER1206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1202B MET 3.1 9.3 + - - -
1203B VAL* 2.7 23.5 + - - -
1205B PHE* 1.3 75.8 - - - +
1207B GLY* 1.3 65.1 + - - +
1209B MET* 3.3 2.3 + - - +
1210B LYS 3.1 15.1 + - - -
1233B TYR* 3.2 39.2 - - - -
1252B ASN* 3.5 21.2 + - - -
1255B LEU* 5.4 2.9 - - - -
1690B PHE* 4.1 9.8 - - - -
1694B HIS* 3.4 13.4 + - - -
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Residues in contact with GLY1207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1203B VAL 3.3 2.1 + - - -
1204B GLY 3.1 7.5 + - - -
1206B SER* 1.3 82.7 + - - +
1208B VAL* 1.3 63.9 + - - +
1210B LYS* 2.9 14.7 + - - +
1211B ALA 3.1 8.3 + - - -
1694B HIS* 3.5 36.3 - - - -
1698B HIS* 3.9 13.8 - - - -
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Residues in contact with VAL1208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1204B GLY 3.2 12.3 + - - +
1205B PHE* 3.2 15.2 + - + +
1207B GLY* 1.3 73.8 - - - +
1209B MET* 1.3 58.6 - - - +
1211B ALA* 2.9 8.4 + - - +
1212B LEU* 2.9 37.7 + - + +
1574B PHE* 3.3 59.5 - - + -
1576B PHE* 4.0 6.3 - - + -
1697B MET* 3.7 22.4 + - + -
1701B THR* 3.7 10.3 - - - +
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Residues in contact with MET1209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1192B ILE* 4.7 2.0 - - - -
1205B PHE* 2.8 48.6 + - + +
1206B SER 3.7 4.5 - - - +
1208B VAL* 1.3 73.6 - - - +
1210B LYS* 1.3 62.2 + - - +
1212B LEU* 4.0 18.2 - - - +
1213B TYR* 2.9 25.8 + - - +
1218B LEU* 3.6 35.9 - - + +
1224B VAL* 4.4 16.6 - - + -
1233B TYR* 3.6 27.8 - - + +
1234B MET* 6.2 1.3 - - + -
1237B LEU* 4.2 18.2 - - + -
1238B TYR* 5.4 4.5 - - + +
1243B PHE* 6.0 0.2 - - + -
1248B PRO* 4.0 8.4 - - + +
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Residues in contact with LYS1210 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1206B SER 3.1 11.9 + - - +
1207B GLY 2.9 11.0 + - - +
1209B MET* 1.3 76.8 - - - +
1211B ALA* 1.3 60.3 + - - +
1213B TYR* 3.4 1.7 - - + +
1214B GLU* 3.0 59.8 + - + +
1248B PRO* 3.8 9.8 - - + +
1249B GLU* 4.3 36.1 - - + +
1252B ASN* 3.8 12.3 - - + +
1694B HIS* 3.5 27.3 + - + +
1698B HIS* 3.6 24.2 + - - +
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Residues in contact with ALA1211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1207B GLY 3.1 6.2 + - - +
1208B VAL 2.9 9.7 + - - +
1210B LYS* 1.3 74.8 - - - +
1212B LEU* 1.3 57.8 + - - +
1213B TYR 3.0 1.6 + - - -
1214B GLU* 3.3 1.3 + - - -
1215B SER* 2.6 36.6 + - - -
1698B HIS* 3.4 30.9 + - - +
1701B THR* 3.4 28.5 - - + -
1702B LEU* 3.8 10.3 - - + +
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Residues in contact with LEU1212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1192B ILE* 3.8 34.3 - - + -
1208B VAL* 2.9 43.8 + - + +
1209B MET* 4.0 13.9 - - - +
1211B ALA* 1.3 71.4 - - - +
1213B TYR* 1.3 65.1 + - - +
1215B SER* 3.4 5.8 - - - -
1216B GLY 3.3 1.2 + - - -
1217B ILE* 3.0 34.7 + - + -
1218B LEU* 3.0 39.2 + - + +
1572B ILE* 5.4 0.7 - - + -
1574B PHE* 4.1 10.5 - - + -
1701B THR* 3.9 16.4 - - + -
1708B ILE* 4.8 5.6 - - + -
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Residues in contact with TYR1213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1209B MET 2.9 19.9 + - - +
1210B LYS* 3.4 4.9 - - + +
1212B LEU* 1.3 76.0 - - - +
1214B GLU* 1.3 77.5 + - + +
1216B GLY* 2.9 15.8 + - - -
1218B LEU* 4.1 22.6 - - + +
1219B ASP* 4.2 9.7 - - - +
1243B PHE* 5.2 4.3 - + - -
1244B PRO* 3.3 28.1 + - + -
1245B GLU 4.0 5.5 + - - -
1247B GLY* 3.7 23.1 + - - -
1248B PRO* 3.7 21.1 - - + -
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Residues in contact with GLU1214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1210B LYS* 3.0 47.5 + - + +
1211B ALA* 3.9 1.3 - - - +
1213B TYR* 1.3 90.3 - - + +
1215B SER* 1.3 59.8 + - - +
1216B GLY* 3.0 6.2 + - - -
1249B GLU* 5.6 3.5 - - - +
1698B HIS* 2.8 27.0 + - - -
1702B LEU* 3.9 10.0 - - + +
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Residues in contact with SER1215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1172B LEU* 3.8 17.3 - - - +
1211B ALA 2.6 26.1 + - - -
1212B LEU* 3.4 10.9 + - - -
1214B GLU* 1.3 75.7 - - - +
1216B GLY* 1.3 58.8 + - - +
1217B ILE* 3.5 12.5 + - - +
1701B THR* 5.4 1.2 - - - +
1702B LEU* 3.7 6.3 - - - +
1705B ILE* 3.2 34.9 - - - +
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Residues in contact with GLY1216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1168B SER* 5.0 1.6 - - - +
1172B LEU* 4.8 3.9 - - - +
1213B TYR 2.9 15.7 + - - -
1214B GLU 3.0 3.1 + - - -
1215B SER* 1.3 77.9 - - - +
1217B ILE* 1.3 65.6 + - - +
1218B LEU 3.3 1.8 - - - -
1219B ASP* 3.2 28.2 + - - +
1220B CYS* 3.6 11.1 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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