Contacts of the helix formed by residues 1205 - 1221 (chain B) in PDB entry 1CM8
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 GLN1205 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1145B HIS* 3.1 69.0 + - + +
1148B GLY* 3.8 12.1 - - - -
1149B ILE 3.1 23.1 + - - +
1150B ILE* 3.8 11.8 - - + +
1178B ALA* 3.9 19.9 - - + +
1204B THR* 1.3 79.4 - - - +
1206B THR* 1.3 61.6 + - - +
1207B VAL 3.1 1.5 + - - -
1208B ASP* 3.2 8.7 + - - +
1209B ILE 4.0 0.9 + - - -
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Residues in contact with THR1206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1195B GLU* 4.5 0.3 + - - -
1204B THR* 2.6 25.3 + - - +
1205B GLN* 1.3 77.2 - - - +
1207B VAL* 1.3 60.0 + - - +
1208B ASP 3.1 0.2 - - - -
1209B ILE* 2.8 25.2 + - + +
1210B TRP 3.1 9.2 + - - -
1296B ALA* 3.7 35.4 + - - +
1299B ARG* 3.8 30.4 + - + +
1300B VAL 4.3 8.7 - - - +
1301B THR* 5.1 9.9 - - + -
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Residues in contact with VAL1207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1150B ILE* 4.3 10.3 - - + -
1152B ARG* 4.8 2.2 - - - -
1187B VAL* 4.4 18.6 - - + +
1191B TYR 4.7 0.3 - - - +
1193B ALA* 4.4 6.6 + - + +
1195B GLU* 3.4 23.1 - - - +
1196B VAL* 4.4 8.5 - - + -
1203B TYR* 3.4 31.2 - - + -
1204B THR 2.9 19.4 + - - +
1206B THR* 1.3 78.1 - - - +
1208B ASP* 1.3 78.6 + - - +
1210B TRP* 3.2 10.0 + - - +
1211B SER* 3.1 24.2 + - - +
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Residues in contact with ASP1208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1141B LEU* 3.8 13.5 - - + +
1145B HIS* 2.9 24.9 + - - +
1150B ILE* 3.7 4.9 - - - +
1151B HIS* 3.0 31.4 + - - +
1152B ARG* 2.9 26.6 + - - -
1153B ASP 4.3 1.9 + - - -
1154B LEU* 3.9 10.9 + - + +
1187B VAL* 5.7 0.2 - - - +
1205B GLN 3.2 8.9 + - - +
1206B THR 3.1 0.4 - - - -
1207B VAL* 1.3 84.4 - - - +
1209B ILE* 1.3 60.7 + - - +
1211B SER* 3.6 7.2 + - - -
1212B VAL* 3.0 30.8 + - - +
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Residues in contact with ILE1209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1138B LEU* 4.1 11.2 - - + -
1141B LEU* 3.7 21.3 - - + -
1145B HIS* 4.9 2.5 - - + -
1205B GLN 4.5 3.6 - - - +
1206B THR* 2.8 20.2 + - + +
1208B ASP* 1.3 74.9 - - - +
1210B TRP* 1.3 66.8 + - - +
1212B VAL* 3.2 4.4 + - + +
1213B GLY* 3.0 18.5 + - - -
1291B MET* 3.8 35.9 - - + +
1299B ARG* 4.3 3.1 - - + -
1300B VAL* 3.5 28.0 - - + +
1301B THR* 4.0 2.7 - - - +
1302B ALA* 3.6 30.1 - - + +
1305B ALA* 5.0 1.1 - - + -
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Residues in contact with TRP1210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1190B TRP 5.2 0.4 + - - -
1191B TYR 3.3 19.7 - - - -
1192B ARG 3.3 10.5 + - - -
1193B ALA* 3.3 24.2 - - + -
1194B PRO* 3.7 20.4 - - + -
1206B THR 3.1 8.2 + - - +
1207B VAL 3.2 11.6 + - - +
1209B ILE* 1.3 74.9 - - - +
1211B SER* 1.3 54.4 + - - +
1213B GLY* 2.7 24.6 + - - -
1214B CYS* 3.0 27.2 + - - -
1226B PHE* 3.5 26.0 - + - -
1238B ILE* 3.7 24.0 - - + -
1242B THR* 4.1 7.0 - - + -
1291B MET 4.3 3.3 + - - -
1292B LEU* 3.4 48.0 - - + +
1293B VAL 3.5 11.9 - - - -
1294B LEU* 4.6 0.9 - - + -
1299B ARG* 3.4 24.7 - - - +
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Residues in contact with SER1211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1153B ASP 5.5 0.2 + - - -
1154B LEU* 3.3 35.5 + - - -
1187B VAL* 3.7 12.5 - - - +
1191B TYR* 2.8 27.3 + - - -
1207B VAL 3.1 10.1 + - - -
1208B ASP* 3.7 11.0 + - - -
1210B TRP* 1.3 78.8 - - - +
1212B VAL* 1.3 57.4 + - - +
1213B GLY 3.1 0.2 + - - -
1214B CYS* 3.2 3.7 + - - +
1215B ILE* 2.8 35.2 + - - +
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Residues in contact with VAL1212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1134B VAL* 4.3 14.1 - - + -
1137B MET* 4.4 21.2 - - + +
1138B LEU* 4.1 20.9 - - + -
1141B LEU* 3.9 20.4 - - + -
1154B LEU* 4.0 13.2 - - + -
1208B ASP 3.0 18.9 + - - +
1209B ILE* 3.6 8.1 - - - +
1210B TRP 3.2 0.2 - - - -
1211B SER* 1.3 75.0 - - - +
1213B GLY* 1.3 57.5 + - - +
1215B ILE* 3.7 8.1 - - + +
1216B MET* 2.7 27.4 + - - +
1291B MET* 4.1 16.4 - - + -
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Residues in contact with GLY1213 (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 ILE 3.0 8.7 + - - -
1210B TRP 2.7 16.1 + - - -
1212B VAL* 1.3 69.6 - - - +
1214B CYS* 1.3 56.5 + - - -
1217B ALA* 2.8 31.9 + - - +
1288B LEU* 3.3 19.2 - - - +
1291B MET* 4.2 9.6 - - - -
1292B LEU* 4.1 16.2 - - - -
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Residues in contact with CYS1214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1190B TRP 3.8 16.6 - - - +
1191B TYR* 3.7 21.3 - - + -
1210B TRP* 3.0 46.9 + - - -
1211B SER 3.7 5.8 - - - +
1213B GLY* 1.3 75.1 - - - +
1215B ILE* 1.3 57.7 + - - +
1217B ALA* 3.5 7.3 - - - +
1218B GLU* 2.9 30.8 + - - +
1225B LEU* 4.4 13.3 + - + +
1226B PHE* 4.1 15.0 - - - -
1292B LEU* 4.2 3.9 - - - +
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Residues in contact with ILE1215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1116B LEU* 3.9 26.5 - - + -
1120B MET* 4.8 0.7 - - + -
1137B MET* 4.4 9.0 - - - -
1154B LEU* 3.4 39.3 - - + +
1155B LYS* 3.4 9.6 - - - +
1156B PRO* 4.2 11.0 - - + -
1159B LEU* 4.1 14.4 - - + -
1191B TYR* 3.7 19.3 - - + -
1211B SER 2.8 29.5 + - - +
1212B VAL* 3.7 7.9 - - + +
1214B CYS* 1.3 74.5 - - - +
1216B MET* 1.3 65.4 + - - +
1218B GLU* 3.1 7.2 + - - +
1219B MET* 3.0 23.6 + - - +
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Residues in contact with MET1216 (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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1130B ILE* 4.7 3.1 - - + -
1134B VAL* 3.5 27.6 - - + -
1137B MET* 5.6 0.8 - - - -
1212B VAL 2.7 21.4 + - - +
1213B GLY 3.8 3.1 - - - +
1215B ILE* 1.3 73.3 - - - +
1217B ALA* 1.3 62.2 + - - +
1219B MET* 3.3 11.7 + - - +
1220B ILE* 3.1 37.4 + - + +
1284B ALA* 4.1 19.5 - - + +
1287B LEU* 4.1 7.2 - - + -
1288B LEU* 3.8 15.7 - - + -
1291B MET* 3.7 25.4 - - + -
1310B TYR* 3.2 45.1 - - + +
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Residues in contact with ALA1217 (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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1213B GLY 2.8 18.7 + - - +
1214B CYS 3.5 4.9 - - - +
1216B MET* 1.3 77.8 - - - +
1218B GLU* 1.3 55.9 + - - +
1220B ILE* 3.3 3.9 + - - +
1221B THR* 3.1 35.1 + - + +
1223B LYS 5.0 0.2 - - - -
1225B LEU* 3.6 31.2 - - + -
1277B LEU* 4.8 7.2 - - + -
1288B LEU* 4.1 20.2 - - + +
1292B LEU* 4.9 0.4 - - + -
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Residues in contact with GLU1218 (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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1120B MET* 4.3 14.6 - - + +
1156B PRO* 4.1 12.2 - - - +
1191B TYR* 2.5 38.5 + - - -
1214B CYS 2.9 16.3 + - - +
1215B ILE* 3.1 6.0 + - - +
1217B ALA* 1.3 75.2 - - - +
1219B MET* 1.3 60.0 + - - +
1222B GLY* 2.8 34.9 + - - +
1223B LYS 3.3 26.6 - - - +
1224B THR* 4.0 22.6 + - - +
1225B LEU* 5.0 1.4 + - - +
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Residues in contact with MET1219 (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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1116B LEU* 3.9 11.2 - - + -
1120B MET* 3.9 23.7 - - + +
1124B LYS* 4.4 11.6 - - - +
1125B LEU* 3.5 26.6 + - + +
1130B ILE* 3.9 26.7 - - + +
1133B LEU* 3.4 46.7 - - + -
1134B VAL* 3.9 21.3 - - - -
1137B MET* 3.9 9.9 - - + -
1215B ILE 3.0 18.8 + - - +
1216B MET* 3.3 8.3 + - - +
1218B GLU* 1.3 78.1 - - - +
1220B ILE* 1.3 63.1 + - - +
1222B GLY* 4.2 2.3 + - - -
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Residues in contact with ILE1220 (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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1124B LYS* 3.8 10.9 + - - -
1130B ILE* 4.1 24.4 - - + +
1216B MET* 3.1 33.2 + - + +
1217B ALA* 3.7 5.2 - - - +
1218B GLU 3.2 0.2 - - - -
1219B MET* 1.3 77.5 - - - +
1221B THR* 1.3 69.3 + - + +
1277B LEU* 5.0 3.6 - - + -
1279B ASN* 4.0 16.7 + - - +
1280B ALA* 3.6 40.6 - - + +
1284B ALA* 4.5 7.0 - - + -
1288B LEU* 3.9 24.9 - - + -
1310B TYR* 5.6 0.2 - - - +
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Residues in contact with THR1221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1124B LYS* 3.6 16.5 + - - -
1217B ALA* 3.1 15.6 + - + +
1220B ILE* 1.3 77.4 - - + +
1222B GLY* 1.3 68.4 + - - +
1223B LYS* 2.9 31.7 + - - +
1225B LEU* 5.9 4.0 - - + -
1276B ILE* 4.6 9.0 - - + +
1277B LEU* 3.9 34.3 - - + -
1278B THR* 5.3 5.4 - - - +
1279B ASN* 5.3 3.9 + - - +
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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) + - + + + + + -
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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