Contacts of the helix formed by residues 1220 - 1238 (chain B) in PDB entry 1Q6P
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 GLY1220 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1219B ILE* 1.3 73.8 - - - +
1221B ARG* 1.3 55.3 + - - +
1224B THR* 2.8 34.8 + - - -
1261B ILE* 3.7 2.3 - - - -
1262B GLN* 3.9 10.3 - - - -
1266B GLN* 3.5 18.8 - - - +
1301B 213 2.7 33.2 + - - -
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Residues in contact with ARG1221 (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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1110B LEU* 3.4 21.9 - - + +
1111B ASN* 3.6 23.2 - - - +
1112B ARG 5.0 0.8 - - - +
1179B TRP* 2.8 70.3 + - + +
1180B PRO* 3.6 8.4 + - - +
1181B ASP* 3.2 35.3 + - - +
1215B CYS* 3.8 9.8 - - + +
1216B SER* 3.6 15.6 - - - +
1220B GLY* 1.3 70.0 - - - +
1222B SER* 1.3 60.7 + - - +
1224B THR 3.1 0.9 + - - -
1225B PHE* 2.8 26.2 + - - +
1266B GLN* 4.2 8.3 - - - +
1301B 213 2.9 48.0 + - - +
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Residues in contact with SER1222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1083B LEU* 4.0 20.6 - - - -
1110B LEU* 3.6 10.0 - - - +
1213B VAL* 3.6 13.1 - - - +
1214B HIS* 3.3 25.5 + - - -
1215B CYS* 3.2 22.0 - - - +
1218B GLY* 3.9 8.3 - - - -
1220B GLY 3.4 0.4 - - - -
1221B ARG* 1.3 78.2 - - - +
1223B GLY* 1.3 63.0 + - - +
1225B PHE* 3.4 0.9 + - - +
1226B CYS* 3.0 30.0 + - - -
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Residues in contact with GLY1223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1083B LEU* 4.3 3.5 - - - +
1219B ILE 3.2 22.7 + - - -
1221B ARG 3.2 0.8 - - - -
1222B SER* 1.3 80.6 - - - +
1224B THR* 1.3 57.0 + - - +
1226B CYS* 3.9 1.6 - - - +
1227B LEU* 2.9 32.9 + - - +
1250B LEU* 5.4 0.2 - - - +
1253B MET* 4.6 2.8 - - - +
1260B LEU* 4.1 22.5 - - - +
1261B ILE* 3.8 7.2 - - - +
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Residues in contact with THR1224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1179B TRP* 3.7 22.0 - - + -
1191B PHE* 4.9 1.8 - - + -
1220B GLY 2.8 19.2 + - - -
1221B ARG 3.1 7.2 + - - -
1223B GLY* 1.3 74.2 - - - +
1225B PHE* 1.3 65.9 + - - +
1227B LEU* 3.8 1.2 - - - +
1228B ALA* 3.0 24.1 + - + +
1261B ILE* 3.7 16.2 - - - +
1266B GLN* 3.6 28.7 + - + +
1269B PHE* 4.3 13.2 - - + -
1270B SER* 4.0 21.3 - - - -
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Residues in contact with PHE1225 (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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1081B TYR* 5.2 4.9 - + - -
1108B VAL* 4.2 25.1 - - + -
1110B LEU* 3.7 23.3 - - + -
1179B TRP* 4.0 1.0 - - + -
1191B PHE* 3.8 26.3 - + + -
1194B PHE* 3.8 26.0 - + - -
1195B LEU* 3.8 31.1 - - + +
1198B VAL* 4.4 11.2 - - + -
1204B LEU* 5.7 5.4 - - + -
1213B VAL* 4.3 14.8 - - + -
1221B ARG 2.8 16.8 + - - +
1222B SER 3.5 3.6 - - - +
1224B THR* 1.3 78.1 - - - +
1226B CYS* 1.3 77.7 + - - +
1228B ALA* 3.3 3.3 + - - +
1229B ASP* 3.0 24.6 + - + +
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Residues in contact with CYS1226 (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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1072B ILE* 6.0 0.7 - - + -
1081B TYR* 3.6 46.4 + - + -
1083B LEU* 3.9 21.1 - - + -
1213B VAL* 4.0 8.3 - - - -
1222B SER 3.0 21.6 + - - +
1223B GLY* 4.2 1.8 - - - +
1225B PHE* 1.3 87.0 - - - +
1227B LEU* 1.3 67.0 + - - +
1229B ASP* 4.4 0.7 - - - +
1230B THR* 2.9 27.9 + - - -
1253B MET* 4.1 13.0 - - - -
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Residues in contact with LEU1227 (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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1223B GLY 2.9 19.9 + - - +
1224B THR 3.8 3.1 - - - +
1226B CYS* 1.3 76.0 - - - +
1228B ALA* 1.3 64.0 + - - +
1230B THR* 3.9 0.5 - - - -
1231B CYS* 2.9 48.5 + - - -
1246B ILE* 3.7 17.3 - - + +
1249B VAL* 3.9 1.1 - - + -
1250B LEU* 3.5 35.4 - - + +
1253B MET* 3.3 28.8 - - + -
1261B ILE* 3.3 27.6 - - + -
1267B LEU* 4.6 0.7 - - + -
1270B SER* 3.5 18.4 - - - +
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Residues in contact with ALA1228 (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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1191B PHE* 3.5 33.9 - - + -
1195B LEU* 4.9 1.3 - - + -
1224B THR* 3.0 18.7 + - + +
1225B PHE 3.6 0.2 - - - +
1227B LEU* 1.3 78.9 - - - +
1229B ASP* 1.3 62.9 + - - +
1231B CYS* 3.3 1.7 + - - +
1232B LEU* 3.0 32.8 + - + +
1269B PHE* 6.4 0.2 - - + -
1270B SER* 5.0 6.9 - - - +
1273B ALA* 5.0 5.6 - - + -
1274B VAL* 4.0 19.0 - - + +
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Residues in contact with ASP1229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1079B ARG* 3.0 25.9 + - - -
1081B TYR* 2.7 29.0 + - + +
1195B LEU* 3.8 21.7 - - + +
1199B ARG* 2.8 44.6 + - - +
1204B LEU* 3.9 5.0 - - - +
1225B PHE* 3.0 18.7 + - + +
1226B CYS* 3.3 3.3 + - - +
1228B ALA* 1.3 77.3 - - - +
1230B THR* 1.3 62.6 + - - +
1232B LEU 3.4 0.3 + - - -
1233B LEU* 3.1 19.8 + - - +
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Residues in contact with THR1230 (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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1074B MET* 3.8 20.5 - - + +
1077B ALA* 3.9 17.1 - - + +
1079B ARG* 5.2 0.2 - - - +
1081B TYR* 2.7 31.7 + - - -
1226B CYS 2.9 15.4 + - - -
1227B LEU 3.9 2.5 - - - -
1229B ASP* 1.3 76.0 - - - +
1231B CYS* 1.3 64.4 + - - +
1233B LEU* 3.1 10.7 + - - +
1234B LEU* 3.0 26.3 + - + +
1249B VAL* 3.6 24.0 - - + -
1253B MET* 4.3 6.1 - - - +
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Residues in contact with CYS1231 (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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1227B LEU* 2.9 43.1 + - - +
1230B THR* 1.3 76.8 - - - +
1232B LEU* 1.3 58.5 + - - +
1234B LEU* 3.4 4.2 + - - +
1235B MET* 3.0 34.6 + - - +
1244B VAL* 4.2 10.2 - - + +
1246B ILE* 3.8 23.1 - - - -
1249B VAL* 3.9 21.1 - - - -
1274B VAL* 3.7 25.4 - - + -
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Residues in contact with LEU1232 (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 LEU* 4.1 17.0 - - + -
1195B LEU* 3.8 25.4 - - + -
1196B PHE* 5.0 2.0 - - + -
1199B ARG* 3.4 19.1 - - - +
1228B ALA* 3.0 23.4 + - + +
1231B CYS* 1.3 73.8 - - - +
1233B LEU* 1.3 66.9 + - - +
1235B MET* 3.3 4.4 + - + +
1236B ASP* 3.0 26.0 + - - +
1273B ALA 4.8 2.9 - - - +
1274B VAL* 3.4 33.7 - - + +
1277B GLY* 3.7 7.2 - - - +
1278B ALA* 3.6 21.8 - - + +
1281B ILE* 4.1 14.7 - - + +
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Residues in contact with LEU1233 (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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1077B ALA* 3.7 33.9 - - + +
1079B ARG* 3.5 57.7 - - + +
1199B ARG* 3.9 10.8 - - - +
1229B ASP* 3.1 21.0 + - - +
1230B THR* 3.1 10.0 + - - +
1232B LEU* 1.3 79.1 - - - +
1234B LEU* 1.3 57.5 + - - +
1236B ASP* 3.5 4.9 + - + +
1237B LYS* 3.0 32.7 + - - +
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Residues in contact with LEU1234 (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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1074B MET* 6.1 0.4 - - + -
1076B GLU* 3.2 41.5 - - + +
1077B ALA* 3.8 22.0 - - + +
1230B THR* 3.0 26.6 + - + +
1231B CYS* 3.8 5.4 - - - +
1232B LEU 3.2 0.2 - - - -
1233B LEU* 1.3 75.2 - - - +
1235B MET* 1.3 58.1 + - - +
1237B LYS* 3.0 4.2 + - + -
1238B ARG* 2.7 54.4 + - + +
1244B VAL* 3.9 15.5 - - + -
1249B VAL* 3.8 29.8 - - + -
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Residues in contact with MET1235 (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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1003B MET* 3.2 20.9 - - + -
1231B CYS 3.0 21.3 + - - +
1232B LEU* 3.3 7.4 + - + +
1234B LEU* 1.3 76.8 - - - +
1236B ASP* 1.3 62.6 + - - +
1237B LYS 3.5 0.2 + - - -
1238B ARG 3.5 13.0 + - - +
1241B PRO* 3.0 49.1 - - + +
1244B VAL* 3.5 27.1 - - + +
1246B ILE* 5.7 2.7 - - + -
1274B VAL* 3.6 25.4 - - + -
1275B ILE* 5.5 3.8 - - + -
1278B ALA* 3.5 31.9 - - + -
1282B MET* 5.2 5.3 - - - +
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Residues in contact with ASP1236 (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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1232B LEU 3.0 17.0 + - - +
1233B LEU* 3.8 5.3 - - + +
1235B MET* 1.3 79.2 - - - +
1237B LYS* 1.3 61.0 + - - +
1238B ARG 3.9 3.8 - - - +
1281B ILE* 4.0 16.1 - - + +
1282B MET* 3.2 34.3 - - + +
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Residues in contact with LYS1237 (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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1076B GLU* 3.0 46.8 + - + +
1077B ALA* 4.6 5.4 - - - +
1078B GLN* 3.1 31.4 + - - +
1233B LEU* 3.0 16.7 + - - +
1234B LEU* 3.9 7.0 - - + +
1236B ASP* 1.3 77.9 + - - +
1238B ARG* 1.3 67.1 + - - +
1239B LYS 3.9 0.2 + - - -
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Residues in contact with ARG1238 (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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1076B GLU* 2.5 42.3 + - - +
1234B LEU* 2.7 44.0 + - - +
1235B MET* 3.5 11.6 - - - +
1236B ASP 3.5 4.2 - - - +
1237B LYS* 1.3 78.6 - - + +
1239B LYS* 1.3 64.8 + - - +
1240B ASP 3.2 7.9 - - - +
1241B PRO* 4.8 0.7 - - - +
1243B SER* 2.9 58.8 + - - +
1244B VAL* 3.4 12.7 - - + +
1245B ASP 5.4 1.6 - - - +
1249B VAL* 5.9 1.8 - - - +
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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
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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