Contacts of the helix formed by residues 1263 - 1283 (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 THR1263 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521A GLN* 4.8 8.5 - - - +
1020B TYR* 3.5 12.4 + - - -
1182B PHE* 3.5 40.1 + - + +
1261B ILE* 3.9 4.3 - - - +
1262B GLN* 1.3 83.9 - - + +
1264B ALA* 1.3 64.5 + - - +
1265B ASP* 3.2 10.3 + - - +
1266B GLN* 2.9 35.4 + - - +
1267B LEU* 3.2 10.6 + - - +
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Residues in contact with ALA1264 (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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1016B TRP* 4.1 29.1 - - + +
1017B ALA* 4.1 14.6 - - + +
1020B TYR* 3.7 24.1 - - + -
1263B THR* 1.3 73.4 - - - +
1265B ASP* 1.3 58.1 + - - +
1267B LEU* 3.2 5.4 + - - +
1268B ARG* 2.9 26.7 + - - +
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Residues in contact with ASP1265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1183B GLY* 6.0 0.2 - - - -
1184B VAL* 3.5 26.8 - - + +
1263B THR* 3.1 8.6 + - - +
1264B ALA* 1.3 77.2 - - - +
1266B GLN* 1.3 60.0 + - - +
1268B ARG* 3.1 25.9 + - - +
1269B PHE* 2.8 28.6 + - - +
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Residues in contact with GLN1266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1179B TRP* 5.2 1.8 - - + +
1182B PHE* 3.8 20.4 - - - +
1183B GLY 3.2 30.2 + - - +
1184B VAL* 4.2 7.4 - - + -
1220B GLY* 3.5 21.5 - - - +
1221B ARG* 4.2 10.9 - - - +
1224B THR* 3.6 18.6 + - + +
1261B ILE* 3.6 8.6 - - + -
1262B GLN* 2.7 33.1 + - - +
1263B THR* 2.9 25.9 + - + +
1265B ASP* 1.3 76.3 - - - +
1267B LEU* 1.3 64.1 + - - +
1269B PHE* 3.3 2.9 + - - +
1270B SER* 2.9 24.4 + - - -
1301B 213 5.0 0.6 + - - -
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Residues in contact with LEU1267 (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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1016B TRP* 4.4 10.5 - - + +
1019B ILE* 3.8 30.3 - - + -
1020B TYR* 4.0 20.6 - - + +
1023B ILE* 4.0 12.3 - - + -
1227B LEU* 4.6 3.4 - - + -
1246B ILE* 4.9 1.8 - - + -
1247B LYS* 5.8 0.7 - - - -
1250B LEU* 3.8 28.5 - - + -
1261B ILE* 3.7 10.7 - - + +
1263B THR 3.2 9.0 + - - +
1264B ALA* 3.3 10.8 - - - +
1265B ASP 3.1 0.4 - - - -
1266B GLN* 1.3 80.0 - - - +
1268B ARG* 1.3 62.7 + - - +
1270B SER* 2.7 26.9 + - - +
1271B TYR* 3.2 32.1 + - + -
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Residues in contact with ARG1268 (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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1007B PHE* 3.9 14.2 - - + -
1011B ASP* 2.7 35.3 + - - -
1016B TRP* 3.4 48.0 - - + +
1264B ALA 2.9 13.5 + - - +
1265B ASP* 3.1 25.6 + - - +
1267B LEU* 1.3 77.0 - - - +
1269B PHE* 1.3 65.9 + - - +
1271B TYR* 2.9 15.1 + - - +
1272B LEU* 2.9 31.2 + - - +
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Residues in contact with PHE1269 (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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1184B VAL* 3.9 18.4 - - + -
1185B PRO* 3.4 47.6 - - + -
1187B SER* 3.8 6.3 - - - -
1188B PRO* 3.7 33.9 - - + -
1191B PHE* 3.5 32.3 - + + -
1224B THR* 4.3 11.7 - - + -
1265B ASP* 2.8 21.0 + - - +
1266B GLN* 3.6 4.5 - - - +
1268B ARG* 1.3 77.1 - - - +
1270B SER* 1.3 61.1 + - - +
1272B LEU* 3.1 13.6 + - + +
1273B ALA* 2.7 36.9 + - + -
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Residues in contact with SER1270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1224B THR* 4.0 20.6 - - - -
1227B LEU* 3.5 29.9 - - - +
1228B ALA* 5.0 6.0 - - - +
1246B ILE* 4.5 1.3 - - - +
1261B ILE* 4.1 1.1 - - - +
1266B GLN 2.9 14.3 + - - -
1267B LEU* 2.7 23.7 + - - +
1269B PHE* 1.3 82.4 - - - +
1271B TYR* 1.3 61.8 + - - +
1273B ALA* 4.0 3.5 - - - +
1274B VAL* 3.0 33.2 + - - +
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Residues in contact with TYR1271 (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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1006B GLU* 6.4 0.4 - - - -
1007B PHE* 3.7 18.2 - + + -
1010B ILE* 4.4 12.3 - - + -
1016B TRP* 3.5 33.9 - + + -
1019B ILE* 4.3 12.5 - - + +
1245B ASP* 5.1 0.9 + - - -
1246B ILE* 3.7 44.7 + - + +
1247B LYS* 3.7 24.7 + - - +
1267B LEU* 3.2 37.6 + - + -
1268B ARG 2.9 9.2 + - - +
1270B SER* 1.3 73.2 + - - +
1272B LEU* 1.3 68.3 + - - +
1274B VAL* 3.2 2.6 + - - +
1275B ILE* 3.1 32.6 + - + +
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Residues in contact with LEU1272 (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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1007B PHE* 3.8 20.6 - - + -
1188B PRO* 3.1 38.8 - - + -
1268B ARG* 2.9 37.3 + - - +
1269B PHE* 3.3 15.9 - - + +
1271B TYR* 1.3 77.9 - - - +
1273B ALA* 1.3 60.9 + - - +
1275B ILE* 3.4 5.8 + - - +
1276B GLU* 3.2 32.0 + - + +
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Residues in contact with ALA1273 (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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1188B PRO* 4.6 5.4 - - + -
1191B PHE* 3.9 31.9 - - + -
1192B LEU* 3.7 13.7 - - + +
1228B ALA* 5.0 2.2 - - + -
1232B LEU* 4.8 0.6 - - - +
1269B PHE* 2.7 32.5 + - + +
1270B SER* 4.0 5.4 - - - +
1272B LEU* 1.3 74.6 - - - +
1274B VAL* 1.3 65.7 + - - +
1276B GLU* 4.5 3.6 - - - -
1277B GLY* 3.0 21.0 + - - -
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Residues in contact with VAL1274 (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* 6.0 0.2 - - + -
1228B ALA* 4.0 22.2 - - - +
1231B CYS* 3.7 31.9 - - + -
1232B LEU* 3.4 13.1 - - + +
1235B MET* 3.6 32.3 - - + -
1246B ILE* 4.2 15.7 - - + -
1270B SER* 3.0 27.5 + - - +
1271B TYR 3.2 4.0 + - - +
1273B ALA* 1.3 75.5 - - - +
1275B ILE* 1.3 61.3 + - + +
1278B ALA* 2.9 27.5 + - - +
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Residues in contact with ILE1275 (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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1000B PHE* 5.1 4.7 - - + -
1003B MET* 4.4 28.7 - - + +
1004B GLU* 3.5 33.7 - - + +
1007B PHE* 4.0 33.7 - - + -
1235B MET* 5.4 3.6 - - + -
1271B TYR* 3.1 23.3 + - + +
1272B LEU* 3.8 4.7 - - - +
1274B VAL* 1.3 80.2 - - + +
1276B GLU* 1.3 67.3 + - - +
1278B ALA* 3.0 9.0 + - - +
1279B LYS* 3.0 23.9 + - + +
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Residues in contact with GLU1276 (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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1004B GLU* 4.7 1.4 - - - +
1188B PRO* 4.1 11.3 - - + +
1192B LEU* 3.6 17.5 - - + -
1272B LEU* 3.2 36.2 + - + +
1273B ALA 3.8 0.7 - - - +
1275B ILE* 1.3 78.2 - - - +
1277B GLY* 1.3 63.8 + - - +
1279B LYS* 2.9 43.3 + - - +
1280B PHE* 3.0 13.1 + - - +
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Residues in contact with GLY1277 (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* 3.4 20.8 - - - +
1196B PHE* 4.6 5.4 - - - -
1232B LEU* 3.7 12.8 - - - -
1273B ALA 3.0 12.1 + - - -
1274B VAL 3.9 0.7 - - - -
1276B GLU* 1.3 80.6 - - - +
1278B ALA* 1.3 56.5 + - - +
1280B PHE* 3.7 6.2 - - - +
1281B ILE* 2.9 35.9 + - - +
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Residues in contact with ALA1278 (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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1000B PHE* 3.3 20.2 - - + -
1003B MET* 5.6 0.2 - - - -
1232B LEU* 3.6 5.4 - - - +
1235B MET* 3.5 26.9 - - + -
1274B VAL 2.9 19.5 + - - +
1275B ILE* 3.0 8.0 + - - +
1277B GLY* 1.3 76.4 - - - +
1279B LYS* 1.3 66.1 + - - +
1281B ILE* 4.7 0.4 - - - -
1282B MET* 2.9 36.4 + - - +
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Residues in contact with LYS1279 (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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1000B PHE* 3.2 34.5 - - + -
1004B GLU* 3.0 34.7 + - - +
1275B ILE 3.0 9.5 + - - +
1276B GLU* 2.9 33.5 + - - +
1278B ALA* 1.3 73.5 - - - +
1280B PHE* 1.3 67.3 + - - +
1282B MET* 3.8 1.3 - - - +
1283B GLY* 2.9 21.5 + - - -
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Residues in contact with PHE1280 (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* 6.0 1.3 - - + -
1196B PHE* 4.3 24.9 - + + -
1276B GLU 3.0 11.4 + - - +
1277B GLY* 3.7 11.2 - - - +
1279B LYS* 1.3 76.2 - - - +
1281B ILE* 1.3 60.6 + - + +
1283B GLY* 2.7 29.5 + - - +
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Residues in contact with ILE1281 (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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1196B PHE* 4.0 21.1 - - + -
1199B ARG* 3.8 25.4 - - - +
1232B LEU* 4.1 24.2 - - + +
1236B ASP* 4.0 14.8 - - + +
1277B GLY 2.9 25.0 + - - +
1278B ALA* 4.6 0.7 - - - -
1280B PHE* 1.3 79.1 - - + +
1282B MET* 1.3 86.8 + - + +
1283B GLY 3.3 7.3 + - - +
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Residues in contact with MET1282 (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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1000B PHE* 3.7 26.7 - - + -
1235B MET* 5.2 5.6 - - - +
1236B ASP* 3.2 40.6 - - - +
1241B PRO* 5.1 7.2 - - + -
1278B ALA* 2.9 29.1 + - - +
1279B LYS* 4.1 2.5 - - - +
1281B ILE* 1.3 90.9 - - + +
1283B GLY* 1.3 63.4 - - - +
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Residues in contact with GLY1283 (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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1279B LYS 2.9 11.6 + - - -
1280B PHE* 2.7 17.4 + - - +
1281B ILE 3.5 8.0 - - - +
1282B MET* 1.3 83.1 - - - +
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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
------------------------------------------------------------
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