Contacts of the helix formed by residues 1187 - 1204 (chain B) in PDB entry 1RQQ
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 THR1187 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1129B VAL* 3.2 17.2 - - - +
1157B ILE* 5.0 0.2 - - - -
1161B ASP 4.0 11.2 - - - +
1162B PTR 3.7 19.5 - - + -
1179B GLU* 4.7 4.4 + - + +
1185B VAL* 4.6 11.4 - - + +
1186B PHE* 1.3 81.6 - - - +
1188B THR* 1.3 65.3 + - - +
1189B SER* 3.0 26.7 + - - -
1190B SER* 2.8 22.7 + - - -
1191B ASP 3.2 5.2 + - - -
1250B PRO* 5.1 1.0 - - - +
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Residues in contact with THR1188 (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 ASN* 3.3 44.7 + - + +
1128B PHE 5.3 1.3 + - - -
1129B VAL* 4.3 2.6 - - - +
1157B ILE* 4.9 9.6 - - - +
1161B ASP 4.9 2.4 + - - -
1187B THR* 1.3 74.7 - - - +
1189B SER* 1.3 58.1 + - - +
1191B ASP* 3.2 11.1 + - + +
1192B MET* 3.0 26.1 + - + +
1255B THR* 5.6 7.2 - - + -
1256B PHE* 3.8 28.3 - - + +
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Residues in contact with SER1189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1187B THR* 2.9 14.0 + - - -
1188B THR* 1.3 77.5 - - - +
1190B SER* 1.3 62.2 + - - +
1192B MET* 3.2 18.5 + - - +
1193B TRP 3.2 6.1 + - - -
1250B PRO* 3.1 41.7 + - - +
1251B ASN* 5.1 1.4 + - - -
1253B ARG* 3.0 19.2 + - - +
1254B PRO 5.7 1.4 + - - -
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Residues in contact with SER1190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1129B VAL* 4.6 0.7 - - - +
1175B TRP 4.8 0.5 - - - +
1176B MET* 5.7 0.2 - - - -
1177B ALA* 3.9 11.1 + - - +
1179B GLU* 4.3 5.1 + - - -
1180B SER* 3.3 24.0 - - - -
1185B VAL 4.5 0.9 - - - -
1186B PHE* 3.3 14.8 - - - +
1187B THR* 2.8 34.4 + - - -
1189B SER* 1.3 80.4 - - - +
1191B ASP* 1.3 64.1 + - - +
1193B TRP* 3.1 13.5 + - - +
1194B SER* 3.1 15.4 + - - -
1253B ARG* 3.8 8.5 - - - +
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Residues in contact with ASP1191 (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* 3.7 10.6 - - + +
1128B PHE 4.8 0.9 - - - +
1129B VAL* 3.4 17.8 - - - +
1130B HIS* 2.8 33.6 + - - +
1131B ARG* 2.9 27.6 + - - -
1132B ASP 4.6 0.2 + - - -
1133B LEU* 3.8 6.7 + - + +
1187B THR 3.2 5.3 + - - +
1188B THR* 3.3 14.0 - - - +
1190B SER* 1.3 80.5 + - - +
1192B MET* 1.3 55.7 + - - +
1194B SER* 3.1 11.8 + - - -
1195B PHE* 2.9 26.3 + - - +
1256B PHE* 3.9 14.3 - - + -
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Residues in contact with MET1192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1188B THR* 3.0 12.4 + - + +
1189B SER* 3.3 13.5 - - - +
1190B SER 3.2 0.2 - - - -
1191B ASP* 1.3 74.1 - - - +
1193B TRP* 1.3 65.4 + - - +
1195B PHE* 3.2 15.3 + - - +
1196B GLY 3.0 17.2 + - - -
1245B CYS* 3.4 28.5 - - - -
1253B ARG* 4.1 14.8 - - + -
1254B PRO* 3.2 36.1 - - + +
1255B THR* 3.4 4.0 - - - -
1256B PHE* 3.3 50.2 - - + +
1259B ILE* 3.7 9.0 - - + -
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Residues in contact with TRP1193 (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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1174B ARG 5.1 1.2 + - - -
1175B TRP 3.4 20.5 + - - -
1176B MET 3.2 19.1 + - - -
1177B ALA* 3.6 15.0 - - + -
1178B PRO* 3.7 20.6 - - + -
1189B SER 3.2 4.6 + - - -
1190B SER 3.1 10.9 + - - +
1192B MET* 1.3 75.8 - - - +
1194B SER* 1.3 63.4 + - - +
1196B GLY 3.0 10.4 + - - -
1197B VAL* 3.2 21.7 + - + +
1210B TYR* 4.3 15.0 + - - -
1222B VAL* 3.9 17.9 - - + -
1226B GLY 4.1 15.5 - - - -
1227B TYR* 4.5 3.6 - + + -
1245B CYS 3.5 24.0 + - - +
1246B TRP* 3.4 51.0 + + + -
1247B GLN 4.0 4.7 - - - -
1248B PHE* 5.1 1.1 - + - -
1253B ARG* 3.6 20.9 - - - +
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Residues in contact with SER1194 (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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1131B ARG 5.3 4.0 + - - -
1133B LEU* 3.4 33.8 + - - +
1175B TRP* 2.8 26.3 + - - +
1176B MET* 4.9 0.9 - - - +
1190B SER 3.1 9.6 + - - -
1191B ASP* 3.1 14.0 + - - -
1193B TRP* 1.3 80.7 - - - +
1195B PHE* 1.3 56.3 + - - +
1197B VAL* 3.0 9.1 + - - +
1198B VAL* 2.9 32.3 + - - +
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Residues in contact with PHE1195 (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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1113B ALA* 3.7 23.8 - - + -
1116B ILE* 3.8 33.2 - - + -
1117B ALA* 4.2 5.2 - - + -
1133B LEU* 3.7 9.6 - - + +
1191B ASP 2.9 12.7 + - - +
1192B MET* 3.2 26.2 - - - +
1193B TRP 3.1 0.2 - - - -
1194B SER* 1.3 74.1 - - - +
1196B GLY* 1.3 65.0 + - - +
1198B VAL* 3.0 9.1 + - + +
1199B LEU* 3.0 58.6 + - + +
1241B LEU* 5.5 1.1 - - + -
1245B CYS* 3.8 7.4 - - - -
1256B PHE* 3.7 19.7 - + + -
1259B ILE* 3.9 31.2 - - + -
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Residues in contact with GLY1196 (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 MET 3.0 7.5 + - - -
1193B TRP 3.0 8.6 + - - -
1195B PHE* 1.3 77.5 - - - +
1197B VAL* 1.3 61.0 + - - +
1199B LEU* 3.2 10.2 + - - +
1200B TRP 3.1 16.5 + - - -
1242B MET* 3.5 6.6 - - - +
1245B CYS* 3.6 25.6 - - - -
1246B TRP* 3.5 18.2 - - - -
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Residues in contact with VAL1197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1174B ARG 4.1 16.6 - - - +
1175B TRP* 3.3 33.4 - - + +
1193B TRP* 3.4 30.5 - - + +
1194B SER* 3.0 10.2 + - - +
1196B GLY* 1.3 74.0 - - - +
1198B VAL* 1.3 61.8 + - - +
1200B TRP* 3.2 4.9 + - + +
1201B GLU* 2.8 28.5 + - + +
1209B PRO* 4.5 8.1 - - + -
1210B TYR* 5.4 1.1 - - - +
1228B LEU* 4.3 16.4 - - + -
1246B TRP* 3.9 18.6 - - + +
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Residues in contact with VAL1198 (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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1084B LEU* 4.6 1.3 - - + -
1116B ILE* 4.3 18.2 - - + -
1133B LEU* 3.9 12.1 - - + -
1134B ALA* 3.5 34.3 - - - +
1135B ALA* 4.2 17.0 - - + +
1138B CYS* 4.5 4.5 - - - -
1175B TRP* 4.7 0.2 - - + -
1194B SER 2.9 19.9 + - - +
1195B PHE* 3.0 10.5 + - + +
1197B VAL* 1.3 76.4 - - - +
1199B LEU* 1.3 55.4 + - + +
1201B GLU* 2.8 11.6 + - - +
1202B ILE* 2.7 49.6 + - + +
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Residues in contact with LEU1199 (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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1113B ALA* 3.9 17.9 - - + -
1195B PHE* 3.0 56.1 + - + +
1196B GLY* 3.2 9.8 + - - +
1198B VAL* 1.3 76.2 - - + +
1200B TRP* 1.3 58.2 + - - +
1202B ILE* 3.1 19.4 + - + +
1203B THR* 2.9 34.1 + - - +
1238B VAL* 4.3 15.7 - - + -
1241B LEU* 3.8 33.4 - - + -
1242B MET* 4.0 15.7 - - + +
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Residues in contact with TRP1200 (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 GLY 3.1 9.2 + - - +
1197B VAL* 3.3 14.8 - - + +
1199B LEU* 1.3 77.6 - - - +
1201B GLU* 1.3 73.1 + - + +
1203B THR* 3.3 7.8 + - - -
1204B SER* 2.8 40.8 + - - -
1207B GLU* 3.0 40.2 - - + -
1208B GLN 3.6 6.3 - - - -
1209B PRO* 3.3 41.1 - - + -
1210B TYR 4.9 0.9 - - - -
1228B LEU* 3.8 27.2 - - + +
1229B ASP 3.0 28.8 + - - +
1231B PRO* 3.6 19.4 - - + +
1242B MET* 3.7 13.8 - - - -
1246B TRP* 4.1 5.2 - + + -
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Residues in contact with GLU1201 (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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1085B LYS* 4.4 14.4 + - - +
1088B LEU* 4.0 1.6 - - + -
1134B ALA 3.8 0.2 - - - -
1135B ALA* 2.8 48.4 + - + +
1136B ARG 4.5 1.4 + - - -
1175B TRP* 2.9 39.1 + - + +
1197B VAL* 2.8 13.3 + - + +
1198B VAL* 3.1 17.3 - - - +
1200B TRP* 1.3 91.2 - - + +
1202B ILE* 1.3 57.0 + - - +
1204B SER* 3.2 6.8 + - - -
1205B LEU 2.9 9.2 + - - -
1206B ALA* 2.6 34.5 + - - +
1207B GLU 4.6 5.7 - - - +
1209B PRO* 5.1 0.7 - - + +
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Residues in contact with ILE1202 (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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1084B LEU* 4.3 11.0 - - + -
1088B LEU* 3.6 27.8 - - + +
1104B PRO* 5.3 2.8 - - + +
1109B MET* 3.9 33.5 - - + +
1112B MET* 3.9 26.7 - - + -
1113B ALA 5.1 1.1 - - - +
1116B ILE* 4.4 15.3 - - + -
1198B VAL* 2.7 30.9 + - + +
1199B LEU* 3.4 26.7 - - + +
1201B GLU* 1.3 73.2 - - - +
1203B THR* 1.3 61.2 + - + +
1204B SER 3.2 4.2 + - - -
1205B LEU* 3.2 17.0 + - - +
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Residues in contact with THR1203 (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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1109B MET* 4.0 24.9 - - + -
1199B LEU 2.9 23.1 + - - +
1200B TRP* 3.3 7.3 + - - -
1202B ILE* 1.3 72.4 - - + +
1204B SER* 1.3 56.4 + - - +
1205B LEU* 3.5 2.1 - - - +
1231B PRO* 2.8 39.6 - - - +
1232B ASP 4.4 8.1 - - - +
1234B CYS* 3.8 25.2 - - - -
1235B PRO* 4.4 4.5 - - + -
1238B VAL* 3.8 17.7 - - + -
1242B MET* 3.8 0.3 - - - +
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Residues in contact with SER1204 (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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1092B ARG* 4.2 1.7 + - - -
1200B TRP* 2.8 30.6 + - - -
1201B GLU* 3.2 6.4 + - - -
1203B THR* 1.3 77.8 - - - +
1205B LEU* 1.3 71.7 + - - +
1207B GLU* 3.2 47.0 + - - +
1231B PRO* 3.8 17.0 - - - -
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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