Contacts of the helix formed by residues 1181 - 1199 (chain C) in PDB entry 3DLS
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 GLY1181 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1125C ILE* 3.7 19.6 - - - +
1153C LEU* 4.5 1.1 - - - -
1179C TYR* 3.6 18.7 - - - +
1180C ARG* 1.3 80.1 - - - +
1182C PRO* 1.4 68.5 - - - +
1183C GLU* 3.1 5.6 + - - -
1184C LEU* 3.1 6.7 + - - +
1185C GLU* 2.9 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1182 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1120C ARG* 3.6 43.3 - - - +
1125C ILE* 3.7 8.5 - - + -
1153C LEU* 4.4 9.6 - - + -
1180C ARG* 3.7 35.2 - - + +
1181C GLY* 1.4 86.7 - - - +
1183C GLU* 1.3 57.7 + - + +
1185C GLU* 3.3 2.9 - - - +
1186C MET* 2.9 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1183 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1172C GLU* 4.4 6.3 - - - +
1179C TYR* 5.8 0.9 - - - +
1180C ARG* 2.7 57.7 + - - +
1181C GLY 4.1 4.3 + - - -
1182C PRO* 1.3 75.1 - - + +
1184C LEU* 1.3 62.3 + - - +
1186C MET* 3.3 6.3 + - - -
1187C TRP 3.2 12.6 + - - -
1236C PRO* 4.0 28.3 - - + +
1239C ARG* 2.9 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1184 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1127C ARG* 5.8 8.7 - - + +
1162C PHE* 4.4 14.8 - - + -
1168C TYR 4.8 1.7 - - - +
1169C CYS* 4.3 10.3 - - - -
1170C ALA* 3.5 41.1 - - + +
1172C GLU* 4.3 1.7 + - - +
1173C VAL* 3.8 19.3 - - + -
1179C TYR* 3.5 48.2 - - + +
1181C GLY* 3.1 9.0 + - - +
1183C GLU* 1.3 75.6 + - - +
1185C GLU* 1.3 65.0 + - - +
1187C TRP* 3.3 4.2 + - - +
1188C SER* 3.1 22.6 + - - -
1239C ARG* 4.2 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1185 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1116C VAL* 3.4 26.2 - - + +
1119C LEU* 5.9 1.9 - - - +
1120C ARG* 2.6 36.9 + - - +
1124C ILE 4.7 2.5 - - - +
1125C ILE* 3.4 26.6 - - + +
1126C HIS* 4.0 9.0 + - - +
1127C ARG 5.0 0.5 + - - -
1129C ILE* 3.6 24.8 - - + +
1181C GLY 2.9 12.3 + - - +
1182C PRO 3.3 9.6 - - - +
1184C LEU* 1.3 76.5 - - - +
1186C MET* 1.3 60.9 + - - +
1188C SER* 2.6 24.4 + - - -
1189C LEU* 3.1 12.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1186 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1120C ARG* 3.6 23.6 - - - +
1182C PRO* 2.9 24.3 + - + +
1183C GLU* 3.6 9.2 - - - +
1184C LEU 3.3 0.4 - - - -
1185C GLU* 1.3 74.4 - - - +
1187C TRP* 1.3 60.8 + - - +
1189C LEU* 3.5 12.9 + - + +
1190C GLY 3.2 15.9 + - - -
1231C LEU* 3.6 29.1 - - + +
1239C ARG* 4.0 9.6 - - - -
1240C THR 3.5 19.3 - - - +
1241C THR* 3.9 4.5 - - - +
1242C LEU* 3.7 29.6 - - + +
1245C LEU* 3.5 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1187 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1167C GLU 5.0 1.4 + - - -
1168C TYR 3.1 25.2 + - - -
1169C CYS 3.2 22.4 + - - -
1170C ALA* 3.7 14.4 - - + -
1171C PRO* 3.7 17.5 - - + -
1183C GLU 3.2 6.0 + - - +
1184C LEU 3.3 8.0 + - - +
1186C MET* 1.3 73.6 - - - +
1188C SER* 1.3 59.6 + - - +
1190C GLY* 3.1 4.7 + - - -
1191C VAL* 3.0 35.2 + - + +
1203C PHE* 3.5 34.9 - + - -
1209C THR* 3.8 27.1 + - + -
1212C ALA* 3.8 6.1 - - + -
1231C LEU 3.7 21.1 - - - -
1232C LEU* 3.4 31.1 - - + +
1233C GLN 3.8 8.3 - - - -
1234C PRO 4.2 1.6 - - - -
1239C ARG* 3.5 25.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1188 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1129C ILE* 3.8 33.1 + - - +
1168C TYR* 3.7 27.5 - - - -
1184C LEU* 3.1 9.4 + - - -
1185C GLU* 2.6 24.4 + - - -
1187C TRP* 1.3 79.6 - - - +
1189C LEU* 1.3 52.3 + - - +
1191C VAL* 3.4 3.0 + - - -
1192C THR* 2.6 36.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1189 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1109C PHE* 3.5 20.2 - - + -
1112C LEU* 3.6 37.9 - - + +
1113C VAL* 5.4 1.8 - - + +
1116C VAL* 4.1 28.3 - - + -
1129C ILE* 3.9 12.3 - - + -
1185C GLU* 3.1 17.7 + - + +
1186C MET* 3.7 34.1 - - + +
1187C TRP 3.2 0.2 - - - -
1188C SER* 1.3 75.5 + - - +
1190C GLY* 1.3 60.9 + - - +
1192C THR* 4.1 2.0 - - - -
1193C LEU* 3.0 28.9 + - - +
1231C LEU* 4.3 5.4 - - + -
1242C LEU* 4.7 0.9 - - + -
1245C LEU* 4.0 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1190 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1186C MET 3.2 7.5 + - - -
1187C TRP 3.1 8.9 + - - -
1189C LEU* 1.3 75.5 - - - +
1191C VAL* 1.3 55.5 + - - +
1193C LEU* 3.4 3.3 + - - +
1194C TYR* 2.9 30.0 + - - +
1228C VAL* 4.7 2.9 - - - +
1231C LEU* 3.7 27.9 - - - +
1232C LEU* 3.7 16.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1191 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1167C GLU 3.9 8.7 - - - +
1168C TYR* 3.5 35.4 - - + -
1187C TRP* 3.0 40.7 + - + +
1188C SER 3.4 0.9 + - - +
1189C LEU 3.4 0.2 - - - -
1190C GLY* 1.3 71.5 - - - +
1192C THR* 1.3 56.6 - - - +
1194C TYR* 3.4 1.7 + - - +
1195C THR* 2.6 39.1 + - - +
1201C ASN* 3.7 21.8 - - - +
1202C PRO* 3.7 20.9 - - + -
1203C PHE* 5.5 2.0 - - + -
1232C LEU* 3.9 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1192 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1090C LEU* 5.3 4.9 - - + -
1109C PHE* 5.1 3.1 - - + -
1112C LEU* 4.0 13.5 - - + -
1129C ILE* 3.8 12.0 + - - +
1130C LYS* 3.9 1.1 - - - -
1131C ASP* 4.3 15.1 - - + +
1134C ILE* 3.9 28.5 - - + -
1168C TYR* 3.6 15.2 - - - -
1188C SER 2.6 23.3 + - - -
1189C LEU* 3.9 7.4 - - - -
1190C GLY 3.4 0.2 - - - -
1191C VAL* 1.3 72.5 - - - +
1193C LEU* 1.3 60.0 + - - +
1195C THR* 3.5 4.8 + - - -
1196C LEU* 2.9 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1193 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1109C PHE* 3.7 32.3 - - + -
1189C LEU 3.0 18.3 + - - +
1190C GLY 3.6 3.8 - - - +
1192C THR* 1.3 77.6 - - - +
1194C TYR* 1.3 62.4 + - - +
1196C LEU* 3.2 6.9 + - + +
1197C VAL* 3.1 34.9 + - + +
1224C LEU* 4.0 3.6 - - + -
1227C LEU* 3.7 31.6 - - + -
1228C VAL* 3.6 24.9 - - + -
1231C LEU* 4.2 6.5 - - + -
1250C TRP* 3.7 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1194 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1190C GLY 2.9 17.4 + - - +
1191C VAL 3.8 0.4 - - - +
1193C LEU* 1.3 76.6 - - - +
1195C THR* 1.3 57.8 + - - +
1197C VAL* 4.2 1.1 - - - -
1198C PHE* 2.9 68.4 + + + +
1200C GLU* 3.0 36.9 + - + +
1201C ASN 3.8 4.1 + - - -
1202C PRO* 3.5 43.3 + - + +
1214C ILE* 3.9 32.3 - - + -
1215C HIS 3.9 8.3 + - - -
1216C PRO* 3.7 10.1 - - + +
1217C PRO* 3.7 18.0 - - - +
1228C VAL* 4.4 7.2 - - + +
1232C LEU* 4.3 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1195 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1094C ILE* 3.6 19.1 - - + +
1131C ASP* 3.8 22.2 - - - +
1168C TYR* 4.0 11.1 + - - +
1191C VAL* 2.6 30.9 + - - +
1192C THR* 3.9 3.8 - - - -
1194C TYR* 1.3 73.4 - - - +
1196C LEU* 1.3 64.9 + - - +
1199C GLU* 3.1 22.3 + - - -
1200C GLU* 3.5 26.8 + - - +
1201C ASN* 4.1 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1196 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1090C LEU* 4.2 21.5 - - + -
1093C PHE* 4.8 4.3 - - + -
1094C ILE* 3.8 14.8 - - + +
1098C PRO* 6.0 0.3 - - - +
1100C LEU* 3.8 33.5 - - + +
1105C ALA* 3.2 37.5 - - + +
1108C ILE* 4.2 27.4 - - + -
1109C PHE* 4.4 13.7 - - + -
1192C THR* 2.9 19.0 + - + +
1193C LEU* 3.2 6.7 + - + +
1195C THR* 1.3 79.1 - - - +
1197C VAL* 1.3 66.4 + - + +
1199C GLU* 4.1 9.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1197 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1100C LEU* 5.7 1.8 - - - +
1102C GLU* 6.1 1.1 - - + -
1105C ALA* 3.8 28.5 - - + -
1193C LEU* 3.1 35.7 + - + +
1194C TYR* 4.2 1.8 - - - -
1196C LEU* 1.3 80.7 - - + +
1198C PHE* 1.3 95.9 + - + +
1199C GLU* 3.3 5.3 + - - +
1218C TYR* 3.3 21.5 - - - -
1220C VAL* 5.5 2.7 - - + -
1224C LEU* 4.0 24.0 - - + -
1228C VAL* 5.3 0.4 - - + -
1250C TRP* 4.2 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1198 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1194C TYR* 2.9 54.2 + + + +
1197C VAL* 1.3 99.3 - - + +
1199C GLU* 1.3 63.4 + - - +
1200C GLU* 3.0 18.7 + - - +
1216C PRO* 3.5 25.6 - - + -
1217C PRO* 3.7 34.5 - - + +
1218C TYR* 3.8 29.7 + + + -
1220C VAL* 3.6 39.7 - - + -
1224C LEU* 4.8 2.7 - - + -
1225C MET* 4.7 2.2 - - - -
1228C VAL* 4.8 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1199 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C MG 2.4 30.9 - - - -
1094C ILE* 4.1 26.3 - - + +
1097C HIS* 4.1 19.6 + - + +
1098C PRO* 2.8 30.8 - - + +
1100C LEU* 5.8 1.7 - - - +
1194C TYR 3.8 0.2 + - - -
1195C THR* 3.1 18.8 + - - +
1196C LEU 4.1 9.8 - - - +
1197C VAL 4.0 7.9 - - - +
1198C PHE* 1.3 77.7 - - - +
1200C GLU* 1.3 58.8 + - - +
1218C TYR* 2.6 26.6 + - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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