Contacts of the helix formed by residues 1190 - 1207 (chain J) in PDB entry 3F5P
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 THR1190 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1132J VAL* 3.0 15.8 - - - +
1160J ILE* 5.4 1.1 - - - -
1164J ASP 3.7 22.0 - - - +
1165J PTR 3.8 10.5 - - + -
1182J GLU* 5.1 3.3 + - + +
1188J VAL* 4.3 11.6 - - + -
1189J PHE* 1.3 82.2 - - - +
1191J THR* 1.3 65.2 + - - +
1192J TYR* 3.1 39.6 + - + +
1193J SER* 2.7 23.6 + - - -
1194J ASP 3.2 1.9 + - - -
1253J PRO* 5.2 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1191 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1127J ASN* 2.8 40.2 + - + +
1132J VAL* 3.6 8.2 - - + +
1160J ILE* 4.1 21.3 - - + +
1164J ASP* 5.9 3.6 - - + +
1190J THR* 1.3 74.2 - - - +
1192J TYR* 1.3 80.6 + - - +
1194J ASP* 3.0 7.4 + - - +
1195J VAL* 3.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1192 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1182J GLU* 4.7 0.2 - - - +
1190J THR* 3.0 23.1 - - + +
1191J THR* 1.3 93.5 + - - +
1193J SER* 1.3 59.9 + - - +
1195J VAL* 3.2 11.7 + - + +
1196J TRP 3.2 12.6 + - - -
1253J PRO* 3.6 46.9 - - + +
1254J LYS* 4.1 27.2 - - + +
1256J ARG* 3.0 22.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1193 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1132J VAL* 4.6 1.2 - - - +
1134J ARG* 5.7 0.6 - - - -
1178J TRP 5.0 0.2 - - - +
1180J SER* 3.5 12.0 + - - -
1182J GLU* 3.9 4.0 + - - -
1183J SER* 3.5 23.3 - - - -
1188J VAL 4.6 1.3 - - - -
1189J PHE* 3.5 14.1 - - - +
1190J THR* 2.7 35.7 + - - -
1192J TYR* 1.3 75.6 - - - +
1194J ASP* 1.3 66.3 + - - +
1196J TRP* 3.3 3.8 + - - +
1197J SER* 3.1 24.5 + - - -
1256J ARG* 3.9 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1194 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1123J MET* 3.2 27.9 - - + +
1126J LEU* 5.2 0.3 - - - +
1127J ASN* 3.7 7.6 + - - -
1132J VAL* 3.6 16.5 - - - +
1133J HIS* 2.7 24.2 + - - +
1134J ARG* 2.8 28.9 + - - -
1136J LEU* 4.2 5.6 - - - +
1190J THR 3.2 4.8 + - - -
1191J THR* 3.0 13.8 + - - +
1193J SER* 1.3 77.4 + - - +
1195J VAL* 1.3 57.8 + - - +
1197J SER* 3.2 9.9 + - - -
1198J PHE* 2.9 24.9 + - - +
1259J PHE* 3.9 9.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1195 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1127J ASN* 5.4 0.2 - - - +
1191J THR* 3.0 18.2 + - - +
1192J TYR* 3.4 11.9 - - + +
1194J ASP* 1.3 74.5 - - - +
1196J TRP* 1.3 68.8 + - - +
1198J PHE* 2.9 12.7 + - - +
1199J GLY 3.0 8.7 + - - -
1248J CYS* 3.5 32.2 - - + +
1256J ARG* 4.0 10.8 - - + -
1257J PRO* 3.5 29.4 - - + +
1258J SER* 4.7 1.6 - - - -
1259J PHE* 3.9 34.5 - - + +
1262J ILE* 4.7 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1196 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1177J ARG 5.2 0.4 + - - -
1178J TRP 3.5 18.4 + - - -
1179J MET 3.2 11.5 + - - -
1180J SER* 3.6 11.9 - - - -
1181J PRO* 3.5 39.5 - - + -
1192J TYR 3.2 3.6 + - - -
1193J SER 3.4 9.2 - - - +
1195J VAL* 1.3 78.6 - - - +
1197J SER* 1.3 68.2 + - - +
1199J GLY* 2.8 15.2 + - - -
1200J VAL* 3.3 18.1 + - + +
1213J TYR* 4.2 13.8 + - - -
1225J VAL* 3.7 16.6 - - + -
1229J GLY 4.7 2.2 - - - -
1230J LEU* 4.5 11.7 - - + -
1248J CYS 3.5 14.8 + - - -
1249J TRP* 3.0 62.8 + + + -
1250J GLN 4.2 2.2 - - - -
1251J TYR* 5.1 0.7 - + - -
1256J ARG* 3.8 22.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1197 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1134J ARG 4.6 10.9 + - - -
1136J LEU* 3.6 30.1 + - - +
1178J TRP* 2.7 28.1 + - - +
1179J MET* 4.9 0.3 - - - -
1180J SER 5.4 0.2 + - - -
1193J SER 3.1 10.6 + - - -
1194J ASP* 3.4 10.4 - - - -
1195J VAL 3.2 0.2 - - - -
1196J TRP* 1.3 79.6 - - - +
1198J PHE* 1.3 64.3 + - - +
1200J VAL* 2.8 18.0 + - - +
1201J VAL* 3.2 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1198 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1116J ALA* 3.4 26.5 - - + -
1119J ILE* 3.3 37.0 - - + -
1120J ALA* 3.7 12.1 - - + -
1136J LEU* 3.7 10.8 - - + -
1194J ASP 2.9 13.1 + - - +
1195J VAL 2.9 9.6 + - - +
1197J SER* 1.3 76.7 - - - +
1199J GLY* 1.3 63.4 + - - +
1201J VAL* 3.0 19.3 + - + +
1202J LEU* 3.1 41.5 + - + +
1248J CYS* 4.2 7.4 - - - -
1259J PHE* 3.7 20.2 - + + -
1262J ILE* 4.0 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1199 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1195J VAL 3.0 5.7 + - - -
1196J TRP 2.8 10.3 + - - -
1198J PHE* 1.3 78.5 - - - +
1200J VAL* 1.3 58.7 + - - -
1202J LEU* 3.4 12.3 - - - +
1203J TRP 3.1 15.1 + - - -
1245J MET* 3.8 4.3 - - - +
1248J CYS* 3.8 19.5 - - - -
1249J TRP* 3.3 25.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1200 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1177J ARG 4.0 14.4 - - - +
1178J TRP* 3.4 34.3 - - + +
1196J TRP* 3.3 19.7 + - + +
1197J SER* 2.8 11.4 + - - +
1199J GLY* 1.3 76.0 - - - +
1201J VAL* 1.3 54.1 + - - +
1202J LEU 3.1 0.2 - - - -
1203J TRP* 3.0 10.9 + - + +
1204J GLU* 2.6 32.0 + - + +
1212J PRO* 4.0 24.0 - - + -
1213J TYR* 5.0 2.0 - - - +
1231J LEU* 4.5 9.9 - - + -
1249J TRP* 4.0 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1201 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1087J LEU* 5.2 2.0 - - + -
1119J ILE* 3.8 30.3 - - + -
1136J LEU* 4.0 19.7 - - + +
1137J ALA* 4.1 10.8 - - - -
1138J ALA* 4.1 8.5 - - - +
1141J CYS* 5.5 0.2 - - - -
1178J TRP* 4.9 0.9 - - + -
1197J SER 3.2 16.2 - - - +
1198J PHE* 3.0 20.2 + - + +
1200J VAL* 1.3 71.4 - - - +
1202J LEU* 1.3 63.1 + - + +
1204J GLU* 3.4 23.0 - - + +
1205J ILE* 2.9 39.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1202 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1112J MET 5.4 0.2 - - - +
1116J ALA* 3.6 31.0 - - + -
1198J PHE* 3.1 43.3 + - + +
1199J GLY* 3.4 11.7 - - - +
1200J VAL 3.1 0.2 - - - -
1201J VAL* 1.3 76.2 - - + +
1203J TRP* 1.3 60.2 + - - +
1205J ILE* 3.1 15.3 + - + +
1206J ALA* 2.9 25.3 + - - +
1241J LEU* 4.3 15.2 - - + +
1244J LEU* 3.9 32.8 - - + -
1245J MET* 3.4 27.8 - - + +
1248J CYS* 4.9 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1203 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1199J GLY 3.1 9.8 + - - +
1200J VAL* 3.0 17.0 + - - +
1202J LEU* 1.3 80.3 - - - +
1204J GLU* 1.3 56.4 + - - +
1206J ALA* 3.2 1.3 + - - -
1207J THR* 2.7 54.9 + - + +
1210J GLU* 3.7 27.6 - - + -
1211J GLN 3.7 13.7 - - - -
1212J PRO* 3.6 27.6 - - + -
1213J TYR 4.6 0.9 - - - -
1231J LEU* 3.7 38.9 - - + +
1232J ASP* 2.9 28.2 + - + -
1234J PRO* 3.7 18.6 - - + +
1242J PHE* 5.3 0.4 - + - -
1245J MET* 3.4 19.2 - - - +
1249J TRP* 3.9 2.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1204 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1088J LYS* 4.3 14.9 + - - +
1091J LEU* 3.5 4.0 - - + +
1138J ALA* 2.9 43.2 + - + +
1139J ARG* 4.6 1.7 + - - +
1178J TRP* 2.9 41.4 + - + +
1200J VAL* 2.6 22.0 + - + +
1201J VAL* 3.5 16.3 - - - +
1202J LEU 3.2 0.2 - - - -
1203J TRP* 1.3 77.3 - - + +
1205J ILE* 1.3 56.1 - - - +
1207J THR* 3.4 5.3 + - - -
1208J LEU 3.0 6.6 + - - -
1209J ALA* 2.6 35.7 + - - +
1210J GLU 4.6 12.8 - - - +
1212J PRO* 4.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1205 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1087J LEU* 4.4 8.3 - - + -
1091J LEU* 3.7 25.1 - - + -
1107J PRO* 5.5 1.3 - - + -
1112J MET* 3.7 38.8 - - + +
1115J MET* 4.3 32.5 - - + -
1116J ALA 5.0 1.6 - - - +
1119J ILE* 4.4 9.2 - - + -
1201J VAL* 2.9 38.7 + - + +
1202J LEU* 3.1 18.4 + - + +
1204J GLU* 1.3 73.5 - - + +
1206J ALA* 1.3 63.0 + - - +
1207J THR 3.0 5.8 + - - -
1208J LEU* 3.3 20.6 + - - +
1241J LEU* 5.2 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1206 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1112J MET* 4.3 15.7 - - - +
1202J LEU 2.9 16.2 + - - +
1203J TRP 3.8 1.6 - - - +
1205J ILE* 1.3 76.7 - - - +
1207J THR* 1.3 61.9 + - - +
1208J LEU* 5.4 1.5 - - - +
1234J PRO* 3.8 27.1 - - + +
1235J ASP 5.0 4.7 - - - +
1237J CYS* 3.8 23.1 - - + +
1238J PRO* 5.6 0.2 - - + -
1241J LEU* 4.1 6.9 - - + +
1245J MET* 3.9 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1207 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1095J ARG* 3.7 2.3 + - - -
1203J TRP* 2.7 42.2 + - + +
1204J GLU* 3.4 5.9 + - - -
1205J ILE 3.0 0.4 - - - -
1206J ALA* 1.3 76.3 - - - +
1208J LEU* 1.3 74.8 + - - +
1210J GLU* 2.9 53.6 + - - +
1234J PRO* 3.4 33.4 - - + -
----------------------------------------------------------
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