Contacts of the helix formed by residues 1223 - 1241 (chain u) in PDB entry 6FF7
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 SER1223 (chain u).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362 G 5.3 0.4 - - - -
372 U 3.8 39.5 - - - -
382 A 6.2 0.4 - - - -
1221u GLU* 3.6 4.3 - - - +
1222u THR* 1.3 80.7 - - - +
1224u PRO* 1.3 63.2 - - - +
1225u HIS* 3.4 4.7 - - - -
1226u VAL* 4.1 13.6 - - - +
1227u ILE* 3.1 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1224 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362 G 4.4 22.5 - - - +
372 U 4.9 1.2 - - - -
1222u THR 3.7 3.5 - - - +
1223u SER* 1.3 72.3 - - - +
1225u HIS* 1.3 58.7 + - - +
1227u ILE* 3.4 4.3 + - + +
1228u GLN* 3.0 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1225 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362 G 5.1 3.8 + - - +
392Z U 4.3 23.6 - - - +
393Z G 5.5 4.5 - - - +
1186u GLN* 5.0 2.7 - - + -
1223u SER* 3.4 2.6 - - - -
1224u PRO* 1.3 77.8 - - - +
1226u VAL* 1.3 58.4 + - - +
1228u GLN* 3.5 3.6 + - - +
1229u ALA* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1226 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1182u LEU* 4.7 16.8 - - + +
1186u GLN* 4.0 24.5 - - + +
1218u ASN 5.3 2.4 - - - +
1221u GLU* 4.9 14.4 - - + -
1223u SER* 3.6 16.2 + - - +
1224u PRO 3.4 0.4 - - - -
1225u HIS* 1.3 78.6 - - - +
1227u ILE* 1.3 58.3 + - - +
1229u ALA* 3.6 1.2 - - - +
1230u VAL* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1227 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1218u ASN 5.9 1.8 - - - -
1219u VAL 5.4 4.0 - - - +
1221u GLU* 4.1 17.2 - - - +
1222u THR 5.3 1.1 - - - -
1223u SER 3.1 19.5 + - - +
1224u PRO* 4.2 4.0 - - + +
1226u VAL* 1.3 78.3 - - - +
1228u GLN* 1.3 57.2 + - - +
1230u VAL* 3.5 4.4 + - - +
1231u MET* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1228 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1224u PRO 3.0 19.0 + - - +
1225u HIS* 4.1 3.4 - - - +
1227u ILE* 1.3 74.4 - - - +
1229u ALA* 1.3 61.6 + - - +
1231u MET* 3.8 5.4 - - - +
1232u GLY* 2.9 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1229 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1186u GLN* 3.8 35.2 - - + +
1189u SER* 3.9 6.6 - - - +
1190u ALA* 5.1 5.4 - - + +
1193u GLN* 5.3 0.5 - - - +
1225u HIS 2.9 19.0 + - - +
1226u VAL 3.6 4.5 - - - +
1227u ILE 3.3 0.2 - - - -
1228u GLN* 1.3 77.3 - - - +
1230u VAL* 1.3 56.8 + - - +
1232u GLY* 3.4 2.3 + - - -
1233u ALA* 2.9 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1230 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1189u SER* 4.2 9.1 - - - -
1215u VAL* 5.2 9.9 - - + +
1218u ASN* 4.6 21.8 - - + +
1219u VAL* 5.3 4.9 - - - -
1226u VAL 2.9 17.3 + - - +
1227u ILE* 4.3 3.4 - - - +
1229u ALA* 1.3 74.6 - - - +
1231u MET* 1.3 60.3 + - - +
1233u ALA* 3.6 8.5 - - + +
1234u LEU* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1231 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1227u ILE 2.9 20.3 + - - +
1228u GLN* 3.8 8.1 - - - +
1230u VAL* 1.3 75.4 - - - +
1232u GLY* 1.3 58.4 + - - +
1234u LEU* 3.3 6.0 + - - +
1235u GLU* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1232 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1193u GLN* 4.0 10.7 - - - +
1228u GLN 2.9 15.7 + - - -
1229u ALA 3.7 3.6 - - - -
1231u MET* 1.3 76.2 - - - +
1233u ALA* 1.3 55.5 + - - +
1235u GLU* 3.5 5.3 + - - +
1236u GLY* 2.9 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1233 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1189u SER* 3.4 32.3 - - - +
1192u VAL* 5.2 5.2 - - + +
1193u GLN* 3.8 15.6 + - + +
1196u SER* 5.6 0.2 - - - -
1215u VAL* 5.5 9.9 - - + -
1229u ALA 2.9 14.5 + - - +
1230u VAL* 3.6 7.4 - - + +
1232u GLY* 1.3 77.3 - - - +
1234u LEU* 1.3 55.3 + - - +
1236u GLY 3.4 0.5 + - - -
1237u LEU* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1234 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1230u VAL 2.9 16.6 + - - +
1231u MET* 3.3 6.9 + - - +
1232u GLY 3.3 0.2 - - - -
1233u ALA* 1.3 76.6 - - - +
1235u GLU* 1.3 55.9 + - - +
1237u LEU* 3.3 5.5 + - - +
1238u ARG* 2.9 28.1 + - - +
1246u MET* 5.8 1.6 - - - +
1268u ILE* 6.2 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1235 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1231u MET 2.9 17.1 + - - +
1232u GLY* 4.2 4.7 - - - +
1234u LEU* 1.3 76.5 - - - +
1236u GLY* 1.3 58.4 + - - +
1238u ARG* 3.7 16.5 - - - +
1239u VAL* 4.7 2.9 + - - +
1271u SER* 5.7 10.1 - - - +
78y GLN* 5.1 10.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1236 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1193u GLN* 4.8 8.5 - - - -
1196u SER* 3.6 23.0 - - - -
1197u LEU* 5.5 3.4 - - - -
1232u GLY 2.9 17.8 + - - -
1233u ALA* 3.8 1.6 - - - -
1235u GLU* 1.3 76.0 - - - +
1237u LEU* 1.3 58.4 + - - +
1238u ARG 3.2 5.5 + - - -
1239u VAL* 3.7 10.0 + - - +
1240u ALA* 4.0 5.7 + - - +
78y GLN* 6.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1237 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1192u VAL 6.0 0.2 - - - +
1196u SER* 4.2 11.6 - - - -
1208u LEU* 5.9 7.4 - - + +
1212u LEU* 5.3 13.0 - - + -
1233u ALA 2.9 18.1 + - - +
1234u LEU* 3.6 4.9 - - - +
1236u GLY* 1.3 72.4 - - - +
1238u ARG* 1.3 63.8 + - - +
1239u VAL 3.2 2.2 + - - -
1240u ALA* 4.1 4.0 - - - +
1241u ILE* 3.8 19.2 + - + +
1242u GLY 4.2 5.4 - - - +
1246u MET* 5.4 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1238 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1234u LEU 2.9 15.8 + - - +
1235u GLU* 3.7 16.2 - - - +
1236u GLY 3.2 0.8 - - - -
1237u LEU* 1.3 77.8 - - - +
1239u VAL* 1.3 58.0 + - + +
1242u GLY 3.1 27.8 - - - -
1243u PRO* 3.2 10.1 - - + +
1246u MET* 4.8 13.0 - - + -
1272u ILE* 5.8 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1239 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1200u TYR* 6.0 4.0 - - + -
1235u GLU 4.7 2.9 + - - +
1236u GLY 3.7 6.9 + - - +
1237u LEU 3.2 0.6 - - - -
1238u ARG* 1.3 81.6 - - + +
1240u ALA* 1.3 65.7 + - - +
1241u ILE 3.6 0.4 - - - -
1242u GLY* 3.7 6.7 + - - -
1165v SER* 5.5 3.8 - - - -
1169v PRO* 3.9 10.4 - - - +
77y ILE* 5.0 11.7 - - + +
78y GLN* 6.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1240 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1196u SER* 3.9 37.7 - - - +
1199u VAL 5.5 1.6 - - - +
1200u TYR* 4.7 15.9 - - + +
1201u GLY 5.6 3.1 + - - +
1205u GLU* 4.7 7.7 - - - +
1208u LEU* 5.7 7.0 - - + -
1236u GLY 4.0 2.9 + - - +
1237u LEU* 3.8 3.9 + - - +
1238u ARG 3.7 0.2 - - - -
1239u VAL* 1.3 79.6 - - - +
1241u ILE* 1.3 60.4 + - - +
1169v PRO* 3.3 19.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1241 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1205u GLU* 4.4 27.2 - - + +
1208u LEU* 5.2 9.4 - - + -
1209u ASN* 5.4 7.6 - - + +
1237u LEU* 3.8 12.3 + - + +
1240u ALA* 1.3 79.0 - - + +
1242u GLY* 1.3 60.6 + - - +
1244u CYS* 5.9 0.7 - - - +
1245u ARG* 4.8 16.9 + - + +
1169v PRO* 4.7 5.3 - - - +
----------------------------------------------------------
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