Contacts of the helix formed by residues 1231 - 1242 (chain B) in PDB entry 1CM8
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 HIS1231 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1185B PTR 3.5 27.6 + + + +
1189B ARG* 3.5 5.1 - - - +
1192B ARG* 3.4 26.5 - - - +
1197B ILE* 3.3 32.2 - - + +
1200B TRP* 6.5 1.3 - + - -
1230B ASP* 1.3 79.6 - - + +
1232B LEU* 1.3 82.5 + - + +
1234B GLN* 3.4 16.7 - - - +
1235B LEU* 3.7 4.7 + - - +
1257B GLU* 3.0 36.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1197B ILE* 4.4 13.2 - - + -
1230B ASP* 3.2 10.8 + - - +
1231B HIS* 1.3 88.4 - - + +
1233B ASP* 1.3 66.8 + - - +
1234B GLN 3.1 1.8 - - - -
1235B LEU* 3.0 16.1 + - + +
1257B GLU* 3.7 40.4 - - + +
1258B ALA* 4.9 0.4 - - - -
1261B TYR* 3.0 64.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1227B LYS 4.9 0.2 - - - +
1228B GLY* 3.6 3.6 - - - -
1229B SER* 2.8 34.0 + - - +
1230B ASP* 3.0 31.1 + - - +
1232B LEU* 1.3 77.3 - - - +
1234B GLN* 1.3 56.4 + - - +
1236B LYS* 3.1 26.9 + - - +
1237B GLU* 2.9 32.1 + - - +
1261B TYR* 3.6 8.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1189B ARG* 3.0 44.8 + - + +
1190B TRP* 3.3 8.0 + - - +
1192B ARG* 4.6 7.7 + - + +
1197B ILE* 6.3 0.2 - - + -
1226B PHE* 2.6 49.6 + - - +
1228B GLY* 3.3 16.6 + - - -
1230B ASP 2.8 11.7 + - - +
1231B HIS* 3.4 13.2 - - - +
1232B LEU 3.1 0.2 - - - -
1233B ASP* 1.3 73.7 - - - +
1235B LEU* 1.3 67.8 + - + +
1237B GLU* 3.2 2.8 + - - +
1238B ILE* 2.9 43.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1194B PRO* 3.8 40.8 - - + +
1197B ILE* 3.9 23.3 - - + -
1198B LEU* 3.6 25.6 - - + -
1231B HIS 3.9 8.7 - - - +
1232B LEU* 3.0 16.4 + - + +
1234B GLN* 1.3 77.7 - - + +
1236B LYS* 1.3 51.0 + - - +
1238B ILE* 3.0 9.5 + - + +
1239B MET* 2.7 53.0 + - + +
1258B ALA* 5.3 1.8 - - + -
1261B TYR* 4.0 21.5 - - + -
1262B MET* 4.5 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1232B LEU 3.5 2.2 + - - -
1233B ASP* 3.1 24.1 + - - +
1235B LEU* 1.3 78.8 - - - +
1237B GLU* 1.3 68.9 + - - +
1239B MET* 3.3 8.9 + - - +
1240B LYS* 2.9 25.1 + - + +
1261B TYR* 3.0 26.9 + - - +
1265B LEU* 3.4 25.7 - - + +
1266B PRO* 5.0 8.0 - - + +
1268B LEU* 4.6 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1225B LEU 5.2 2.1 - - - +
1226B PHE* 3.7 28.8 - - + -
1227B LYS 3.7 27.3 + - - +
1228B GLY* 4.0 9.0 - - - -
1233B ASP* 2.9 17.4 + - - +
1234B GLN* 3.2 8.5 + - - +
1236B LYS* 1.3 84.3 - - - +
1238B ILE* 1.3 64.0 + - - +
1240B LYS* 3.4 18.3 + - - +
1241B VAL* 3.8 4.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1192B ARG 3.8 22.2 - - - +
1194B PRO* 3.9 23.8 - - + -
1210B TRP* 3.7 27.1 - - + -
1226B PHE* 3.6 30.1 - - + -
1234B GLN* 2.9 31.7 + - + +
1235B LEU* 3.4 8.3 - - + +
1237B GLU* 1.3 75.4 - - - +
1239B MET* 1.3 56.4 + - + +
1241B VAL* 2.8 26.5 + - - +
1242B THR* 2.9 25.9 + - + +
1294B LEU* 4.5 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1194B PRO* 4.7 2.0 - - + -
1198B LEU* 4.0 20.2 - - + -
1235B LEU* 2.7 46.2 + - + +
1236B LYS* 3.6 5.4 - - - +
1238B ILE* 1.3 74.2 - - + +
1240B LYS* 1.3 58.7 + - - +
1242B THR* 3.9 2.0 - - - -
1243B GLY* 2.7 48.4 + - - +
1244B THR* 3.7 16.2 - - + -
1245B PRO* 3.8 9.2 - - + -
1262B MET* 3.5 38.4 - - + -
1265B LEU* 3.9 10.8 - - + -
1268B LEU* 3.8 11.2 - - + +
1294B LEU* 4.6 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1236B LYS* 2.9 15.9 + - + +
1237B GLU* 3.6 18.4 - - - +
1238B ILE 3.2 0.4 - - - -
1239B MET* 1.3 75.5 - - - +
1241B VAL* 1.3 60.3 + - + +
1268B LEU* 3.9 22.2 - - + +
1269B GLU 4.3 9.5 - - - +
1271B LYS* 4.7 6.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1225B LEU* 5.3 4.7 - - + +
1226B PHE* 3.3 35.4 - - + -
1237B GLU 3.9 5.8 - - - +
1238B ILE 2.8 7.9 + - - +
1240B LYS* 1.3 84.2 - - + +
1242B THR* 1.3 57.1 + - + +
1243B GLY 3.3 4.3 - - - -
1270B LYS* 3.7 4.9 - - - +
1271B LYS* 3.1 30.0 + - - +
1273B PHE* 3.7 17.9 - - + -
1276B ILE* 3.3 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1210B TRP* 4.1 6.3 - - + -
1226B PHE* 4.7 4.0 - - + -
1238B ILE* 2.9 33.4 + - + +
1239B MET* 3.9 1.0 - - - -
1241B VAL* 1.3 79.7 - - + +
1243B GLY* 1.3 71.9 + - - +
1270B LYS* 3.0 27.5 - - - +
1273B PHE* 4.8 5.6 - - + -
1292B LEU 3.8 21.3 - - - +
1293B VAL* 6.1 0.2 - - - -
1294B LEU* 3.5 30.5 - - + +
----------------------------------------------------------
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