Contacts of the helix formed by residues 1235 - 1246 (chain B) in PDB entry 3ETA
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 PRO1235 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1106B LEU* 3.4 38.1 - - + -
1109B MET* 5.7 4.3 - - - -
1203B THR* 5.0 5.8 - - + -
1233B ASN 3.7 6.5 - - - +
1234B CYS* 1.3 92.7 - - - +
1236B GLU* 1.3 65.9 + - - +
1237B ARG* 2.9 8.3 + - + +
1238B VAL* 3.1 26.3 + - + -
1239B THR* 3.1 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1234B CYS 3.7 1.8 + - - -
1235B PRO* 1.3 71.7 - - - +
1237B ARG* 1.3 52.3 + - - +
1239B THR* 3.4 11.0 + - - +
1240B ASP* 2.8 42.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1106B LEU* 6.1 1.8 - - - +
1110B ILE* 4.3 21.3 - - - +
1235B PRO* 2.9 4.4 + - + -
1236B GLU* 1.3 75.1 - - - +
1238B VAL* 1.3 67.4 + - + +
1240B ASP* 3.5 8.9 + - - +
1241B LEU* 3.3 26.5 + - + +
1262B LEU* 3.2 27.0 + - + +
1263B LEU* 3.9 30.2 + - + +
1265B ASP* 5.6 2.0 - - - +
1266B ASP* 3.0 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1106B LEU* 4.8 1.6 - - + -
1109B MET* 5.9 4.7 - - + -
1110B ILE* 4.0 26.7 - - + -
1113B ALA* 6.3 0.4 - - + -
1199B LEU* 4.2 23.1 - - + -
1203B THR* 4.3 15.9 - - + -
1234B CYS* 4.2 5.4 - - - -
1235B PRO* 3.1 24.7 + - + +
1237B ARG* 1.3 76.5 - - + +
1239B THR* 1.3 63.8 + - - +
1241B LEU* 3.3 13.2 + - + +
1242B MET* 3.1 40.3 + - + +
1263B LEU* 5.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1230B GLN* 2.9 44.3 + - + +
1234B CYS* 3.4 20.3 + - - +
1235B PRO 3.1 9.3 + - - -
1236B GLU* 3.4 14.3 - - - +
1238B VAL* 1.3 76.7 - - - +
1240B ASP* 1.3 67.5 + - - +
1242B MET* 3.3 5.9 + - - +
1243B ARG* 3.0 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1236B GLU* 2.8 27.4 + - - +
1237B ARG* 3.6 9.5 - - - +
1239B THR* 1.3 77.9 - - - +
1241B LEU* 1.3 63.3 + - + +
1243B ARG* 3.3 10.2 + - - +
1244B MET* 3.0 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1113B ALA* 5.7 0.9 - - + -
1199B LEU* 3.8 22.9 - - + -
1237B ARG* 3.3 16.7 + - + +
1238B VAL* 3.3 14.1 + - + +
1240B ASP* 1.3 77.4 - - + +
1242B MET* 1.3 51.7 + - - +
1244B MET* 3.1 9.2 + - + +
1245B CYS* 2.8 40.3 + - - -
1254B PRO* 4.8 1.5 - - + +
1259B ILE* 3.6 42.2 - - + -
1262B LEU* 3.7 27.8 - - + -
1263B LEU* 4.4 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1196B GLY 3.5 18.8 - - - +
1199B LEU* 3.9 12.7 - - + +
1200B TRP* 3.9 20.4 - - - -
1203B THR* 4.0 11.0 - - - +
1230B GLN* 3.5 17.7 - - - +
1231B PRO* 4.6 0.7 - - + -
1234B CYS* 3.5 31.9 - - - -
1238B VAL* 3.1 25.6 + - + +
1239B THR 3.4 9.0 - - - +
1241B LEU* 1.3 76.9 - - - +
1243B ARG* 1.3 63.7 + - - +
1245B CYS* 3.2 8.9 + - - +
1246B TRP* 3.0 58.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1227B TYR* 4.3 27.4 - - - -
1230B GLN* 4.4 15.7 - - - +
1239B THR* 3.0 25.3 + - + +
1240B ASP* 3.6 11.4 - - - +
1242B MET* 1.3 75.3 - - - +
1244B MET* 1.3 70.9 + - + +
1246B TRP* 3.3 15.2 + - - +
1247B GLN* 3.4 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1240B ASP 3.0 16.3 + - - +
1241B LEU* 3.1 11.6 + - + +
1243B ARG* 1.3 79.9 - - + +
1245B CYS* 1.3 65.5 + - - +
1247B GLN* 3.1 55.6 + - - +
1252B MET* 4.7 7.9 - - - +
1253B ARG* 3.5 2.6 - - - +
1254B PRO* 3.5 27.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1192B MET* 3.5 43.1 - - - +
1193B TRP* 3.6 11.8 - - - -
1195B PHE* 4.0 9.4 - - - -
1196B GLY* 3.6 24.2 - - - -
1199B LEU* 5.0 1.1 - - - -
1241B LEU 2.8 19.7 + - - -
1242B MET 3.2 8.9 + - - +
1244B MET* 1.3 76.7 - - - +
1246B TRP* 1.3 60.1 + - + +
1247B GLN 3.3 0.9 - - - -
1253B ARG* 3.2 25.8 + - - -
1254B PRO* 4.1 10.3 - - - -
1259B ILE* 4.9 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1193B TRP* 3.4 61.4 + + + -
1196B GLY 3.3 25.3 - - - -
1197B VAL* 3.5 13.4 - - + +
1200B TRP* 4.0 5.6 - + + -
1210B TYR* 5.9 0.4 - - - -
1227B TYR* 4.1 40.0 - + + -
1228B LEU* 3.7 46.2 - - + -
1230B GLN* 3.9 10.8 - - - -
1242B MET* 3.0 49.3 + - + +
1243B ARG* 3.3 10.9 + - - +
1244B MET 3.1 0.8 - - - -
1245B CYS* 1.3 83.3 - - + +
1247B GLN* 1.3 64.9 + - - +
1248B PHE* 3.3 2.6 + - - -
----------------------------------------------------------
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