Contacts of the helix formed by residues 1364 - 1373 (chain C) in PDB entry 5Y3R
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 CYS1364 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1296C PHE* 3.4 31.6 - - + +
1297C PHE* 6.0 0.2 - - - -
1299C GLU* 4.6 6.3 - - + +
1300C SER* 5.1 6.7 - - - +
1362C ASP* 3.4 22.4 - - - -
1363C LEU* 1.3 75.7 - - - +
1365C ASN* 1.3 58.0 - - - +
1366C THR 3.2 2.9 - - - -
1367C HIS* 2.7 24.4 + - + -
1368C LEU* 2.5 62.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1365 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1356C TRP* 5.5 0.5 - - - -
1360C LYS 4.8 0.6 + - - -
1362C ASP* 2.5 60.1 + - - +
1363C LEU* 3.1 8.2 - - - +
1364C CYS* 1.3 78.1 - - - +
1366C THR* 1.3 64.1 + - + +
1368C LEU* 4.1 5.3 - - - +
1369C MET* 3.6 22.3 + - - +
1411C TYR* 2.5 38.6 + - - +
1414C ILE* 4.9 10.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1366 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1363C LEU 4.6 1.6 + - - -
1365C ASN* 1.3 80.0 - - + +
1367C HIS* 1.3 70.6 + - - +
1369C MET* 3.3 6.3 + - - +
1370C ARG* 2.4 64.7 + - - +
1417C THR* 6.2 0.2 - - - +
1421C GLU* 5.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1367 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1299C GLU 5.8 0.7 - - - -
1300C SER* 3.2 37.0 + - - +
1303C MET* 3.6 26.7 - - + +
1304C HIS* 4.3 7.6 + + - -
1363C LEU* 3.0 30.5 + - + -
1364C CYS* 2.7 25.1 + - + +
1366C THR* 1.3 72.9 + - - +
1368C LEU* 1.3 56.3 + - - +
1370C ARG* 2.7 49.7 + - - +
1371C VAL* 2.9 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1368 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1299C GLU* 3.5 38.1 - - + +
1342C MET* 4.1 13.9 - - + +
1345C THR* 5.1 13.9 - - + -
1362C ASP* 3.9 14.4 - - + +
1364C CYS* 2.5 43.8 + - + +
1365C ASN* 4.1 4.5 - - - +
1367C HIS* 1.3 71.4 - - + +
1369C MET* 1.3 77.2 + - + +
1371C VAL* 2.9 25.7 - - + +
1372C LEU* 3.0 15.8 + - - +
1402C LEU* 5.9 3.4 - - + -
1406C LEU* 5.7 7.6 - - + -
1414C ILE* 5.9 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1369 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1365C ASN 3.6 14.8 + - - +
1366C THR* 3.3 8.4 + - - +
1367C HIS 3.1 0.8 - - - -
1368C LEU* 1.3 98.3 - - + +
1370C ARG* 1.3 57.6 + - - +
1372C LEU* 5.1 1.6 - - + -
1373C VAL* 3.1 10.2 + - - +
1402C LEU* 4.7 8.7 - - + -
1403C MET* 3.9 8.7 - - - -
1406C LEU* 3.7 23.6 - - + -
1413C ASP 5.0 0.7 - - - +
1414C ILE* 2.9 42.4 - - + +
1417C THR* 5.4 2.0 - - - +
1418C HIS* 2.7 56.3 + - + +
1421C GLU* 3.2 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1370 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1303C MET* 3.4 31.9 - - + +
1366C THR* 2.4 50.0 + - - +
1367C HIS* 2.7 48.7 + - - +
1369C MET* 1.3 73.4 - - - +
1371C VAL* 1.3 58.5 + - - +
1373C VAL* 3.1 19.8 - - + +
1374C GLN* 4.3 7.4 + - - +
1421C GLU* 4.1 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1371 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1299C GLU* 5.4 4.5 - - + +
1302C ALA* 6.6 0.4 - - + -
1303C MET* 5.0 16.3 - - + -
1306C ILE* 5.5 11.2 - - + -
1338C VAL* 4.2 21.8 - - + -
1342C MET* 3.9 16.4 - - + -
1367C HIS 2.9 13.8 + - - +
1368C LEU* 2.9 26.2 - - + +
1370C ARG* 1.3 76.5 - - - +
1372C LEU* 1.3 64.8 + - - +
1373C VAL 3.2 0.2 - - - -
1374C GLN* 2.8 27.0 + - - +
1378C GLU* 4.3 10.0 - - + +
1382C ILE* 5.7 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1372 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1338C VAL* 5.8 3.1 - - + -
1342C MET* 4.8 6.3 - - + -
1368C LEU 3.0 16.5 + - - +
1369C MET* 5.0 1.3 - - + -
1371C VAL* 1.3 81.7 - - + +
1373C VAL* 1.3 64.9 + - - +
1374C GLN 3.0 9.1 + - - -
1375C THR* 3.5 6.0 + - - +
1378C GLU* 4.7 11.2 - - - +
1395C LEU* 4.9 7.6 - - + -
1398C VAL* 4.8 10.5 - - + -
1399C CYS* 3.4 38.3 - - + -
1402C LEU* 3.5 29.6 - - + -
1403C MET* 3.6 22.0 - - - -
1418C HIS* 3.9 9.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1373 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1369C MET 3.1 16.1 + - - +
1370C ARG* 3.1 24.2 - - + +
1372C LEU* 1.3 76.0 - - - +
1374C GLN* 1.3 69.8 + - + +
1375C THR* 3.4 6.4 + - - +
1376C LEU* 4.8 6.9 - - - +
1418C HIS* 3.2 21.6 - - + +
1421C GLU* 3.2 30.5 - - + +
1422C LYS* 5.1 8.1 - - + +
----------------------------------------------------------
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