Contacts of the helix formed by residues 1292 - 1308 (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 LYS1292 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1228C GLY 5.2 1.0 + - - -
1232C PRO* 3.3 24.9 - - - +
1261C LEU* 5.1 0.7 - - - -
1265C GLU* 3.2 36.5 + - - +
1275C THR 5.9 0.2 - - - -
1279C LEU* 4.0 31.7 + - - +
1288C SER* 2.7 38.1 + - - +
1291C LEU* 1.3 76.0 - - + +
1293C ALA* 1.3 57.6 + - - +
1295C ALA* 2.9 27.1 + - - +
1296C PHE* 3.0 7.8 + - - -
1344C PHE* 4.7 7.0 - - + -
1358C LEU* 4.8 14.8 - - + -
1361C LYS* 3.1 28.0 + - - +
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Residues in contact with ALA1293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1285C GLU* 4.9 17.0 - - + +
1288C SER 3.3 5.4 + - - +
1289C SER* 3.6 16.6 - - - +
1292C LYS* 1.3 70.1 - - - +
1294C VAL* 1.3 65.1 + - - +
1295C ALA 2.9 4.3 - - - -
1296C PHE* 2.9 20.0 + - + +
1297C PHE* 2.9 40.1 + - + -
1361C LYS* 3.2 16.1 - - + +
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Residues in contact with VAL1294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1233C SER 4.6 2.0 - - - +
1234C GLY* 4.7 1.1 - - - +
1237C ALA* 3.8 14.6 - - + -
1238C GLN* 2.9 35.7 - - + +
1261C LEU* 6.0 0.4 - - + -
1289C SER 3.7 6.2 + - - +
1290C LEU* 3.2 27.6 - - + +
1291C LEU 3.1 21.5 - - - +
1293C ALA* 1.3 78.2 - - - +
1295C ALA* 1.3 55.8 + - - +
1297C PHE* 3.6 12.0 - - + -
1298C LEU* 2.8 39.5 + - + +
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Residues in contact with ALA1295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1261C LEU* 3.9 22.0 - - + -
1291C LEU 3.7 8.5 - - - +
1292C LYS* 2.9 20.2 + - - +
1294C VAL* 1.3 81.2 - - - +
1296C PHE* 1.3 67.1 + - - +
1298C LEU* 3.3 8.1 + - - +
1299C GLU* 2.9 18.2 + - - +
1341C ILE* 3.9 19.2 - - + +
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Residues in contact with PHE1296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1292C LYS 3.0 8.6 + - - -
1293C ALA* 2.9 16.6 + - - +
1295C ALA* 1.3 72.9 - - - +
1297C PHE* 1.3 66.5 + + + +
1298C LEU 2.8 1.0 + - - -
1299C GLU* 2.4 37.6 + - - +
1300C SER* 2.8 9.7 + - - -
1341C ILE* 5.8 0.7 - - - -
1345C THR* 6.1 2.0 - - + -
1348C LEU* 6.5 0.7 - - + -
1358C LEU* 3.3 24.9 - - + -
1361C LYS* 3.0 58.6 - - + -
1362C ASP* 3.2 23.3 - - + -
1363C LEU 4.8 1.8 - - - +
1364C CYS* 3.4 27.6 - - + +
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Residues in contact with PHE1297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1238C GLN* 2.5 39.0 + - - +
1285C GLU* 5.4 6.5 - - - -
1289C SER 5.5 0.4 - - - -
1293C ALA* 2.9 43.6 + - + +
1294C VAL* 3.6 6.7 - - + -
1296C PHE* 1.3 90.1 - + + +
1298C LEU* 1.3 53.9 + - - +
1300C SER* 3.1 15.5 - - - -
1301C ILE* 2.8 16.6 + - - +
1361C LYS 4.5 2.5 - - - -
1363C LEU* 3.6 40.4 - - + -
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Residues in contact with LEU1298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1237C ALA* 3.7 21.3 - - + +
1238C GLN* 3.0 32.7 + - + +
1241C LEU* 4.0 11.0 - - + -
1253C THR* 5.4 2.9 - - + -
1254C LEU* 5.0 8.1 - - + -
1258C ASP* 5.2 10.8 - - - +
1294C VAL* 2.8 41.3 + - + +
1295C ALA* 3.6 8.1 - - - +
1297C PHE* 1.3 73.6 - - - +
1299C GLU* 1.3 60.3 + - - +
1301C ILE* 3.0 25.1 + - + +
1302C ALA* 2.9 22.0 + - - +
1337C VAL* 4.9 3.1 - - - +
1341C ILE* 4.9 7.2 - - + -
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Residues in contact with GLU1299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1295C ALA 2.9 11.9 + - - +
1296C PHE* 2.4 29.7 + - - +
1298C LEU* 1.3 65.9 - - - +
1300C SER* 1.3 55.2 + - - +
1302C ALA* 2.7 30.7 + - + +
1303C MET* 3.0 12.2 + - - +
1337C VAL* 5.0 3.1 - - + -
1338C VAL* 4.2 7.5 - - + +
1341C ILE* 3.1 34.1 - - + +
1342C MET* 3.3 38.3 + - - +
1345C THR* 4.0 6.1 + - - +
1364C CYS* 4.6 10.0 - - + -
1367C HIS* 5.8 0.9 - - - -
1368C LEU* 3.5 22.1 - - + +
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Residues in contact with SER1300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1296C PHE 2.8 5.5 + - - -
1297C PHE* 3.1 23.6 - - - -
1299C GLU* 1.3 76.5 - - - +
1301C ILE* 1.3 54.2 + - - -
1303C MET* 3.3 3.0 + - - +
1304C HIS* 2.7 65.9 + - - -
1363C LEU 6.4 0.2 - - - -
1364C CYS* 5.1 5.9 - - - +
1367C HIS* 3.2 34.1 + - - -
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Residues in contact with ILE1301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1238C GLN* 3.1 34.3 - - + +
1241C LEU* 3.6 23.3 - - + -
1242C LEU* 3.6 40.6 - - + -
1297C PHE 2.8 20.9 + - - +
1298C LEU* 3.0 16.7 + - + +
1300C SER* 1.3 73.0 - - - +
1302C ALA* 1.3 60.5 + - - +
1304C HIS* 3.1 26.7 - - + +
1305C ASP* 2.8 29.6 + - + +
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Residues in contact with ALA1302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1298C LEU 2.9 6.5 + - - +
1299C GLU* 2.7 20.0 + - + +
1301C ILE* 1.3 70.0 - - - +
1303C MET* 1.3 67.0 + - - +
1305C ASP* 2.5 39.1 + - - +
1306C ILE* 3.0 11.4 + - + +
1334C LYS* 5.1 4.5 - - + +
1337C VAL* 3.7 31.0 - - + -
1338C VAL* 5.5 3.4 - - + +
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Residues in contact with MET1303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1299C GLU 3.0 10.2 + - - +
1300C SER* 3.5 11.0 - - - +
1302C ALA* 1.3 74.2 - - - +
1304C HIS* 1.3 62.0 + - + +
1306C ILE* 3.1 12.9 + - - +
1307C ILE* 2.9 45.2 + - + +
1367C HIS* 3.6 47.3 - - + +
1370C ARG* 3.4 42.8 - - + +
1371C VAL* 5.0 14.9 - - + +
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Residues in contact with HIS1304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1238C GLN* 5.4 1.1 - - - -
1242C LEU* 5.4 3.1 - - + +
1300C SER* 2.7 47.3 + - - +
1301C ILE* 3.1 35.0 - - + +
1303C MET* 1.3 81.7 - - + +
1305C ASP* 1.3 56.9 + - - +
1307C ILE* 2.6 41.4 + - + +
1308C ALA* 3.4 7.4 + - - +
1367C HIS* 4.3 8.1 + + - -
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Residues in contact with ASP1305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1245C ARG* 5.8 6.7 - - - +
1301C ILE* 2.8 16.0 + - + +
1302C ALA* 2.5 42.7 + - - +
1304C HIS* 1.3 72.1 - - - +
1306C ILE* 1.3 73.4 + - - +
1308C ALA 4.8 5.5 - - - +
1330C TYR* 3.8 18.6 + - - +
1334C LYS* 3.0 44.1 - - - +
1337C VAL* 5.6 1.6 - - - +
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Residues in contact with ILE1306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1302C ALA* 3.0 29.8 + - + +
1303C MET* 3.7 8.5 - - - +
1305C ASP* 1.3 92.7 + - - +
1307C ILE* 1.3 66.8 + - + +
1308C ALA 3.4 6.3 - - - +
1334C LYS* 4.8 1.8 - - + -
1371C VAL* 5.5 10.1 - - + -
1374C GLN* 6.1 1.6 - - - +
1377C CYS* 6.2 2.7 - - + -
1381C SER* 4.5 20.0 - - - +
1382C ILE* 3.5 34.8 - - + -
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Residues in contact with ILE1307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1303C MET* 2.9 47.8 + - + +
1304C HIS* 2.6 32.7 + - + +
1306C ILE* 1.3 74.1 - - + +
1308C ALA* 1.3 69.6 + - + +
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Residues in contact with ALA1308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1245C ARG* 6.5 0.9 - - - -
1304C HIS 3.4 6.0 + - - +
1305C ASP 4.8 4.6 - - - +
1306C ILE 3.4 9.3 - - - +
1307C ILE* 1.3 91.1 - - + +
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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
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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) + - + + + + + -
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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