Contacts of the helix formed by residues 1295 - 1309 (chain C) in PDB entry 2OM2
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 THR1295 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1278C ILE* 4.1 3.8 - - - -
1293C SER* 3.0 30.1 + - - +
1294C ASN* 1.3 79.8 - - - +
1296C TYR* 1.3 66.0 + - - +
1297C GLU* 4.1 10.5 + - - +
1298C GLU* 3.4 17.5 + - - +
1299C ALA* 3.1 22.0 + - - +
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Residues in contact with TYR1296 (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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1227C LEU* 5.7 0.4 - - + -
1271C LYS* 3.6 48.3 + - + +
1274C PHE* 3.7 17.6 - + - -
1275C GLU* 3.6 44.2 - - + +
1278C ILE* 3.9 16.9 - - + +
1295C THR* 1.3 71.8 - - - +
1297C GLU* 1.3 89.6 + - + +
1300C ALA* 3.0 36.9 + - + +
1323C PHE* 4.7 11.4 - + - +
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Residues in contact with GLU1297 (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 THR* 4.1 9.3 - - - +
1296C TYR* 1.3 104.7 + - + +
1298C GLU* 1.3 63.0 + - - +
1300C ALA* 3.9 2.1 - - - +
1301C ALA* 3.0 26.3 + - - +
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Residues in contact with GLU1298 (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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1290C TYR* 3.3 16.8 + - + +
1292C GLY* 3.3 15.1 - - - -
1293C SER* 2.4 41.8 + - - +
1295C THR* 3.4 15.2 + - - +
1297C GLU* 1.3 79.3 - - - +
1299C ALA* 1.3 58.4 - - - +
1301C ALA* 3.5 5.1 + - - +
1302C TYR* 2.9 28.0 + - + +
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Residues in contact with ALA1299 (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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1274C PHE* 3.6 19.5 - - + -
1278C ILE* 3.8 17.0 - - + -
1283C LEU* 3.8 17.5 - - + +
1290C TYR* 3.7 11.1 + - + +
1293C SER 4.4 3.6 - - - +
1295C THR 3.1 18.5 + - - +
1298C GLU* 1.3 74.6 - - - +
1300C ALA* 1.3 65.5 + - - +
1302C TYR* 3.2 3.3 + - - +
1303C ILE* 3.0 26.5 + - - +
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Residues in contact with ALA1300 (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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1227C LEU* 4.7 6.0 - - + +
1268C LEU* 4.6 0.5 - - - +
1274C PHE* 3.6 20.8 - - + -
1296C TYR* 3.0 28.6 + - + +
1297C GLU* 3.9 3.4 - - - +
1299C ALA* 1.3 78.1 - - - +
1301C ALA* 1.3 58.5 + - - +
1303C ILE* 3.2 8.6 + - - +
1304C GLN* 3.0 26.3 + - - +
1323C PHE* 4.0 26.6 - - + -
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Residues in contact with ALA1301 (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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1297C GLU 3.0 19.0 + - - +
1298C GLU* 3.9 5.6 - - - +
1300C ALA* 1.3 76.9 - - - +
1302C TYR* 1.3 58.7 + - - +
1304C GLN* 3.5 18.2 + - - +
1305C CYS* 2.9 27.9 + - - +
1323C PHE* 4.8 4.0 - - + -
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Residues in contact with TYR1302 (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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1283C LEU* 3.6 17.5 - - + -
1287C TYR* 3.8 21.1 - + + -
1289C GLU* 2.6 33.1 + - - +
1290C TYR* 3.5 38.5 - + + -
1298C GLU* 2.9 19.0 + - + +
1299C ALA 3.4 5.2 - - - +
1300C ALA 3.2 0.2 - - - -
1301C ALA* 1.3 75.5 - - - +
1303C ILE* 1.3 65.1 + - - +
1305C CYS* 3.2 6.9 + - + +
1306C GLN* 3.0 63.4 + - + +
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Residues in contact with ILE1303 (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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1225C VAL* 5.1 0.7 - - + -
1227C LEU* 3.7 35.2 - - + +
1230C TYR* 4.4 0.7 - - + -
1243C MET* 4.2 14.6 - - + -
1268C LEU* 4.8 3.8 - - + -
1274C PHE* 3.6 34.3 - - + -
1283C LEU* 4.1 12.6 - - + -
1287C TYR* 4.0 21.3 - - + +
1299C ALA 3.0 13.7 + - - +
1300C ALA* 3.2 6.3 + - - +
1302C TYR* 1.3 74.7 - - - +
1304C GLN* 1.3 68.7 + - - +
1306C GLN* 3.0 17.6 + - - +
1307C PHE* 3.2 33.1 + - + -
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Residues in contact with GLN1304 (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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1266C LEU* 5.2 0.9 - - + -
1268C LEU* 3.4 27.5 - - + +
1300C ALA 3.0 10.4 + - - +
1301C ALA* 3.6 16.0 - - - +
1303C ILE* 1.3 75.0 - - - +
1305C CYS* 1.3 60.4 + - - +
1307C PHE* 3.1 8.1 + - - +
1308C GLU* 3.0 53.2 + - + +
1321C THR* 3.5 26.8 - - + +
1323C PHE* 3.6 21.6 - - + -
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Residues in contact with CYS1305 (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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1301C ALA 2.9 15.5 + - - +
1302C TYR* 3.3 15.3 - - + +
1304C GLN* 1.3 79.1 - - - +
1306C GLN* 1.3 65.1 + - - +
1308C GLU* 4.6 4.7 - - - +
1309C ASP* 2.9 59.2 + - - -
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Residues in contact with GLN1306 (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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1247C MET* 4.0 12.9 - - + +
1287C TYR* 3.6 39.4 - - + +
1289C GLU* 4.1 6.4 - - - +
1302C TYR* 3.0 62.9 + - + +
1303C ILE 3.0 5.4 + - - +
1305C CYS* 1.3 87.7 - - - +
1307C PHE* 1.3 61.3 + - - +
1309C ASP* 4.0 9.4 + - - +
1310C LEU* 3.3 24.6 + - - +
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Residues in contact with PHE1307 (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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1223C PHE* 4.2 0.4 - + - -
1225C VAL* 3.5 37.7 - - + -
1243C MET* 3.8 21.5 - - + -
1246C SER* 3.6 20.6 - - - -
1247C MET* 3.5 38.8 - - + -
1250C PHE* 3.4 39.3 - + + -
1266C LEU* 4.1 18.8 - - + -
1268C LEU* 4.8 3.8 - - + -
1287C TYR* 4.4 1.1 - - - -
1303C ILE* 3.2 28.1 + - + -
1304C GLN 3.1 7.9 + - - +
1305C CYS 3.1 0.6 - - - -
1306C GLN* 1.3 76.1 - - - +
1308C GLU* 1.3 65.9 + - - +
1310C LEU* 3.1 25.0 + - - +
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Residues in contact with GLU1308 (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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1250C PHE* 4.7 4.9 - - - -
1266C LEU* 4.5 4.7 - - + -
1304C GLN* 3.0 42.5 + - + +
1305C CYS* 4.2 3.8 - - - +
1307C PHE* 1.3 75.1 - - - +
1309C ASP* 1.3 59.4 + - - +
1310C LEU 3.0 0.2 - - - -
1311C ASN* 2.9 31.2 + - + +
1314C LYS* 4.0 7.6 - - - +
1319C ILE* 3.4 30.5 - - + +
1321C THR* 2.7 25.9 + - - +
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Residues in contact with ASP1309 (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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1305C CYS* 2.9 42.4 + - - +
1306C GLN* 4.2 11.3 + - - +
1308C GLU* 1.3 77.4 - - - +
1310C LEU* 1.3 63.5 + - + +
1311C ASN 3.3 0.5 + - - -
1312C LYS* 3.7 14.6 + - - -
1314C LYS* 3.4 29.4 + - - +
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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
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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