Contacts of the helix formed by residues 1293 - 1311 (chain C) in PDB entry 3B13
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 MET1293 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1238C THR* 3.4 30.5 - - + +
1242C TYR* 4.5 0.4 - - - +
1288C PHE* 2.8 32.2 + - + +
1291C GLY 3.7 10.3 - - - +
1292C LYS* 1.3 76.3 - - - +
1294C TRP* 1.3 50.9 + - - +
1295C GLU* 2.7 18.3 + - - -
1296C GLU* 2.7 19.8 + - + +
1297C ALA 3.5 2.5 + - - -
1337C ARG* 4.4 0.2 - - - +
1364C ARG* 4.2 14.8 - - - +
1433C PHE* 4.0 16.2 - - + -
1437C ASN* 4.6 1.8 - - - +
1438C TYR* 3.1 49.8 + - + +
1476C PRO* 3.3 26.0 - - + -
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Residues in contact with TRP1294 (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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1289C ASP* 2.9 34.9 + - - -
1292C LYS* 3.1 25.7 + - + -
1293C MET* 1.3 75.0 - - - +
1295C GLU* 1.3 59.4 + - - +
1296C GLU 3.3 0.2 - - - -
1297C ALA* 3.8 7.4 - - + -
1298C ILE* 2.9 36.3 + - - +
1327C LYS* 6.2 0.2 - - - +
1328C PHE* 3.4 34.1 - + + +
1331C SER* 3.7 29.3 + - - -
1332C ILE* 3.7 28.0 - - + -
1335C ILE* 3.5 34.8 - - + -
1337C ARG* 3.4 43.3 - - + -
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Residues in contact with GLU1295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1293C MET 2.7 6.3 + - - -
1294C TRP* 1.3 72.9 - - - +
1296C GLU* 1.3 54.5 + - - -
1298C ILE* 3.6 6.3 + - - +
1299C SER* 3.0 25.6 + - - -
1332C ILE* 3.3 19.1 - - + +
1337C ARG* 2.3 49.1 + - - -
1420C ARG* 5.3 2.9 - - - +
1430C ILE* 5.1 2.1 - - - +
1433C PHE* 3.3 14.8 - - - +
1434C TYR* 3.5 26.9 - - - +
1438C TYR* 3.0 32.0 + - + +
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Residues in contact with GLU1296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1242C TYR* 2.6 40.3 + - - +
1245C LEU* 5.8 2.6 - - - +
1288C PHE* 3.7 29.8 - - + -
1293C MET* 2.7 14.6 + - + +
1295C GLU* 1.3 70.0 - - - +
1297C ALA* 1.3 65.8 + - - +
1299C SER* 2.9 22.6 + - - -
1300C LEU* 3.0 20.9 + - + +
1438C TYR* 3.9 20.7 - - + +
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Residues in contact with ALA1297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1285C ILE* 4.0 24.2 - - + +
1288C PHE* 4.2 13.6 - - + -
1289C ASP 4.8 2.0 - - - +
1293C MET 3.5 2.4 + - - -
1294C TRP* 3.4 16.1 + - - +
1296C GLU* 1.3 78.1 - - - +
1298C ILE* 1.3 64.1 + - - +
1300C LEU* 3.2 2.3 + - - +
1301C CYS* 2.9 28.7 + - - +
1328C PHE* 3.5 29.8 - - + -
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Residues in contact with ILE1298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1294C TRP 2.9 21.2 + - - +
1295C GLU* 3.8 5.8 - - - +
1297C ALA* 1.3 77.0 - - - +
1299C SER* 1.3 57.2 + - - +
1301C CYS* 3.3 7.7 + - - +
1302C LYS* 2.9 33.5 + - + +
1325C GLN* 3.9 11.2 - - - +
1328C PHE* 3.3 34.8 - - + -
1329C TYR* 3.3 63.9 - - + +
1332C ILE* 4.4 9.6 - - + -
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Residues in contact with SER1299 (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 GLU 3.0 14.8 + - - -
1296C GLU* 2.9 21.4 + - - -
1298C ILE* 1.3 77.0 - - - +
1300C LEU* 1.3 67.1 + - - -
1302C LYS* 3.1 16.5 + - - +
1303C GLU* 3.1 22.4 + - - +
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Residues in contact with LEU1300 (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 LEU* 4.0 20.2 - - + -
1281C TYR* 3.9 32.6 - - + +
1284C ILE* 3.3 36.3 - - + -
1285C ILE* 3.6 25.4 - - + -
1288C PHE* 4.5 5.8 - - + -
1296C GLU* 3.0 20.4 + - - +
1297C ALA 3.8 0.9 - - - +
1299C SER* 1.3 77.5 - - - +
1301C CYS* 1.3 68.2 + - - +
1303C GLU* 2.9 24.1 + - - +
1304C LEU* 3.0 14.6 + - - +
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Residues in contact with CYS1301 (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 ILE* 3.9 15.8 - - - +
1297C ALA 2.9 16.4 + - - +
1298C ILE* 3.3 10.1 - - - +
1300C LEU* 1.3 77.9 - - - +
1302C LYS* 1.3 63.9 + - - +
1303C GLU 3.1 0.3 + - - -
1304C LEU* 3.2 0.6 + - - -
1305C ALA 2.8 21.0 + - - -
1321C ASN* 3.4 27.7 + - - +
1324C GLN* 4.4 10.5 - - - -
1325C GLN* 3.6 25.8 - - + -
1328C PHE* 4.1 22.0 - - - -
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Residues in contact with LYS1302 (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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1309A GLU* 3.0 40.0 + - - +
1310A MET* 3.9 12.7 - - - +
1298C ILE* 2.9 26.2 + - + +
1299C SER* 3.1 14.8 + - - +
1301C CYS* 1.3 75.3 - - - +
1303C GLU* 1.3 62.4 + - + +
1305C ALA* 3.3 2.9 + - - +
1306C GLU* 3.0 23.9 + - - +
1325C GLN* 3.7 22.7 - - - +
1329C TYR* 4.5 3.8 - - - -
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Residues in contact with GLU1303 (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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1253C TRP* 3.3 26.4 + - + +
1277C LYS* 4.8 1.9 + - - -
1281C TYR* 2.7 35.4 + - + -
1299C SER 3.1 16.3 + - - +
1300C LEU* 2.9 17.9 + - - +
1302C LYS* 1.3 74.1 - - + +
1304C LEU* 1.3 66.9 + - - +
1306C GLU* 3.2 10.8 + - - +
1307C GLN* 3.0 24.6 + - - +
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Residues in contact with LEU1304 (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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1253C TRP* 3.7 21.7 - - + -
1278C GLU* 3.7 26.5 - - + +
1281C TYR* 3.7 30.9 - - + -
1282C GLU* 4.5 15.0 - - + -
1285C ILE* 3.9 18.6 - - + -
1300C LEU 3.0 3.6 + - - +
1301C CYS 3.7 6.1 - - - +
1303C GLU* 1.3 78.9 - - - +
1305C ALA* 1.3 58.7 + - - +
1307C GLN* 3.0 10.6 + - + +
1308C TYR* 2.9 51.4 + - + +
1321C ASN* 3.7 12.8 - - - +
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Residues in contact with ALA1305 (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 CYS 2.8 10.7 + - - +
1302C LYS* 3.7 4.3 - - - +
1304C LEU* 1.3 73.2 - - - +
1306C GLU* 1.3 67.0 + - - +
1308C TYR* 3.2 10.8 + - - +
1309C GLU* 2.9 28.8 + - - +
1318C LEU* 3.8 15.8 - - + +
1321C ASN* 3.1 26.0 - - - +
1322C LEU* 5.1 3.4 - - + -
1325C GLN* 4.1 8.7 - - - +
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Residues in contact with GLU1306 (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 LYS 3.0 14.1 + - - +
1303C GLU* 3.2 10.7 + - - +
1305C ALA* 1.3 76.5 - - - +
1307C GLN* 1.3 64.3 + - - +
1309C GLU* 4.5 8.5 - - - +
1310C MET* 2.9 49.9 + - + +
1311C GLU* 4.4 4.0 - - - +
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Residues in contact with GLN1307 (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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1253C TRP* 3.3 58.1 - - + +
1274C ARG* 3.0 34.7 + - - +
1303C GLU 3.0 17.1 + - - +
1304C LEU* 3.0 13.1 + - + +
1306C GLU* 1.3 80.0 - - - +
1308C TYR* 1.3 66.3 + - + +
1311C GLU* 2.9 43.8 + - - +
1312C ILE* 3.1 13.2 + - + +
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Residues in contact with TYR1308 (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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1278C GLU* 2.8 41.2 + - - +
1282C GLU* 3.7 9.0 + - - -
1304C LEU* 2.9 46.7 + - + +
1305C ALA* 3.8 6.7 - - - +
1307C GLN* 1.3 79.3 - - + +
1309C GLU* 1.3 59.2 + - - +
1312C ILE* 3.7 24.9 - - + -
1313C PHE* 3.0 27.7 - - - -
1314C ASP* 3.1 20.1 + - + +
1315C TYR* 4.2 1.9 - - - -
1317C LEU* 3.4 48.8 - - + +
1318C LEU* 3.9 11.2 - - + -
1321C ASN* 4.1 9.0 - - + -
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Residues in contact with GLU1309 (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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1302A LYS* 3.1 34.6 + - - -
1329A TYR* 3.5 20.1 + - + +
1420A ARG* 3.6 23.4 + - - +
1305C ALA* 2.9 17.7 + - - +
1306C GLU* 4.2 7.4 - - - +
1308C TYR* 1.3 79.8 - - - +
1310C MET* 1.3 85.9 + - - +
1311C GLU 3.6 0.2 - - - -
1313C PHE* 3.5 23.6 - - - -
1315C TYR* 4.4 6.6 + - + -
1318C LEU* 3.7 18.3 - - + +
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Residues in contact with MET1310 (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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1302A LYS* 5.6 0.9 - - + -
1420A ARG* 3.5 42.9 - - - +
1424A LYS* 4.2 8.0 - - - +
1306C GLU* 2.9 43.0 + - + +
1309C GLU* 1.3 101.0 - - + +
1311C GLU* 1.3 75.5 + - + +
1313C PHE* 3.6 17.5 - - - -
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Residues in contact with GLU1311 (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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1424A LYS* 3.4 27.8 - - - +
1425A PRO* 3.6 15.4 - - - +
1274C ARG* 3.9 15.0 + - - +
1306C GLU* 4.4 3.9 - - - +
1307C GLN* 2.9 45.7 + - - +
1309C GLU 3.6 1.6 - - - -
1310C MET* 1.3 97.0 - - + +
1312C ILE* 1.3 60.9 + - - +
1313C PHE* 3.4 14.3 - - - -
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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
------------------------------------------------------------
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