Contacts of the helix formed by residues 1370 - 1389 (chain A) in PDB entry 5IYB
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 GLY1370 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1365A ILE 3.6 2.0 + - - -
1366A PHE* 3.0 21.4 + - - -
1368A VAL 3.7 0.8 + - - -
1369A LEU* 1.3 79.3 - - - +
1371A ILE* 1.3 52.7 + - - -
1372A GLU* 3.3 2.2 - - - +
1373A ALA* 2.8 33.3 + - - +
1374A VAL* 3.7 3.5 + - - -
177E ASP* 3.0 22.2 - - - -
178E PRO* 4.2 2.8 - - - +
179E VAL* 4.4 4.3 - - - -
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Residues in contact with ILE1371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1366A PHE* 3.8 19.7 - - + -
1370A GLY* 1.3 68.5 - - - -
1372A GLU* 1.3 66.3 + - + +
1373A ALA 3.3 0.2 - - - -
1374A VAL* 3.4 4.5 + - + -
1375A ARG* 3.1 19.4 + - - +
1406A THR* 3.8 26.2 - - + +
1409A GLY 3.3 26.0 - - - +
1411A LEU* 3.9 18.4 - - + -
173E ILE* 3.9 33.7 - - + -
174E GLN* 5.0 1.6 - - - +
177E ASP* 3.5 6.4 + - - +
207E ARG* 3.2 35.2 + - - +
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Residues in contact with GLU1372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1370A GLY 2.9 4.2 + - - +
1371A ILE* 1.3 82.2 - - + +
1373A ALA* 1.3 62.7 + - - +
1375A ARG* 3.1 16.0 + - - +
1376A LYS* 3.2 15.6 + - - +
145E VAL* 5.8 0.9 - - + -
146E PRO* 3.6 23.8 - - + +
148E HIS* 3.6 17.9 - - + +
179E VAL* 6.2 2.4 - - + +
193E ILE* 3.2 36.8 - - + +
195E ARG* 3.0 34.1 + - - -
207E ARG* 2.7 32.1 + - - -
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Residues in contact with ALA1373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1365A ILE* 4.2 4.9 - - + -
1369A LEU* 3.4 33.1 + - + +
1370A GLY 2.8 17.3 + - - +
1372A GLU* 1.3 73.4 - - - +
1374A VAL* 1.3 56.2 + - - +
1376A LYS* 3.3 3.1 + - - +
1377A ALA* 2.8 30.5 + - - +
144E LEU* 3.9 30.2 + - + +
145E VAL* 4.2 6.9 - - + +
146E PRO* 4.9 0.8 - - - +
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Residues in contact with VAL1374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1362A ILE* 3.7 21.8 - - + +
1365A ILE* 3.9 10.1 - - + -
1366A PHE* 3.5 50.9 - - + +
1370A GLY 3.7 2.2 + - - +
1371A ILE* 3.4 8.2 + - + +
1372A GLU 3.2 0.4 - - - -
1373A ALA* 1.3 74.6 - - - +
1375A ARG* 1.3 66.6 + - - +
1377A ALA* 4.4 2.5 - - - +
1378A LEU* 2.8 38.7 + - + +
1406A THR* 4.6 2.5 - - + -
1411A LEU* 3.5 28.9 - - + -
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Residues in contact with ARG1375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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893A GLU* 3.0 25.7 + - - -
1371A ILE 3.1 13.2 + - - +
1372A GLU* 3.1 15.0 + - - +
1374A VAL* 1.3 78.0 - - - +
1376A LYS* 1.3 66.7 + - + +
1378A LEU* 4.2 2.5 - - - +
1379A GLU* 2.3 55.1 + - - +
1395A TYR* 3.3 5.7 + - - -
1399A ALA* 3.5 22.5 + - - +
1402A CYS* 4.3 12.5 - - + +
1403A ASP* 2.8 41.8 + - - +
1406A THR* 4.3 20.8 - - + +
195E ARG* 3.6 25.3 - - - +
207E ARG* 6.0 1.3 - - - +
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Residues in contact with LYS1376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1372A GLU 3.2 11.0 + - - +
1373A ALA 3.7 5.8 - - - +
1375A ARG* 1.3 82.1 - - + +
1377A ALA* 1.3 58.0 + - - +
1379A GLU* 3.0 37.4 + - - +
1380A ARG* 2.9 54.0 + - - +
143E GLU 5.8 1.3 - - - -
144E LEU* 3.7 37.2 - - + +
146E PRO* 5.8 1.6 - - + -
195E ARG* 6.1 6.7 - - + -
196E PRO* 5.5 18.7 + - + +
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Residues in contact with ALA1377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1358A THR* 5.5 1.1 - - - +
1359A SER 5.1 7.4 - - - +
1362A ILE* 4.3 15.3 - - + -
1365A ILE* 4.4 13.5 - - + -
1373A ALA 2.8 20.4 + - - +
1374A VAL 4.2 1.1 - - - +
1376A LYS* 1.3 70.3 - - - +
1378A LEU* 1.3 60.5 + - - +
1380A ARG* 3.2 9.3 + - - +
1381A GLU* 2.8 33.5 + - + +
144E LEU* 4.1 20.8 - - + +
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Residues in contact with LEU1378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1127A LEU* 3.6 41.3 - - + +
1128A ILE* 6.2 0.9 - - + -
1130A ILE* 5.1 2.9 - - + -
1362A ILE* 3.9 19.2 - - + +
1374A VAL* 2.8 30.2 + - + +
1375A ARG 4.2 0.9 - - - +
1377A ALA* 1.3 73.9 - - - +
1379A GLU* 1.3 66.0 + - - +
1381A GLU* 4.0 1.3 - - - +
1382A LEU* 3.1 27.7 + - + +
1402A CYS* 3.7 24.9 - - + +
1405A MET* 3.9 35.0 - - + -
1406A THR* 5.1 4.7 - - + -
1411A LEU* 5.3 0.7 - - + -
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Residues in contact with GLU1379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1375A ARG* 2.3 46.5 + - - +
1376A LYS* 3.0 44.2 + - - +
1378A LEU* 1.3 78.0 - - - +
1380A ARG* 1.3 66.5 + - + +
1382A LEU* 3.5 3.3 + - - +
1383A TYR* 2.8 30.4 + - + +
1395A TYR* 3.0 29.0 + - + -
1398A LEU* 5.0 12.6 - - + +
1399A ALA* 4.6 1.9 - - - -
1402A CYS* 3.5 16.7 - - + -
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Residues in contact with ARG1380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1358A THR* 5.1 11.3 + - - +
1376A LYS* 2.9 35.3 + - - +
1377A ALA* 3.2 8.7 + - - +
1379A GLU* 1.3 80.2 - - + +
1381A GLU* 1.3 61.2 + - + +
1383A TYR* 3.2 7.5 + - + +
1384A HIS* 2.7 30.2 + - - +
143E GLU* 3.9 29.1 + - - +
144E LEU* 4.1 25.7 - - - +
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Residues in contact with GLU1381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1117A VAL* 5.8 0.7 - - - +
1123A ARG* 2.1 43.1 + - - +
1127A LEU* 3.8 23.8 - - + -
1359A SER 4.5 4.6 - - - +
1360A ASN* 3.6 28.4 - - - +
1362A ILE* 4.6 4.5 - - + -
1377A ALA* 2.8 24.1 + - + +
1378A LEU 4.0 1.3 - - - +
1380A ARG* 1.3 75.0 - - + +
1382A LEU* 1.3 61.7 - - - +
1384A HIS* 3.2 14.2 + - - +
1385A VAL* 3.2 26.7 + - - +
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Residues in contact with LEU1382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095A LEU* 4.7 10.3 - - + -
1124A LEU* 3.6 30.1 - - + -
1127A LEU* 3.4 25.4 - - + -
1128A ILE* 4.7 5.8 - - + -
1378A LEU* 3.1 18.4 + - + +
1379A GLU* 3.9 3.8 - - - +
1381A GLU* 1.3 76.3 - - - +
1383A TYR* 1.3 66.3 + - - +
1385A VAL* 3.1 27.2 - - + +
1386A ILE* 3.3 12.0 - - + +
1398A LEU* 4.6 17.7 - - + +
1401A LEU* 3.8 28.0 - - + -
1402A CYS* 4.0 15.7 - - - -
1405A MET* 5.9 0.4 - - - -
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Residues in contact with TYR1383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1379A GLU* 2.8 20.2 + - + +
1380A ARG* 3.2 8.5 + - + +
1382A LEU* 1.3 75.9 - - - +
1384A HIS* 1.3 64.8 + - - +
1386A ILE* 3.5 7.4 + - + +
1387A SER* 3.0 50.5 + - - -
1392A TYR* 5.2 18.8 - + - -
1393A VAL 5.2 4.3 - - - -
1395A TYR* 6.0 4.7 - + + -
1398A LEU* 4.3 22.1 - - + +
198E GLU* 5.4 10.5 - - - -
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Residues in contact with HIS1384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1117A VAL* 5.6 11.0 - - + +
1119A LEU* 6.0 0.6 - - - +
1380A ARG 2.7 20.1 + - - +
1381A GLU* 3.5 18.2 - - - +
1382A LEU 3.1 0.4 - - - -
1383A TYR* 1.3 79.1 - - - +
1385A VAL* 1.3 64.8 + - + +
1387A SER* 3.5 4.6 + - - -
1388A PHE* 3.3 47.6 + + - +
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Residues in contact with VAL1385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1118A THR 5.1 1.1 - - - +
1119A LEU* 4.8 5.9 - - + +
1120A GLY* 4.5 20.5 - - - +
1123A ARG* 3.4 38.1 - - + +
1124A LEU* 5.3 7.6 - - + -
1127A LEU* 6.0 1.6 - - + -
1381A GLU* 3.2 10.8 + - - +
1382A LEU* 3.1 28.3 - - + +
1384A HIS* 1.3 79.1 - - + +
1386A ILE* 1.3 76.0 - - + +
1388A PHE* 3.4 7.1 + - - +
1389A ASP* 3.2 24.3 + - - +
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Residues in contact with ILE1386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095A LEU* 4.2 26.5 - - + +
1098A PRO* 4.4 19.7 - - + -
1099A ALA* 5.4 5.2 - - + +
1124A LEU* 6.5 1.8 - - + -
1382A LEU* 3.3 19.2 + - + +
1383A TYR* 3.7 9.0 - - + +
1385A VAL* 1.3 82.2 - - + +
1387A SER* 1.3 65.4 + - - +
1389A ASP* 3.6 9.6 + - + +
1390A GLY 3.2 9.2 + - - -
1391A SER* 2.8 34.7 + - - +
1392A TYR* 4.5 0.7 - - - -
1393A VAL* 3.9 29.4 - - + +
1398A LEU* 5.2 4.9 - - + -
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Residues in contact with SER1387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1383A TYR* 3.0 50.6 + - - -
1384A HIS* 4.0 5.2 - - - -
1385A VAL 3.4 0.2 - - - -
1386A ILE* 1.3 73.8 - - - +
1388A PHE* 1.3 66.9 + - - +
1390A GLY* 3.0 9.8 + - - -
1391A SER 4.3 4.5 - - - -
297U ARG* 3.1 30.0 + - - -
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Residues in contact with PHE1388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1108A HIS* 3.8 36.3 - + + -
1117A VAL* 6.2 3.4 - - + -
1119A LEU* 3.2 45.8 - - + -
1384A HIS* 3.3 36.0 + + - +
1385A VAL* 3.5 9.6 - - - +
1387A SER* 1.3 75.4 - - - +
1389A ASP* 1.3 57.5 + - - +
1390A GLY 2.7 14.5 + - - -
274U THR* 5.7 10.4 + - + +
297U ARG* 3.5 21.6 + - - +
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Residues in contact with ASP1389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1098A PRO* 4.1 11.5 - - - +
1101A GLN 2.9 24.9 - - - +
1102A MET* 2.9 53.1 - - - +
1103A THR* 4.9 5.6 + - - +
1119A LEU* 5.1 1.3 - - + +
1120A GLY* 6.2 3.6 - - - -
1385A VAL 3.2 14.1 + - - +
1386A ILE* 3.9 8.1 - - + +
1388A PHE* 1.3 78.1 - - - +
1390A GLY* 1.3 55.5 + - - +
1391A SER* 3.1 17.9 + - - -
276U VAL* 6.4 0.7 - - - -
288U PHE* 5.5 3.3 - - - -
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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
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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