Contacts of the helix formed by residues 1362 - 1376 (chain A) in PDB entry 3RYT
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 LYS1362 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1358A GLN 3.8 5.7 + - - +
1359A LEU* 3.3 18.7 + - + +
1360A LEU 3.1 1.5 - - - +
1361A THR* 1.3 75.6 - - - +
1363A LYS* 1.3 67.8 + - - +
1364A HIS* 3.2 1.8 - - + +
1365A PHE* 2.9 23.0 + - + +
1366A LEU 3.2 8.3 + - - -
1401A TYR* 3.7 1.4 + - - -
1877A GLN* 5.4 6.1 - - - +
1879A LEU* 4.1 14.1 - - + -
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Residues in contact with LYS1363 (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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1361A THR 3.0 6.2 + - - -
1362A LYS* 1.3 71.1 - - - +
1364A HIS* 1.3 66.7 + - + +
1366A LEU* 3.5 3.8 + - - +
1367A LEU* 3.1 31.5 + - + +
1401A TYR* 3.6 20.8 + - + -
1405A VAL* 4.9 4.0 - - + +
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Residues in contact with HIS1364 (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 LYS* 3.2 1.4 - - + -
1363A LYS* 1.3 81.1 - - + +
1365A PHE* 1.3 67.4 + - - +
1367A LEU* 3.1 17.1 + - + +
1368A THR* 2.9 37.0 + - - +
1871A ASP* 5.5 4.4 - - + +
1873A GLN* 3.4 33.8 - - + +
1874A ALA* 4.9 6.5 + - + +
1877A GLN* 4.2 20.0 - - - +
1879A LEU* 4.8 4.5 - - + -
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Residues in contact with PHE1365 (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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1356A PHE* 4.7 22.2 - + - -
1359A LEU* 3.2 49.6 - - + +
1360A LEU* 3.5 26.0 - - + -
1362A LYS* 2.9 5.4 + - + +
1364A HIS* 1.3 78.0 - - - +
1366A LEU* 1.3 62.4 + - - +
1368A THR* 3.8 1.0 - - - -
1369A PHE* 2.8 55.7 + + + +
1864A ILE* 5.6 2.2 - - + -
1868A LEU* 4.1 25.7 - - + +
1879A LEU* 3.4 38.4 - - + +
1883A LEU* 4.8 2.5 - - + -
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Residues in contact with LEU1366 (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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1360A LEU* 3.6 37.0 - - + +
1362A LYS 3.2 2.2 + - - -
1363A LYS 4.0 3.4 - - - +
1365A PHE* 1.3 81.9 - - - +
1367A LEU* 1.3 59.8 + - - +
1369A PHE* 4.0 13.9 - - + -
1370A ILE* 3.3 29.6 + - + +
1391A ILE* 4.1 26.5 - - + -
1395A LEU* 3.7 27.4 - - + -
1401A TYR* 3.5 21.3 - - - +
1405A VAL* 4.0 22.2 - - + -
1438A MET* 6.1 2.0 - - + -
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Residues in contact with LEU1367 (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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1363A LYS* 3.1 27.6 - - + +
1364A HIS* 3.1 22.1 + - + +
1366A LEU* 1.3 76.2 - - - +
1368A THR* 1.3 60.8 + - - +
1369A PHE 3.2 1.1 - - - -
1370A ILE* 3.2 3.6 + - - +
1371A ARG* 2.9 30.9 + - - +
1405A VAL* 3.4 31.6 - - + -
1408A GLN* 3.7 32.5 - - + -
1409A LEU* 3.6 21.8 - - + +
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Residues in contact with THR1368 (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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1364A HIS* 2.9 27.7 + - - -
1367A LEU* 1.3 72.0 - - - +
1369A PHE* 1.3 64.8 + - - +
1371A ARG* 4.4 6.3 - - + -
1372A THR* 2.9 32.7 + - - +
1864A ILE* 4.8 0.6 - - - +
1867A ALA* 3.6 35.9 - - + +
1868A LEU* 4.0 26.5 - - + +
1871A ASP* 4.8 11.5 - - + +
1874A ALA* 5.0 3.3 - - + +
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Residues in contact with PHE1369 (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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1356A PHE* 4.9 4.7 - + - -
1360A LEU* 5.4 1.3 - - + -
1365A PHE* 2.8 40.9 + + + +
1366A LEU* 3.9 24.9 - - + +
1367A LEU 3.2 0.2 - - - -
1368A THR* 1.3 78.4 - - - +
1370A ILE* 1.3 64.0 + - + +
1373A LEU* 3.0 57.2 + - + +
1387A VAL* 5.1 7.4 - - + -
1391A ILE* 5.0 8.3 - - + -
1853A ILE* 3.9 34.8 - - + -
1856A TYR* 5.1 3.4 - - + -
1857A ILE* 4.4 22.9 - - + -
1864A ILE* 3.8 26.7 - - + +
1868A LEU* 5.2 2.4 - - - +
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Residues in contact with ILE1370 (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 LEU* 3.3 22.9 + - + +
1367A LEU 3.2 4.3 + - - +
1368A THR 3.2 0.2 - - - -
1369A PHE* 1.3 85.0 - - + +
1371A ARG* 1.3 61.6 + - - +
1372A THR 3.2 2.2 + - - -
1373A LEU* 3.2 4.8 + - + +
1374A GLU* 2.9 43.5 + - - +
1387A VAL* 5.7 2.9 - - + -
1391A ILE* 4.4 20.4 - - + -
1409A LEU* 3.5 39.9 - - + -
1434A VAL* 3.9 32.3 - - + -
1438A MET* 4.5 3.6 - - - -
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Residues in contact with ARG1371 (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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1367A LEU 2.9 17.5 + - - +
1368A THR* 4.2 6.3 - - + +
1370A ILE* 1.3 78.4 - - - +
1372A THR* 1.3 58.6 + - - +
1374A GLU* 4.3 6.3 - - - +
1375A ALA* 3.2 26.0 + - - +
1409A LEU* 5.9 0.9 - - + +
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Residues in contact with THR1372 (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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1368A THR* 2.9 23.5 + - - +
1371A ARG* 1.3 75.2 - - - +
1373A LEU* 1.3 66.4 + - - +
1375A ALA* 3.4 15.7 + - - +
1376A GLN* 3.5 11.6 + - - +
1863A GLU* 3.5 51.6 - - + +
1864A ILE* 3.9 14.8 - - + +
1867A ALA* 3.1 24.9 - - + +
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Residues in contact with LEU1373 (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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1369A PHE* 3.0 50.4 + - + +
1370A ILE* 3.2 5.7 + - - +
1372A THR* 1.3 73.4 - - - +
1374A GLU* 1.3 60.7 + - - +
1375A ALA 3.0 1.3 - - - -
1376A GLN* 2.8 26.8 + - - +
1379A PHE* 3.2 32.4 - - + -
1387A VAL* 5.5 12.1 - - + -
1856A TYR* 5.3 11.0 - - + +
1857A ILE* 6.2 0.2 - - - -
1860A TYR* 3.4 34.5 - - + -
1864A ILE* 3.5 24.7 - - + -
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Residues in contact with GLU1374 (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 ILE* 2.9 26.5 + - - +
1371A ARG* 4.3 5.6 - - - +
1373A LEU* 1.3 77.6 - - - +
1375A ALA* 1.3 61.1 + - - +
1376A GLN 3.3 8.1 + - - +
1377A ARG* 4.8 6.4 + - - -
1379A PHE* 3.5 11.6 - - - -
1384A ARG* 3.3 39.1 + - - +
1413A LEU* 4.6 8.1 - - - +
1416A LYS* 5.2 12.3 + - - +
1433A SER* 3.8 12.4 + - - -
1434A VAL* 4.0 22.8 - - + +
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Residues in contact with ALA1375 (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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1371A ARG 3.2 18.7 + - - +
1372A THR* 3.5 9.6 - - - +
1373A LEU 3.0 0.8 - - - -
1374A GLU* 1.3 78.6 - - - +
1376A GLN* 1.3 60.3 + - - +
1377A ARG* 3.4 25.7 + - - +
1863A GLU* 5.2 4.7 - - - +
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Residues in contact with GLN1376 (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 THR* 3.6 14.4 + - - +
1373A LEU* 2.8 16.1 + - - +
1374A GLU 3.4 10.4 - - - +
1375A ALA* 1.3 80.3 - - - +
1377A ARG* 1.3 61.8 + - - +
1378A SER* 3.2 18.1 + - - +
1379A PHE* 4.7 8.0 + - - +
1384A ARG* 5.2 2.3 + - - -
1860A TYR* 3.3 42.5 - - - +
1863A GLU* 3.0 45.0 - - + +
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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