Contacts of the helix formed by residues 1380 - 1393 (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 SER1380 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1378A SER 4.0 1.6 + - - -
1379A PHE* 1.3 73.7 - - - +
1381A MET* 1.3 66.3 + - - +
1382A ARG* 3.6 18.4 + - - +
1383A ASP* 2.9 17.8 + - - -
1384A ARG* 3.1 17.4 + - - +
1697B GLU* 4.4 14.8 - - - +
1810B TRP* 3.7 35.4 + - - +
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Residues in contact with MET1381 (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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1380A SER* 1.3 76.3 - - - +
1382A ARG* 1.3 63.0 + - - +
1384A ARG* 3.0 17.1 + - + +
1385A GLY* 2.8 29.8 + - - -
1431A THR 5.1 2.0 - - - +
1432A GLU* 3.3 55.4 - - + +
1437A LYS* 4.1 18.4 - - + -
1697B GLU* 6.3 1.8 - - + -
1704B HIS* 6.1 5.6 - - - -
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Residues in contact with ARG1382 (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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1380A SER* 3.0 13.5 + - - +
1381A MET* 1.3 87.8 - - - +
1383A ASP* 1.3 69.2 + - - +
1385A GLY* 3.5 4.5 + - - -
1386A ASN* 3.5 24.6 - - - +
1700B PHE 4.0 18.8 + - - -
1701B SER* 5.6 9.2 - - - +
1702B THR* 5.0 8.1 - - - +
1810B TRP 5.3 1.0 + - - -
1813B ARG* 3.3 44.1 - - - +
1814B TYR* 4.8 4.2 - - - +
1817B ASP* 2.7 32.1 + - - -
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Residues in contact with ASP1383 (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 PHE* 3.0 42.2 - - + +
1380A SER* 2.9 7.2 + - - -
1382A ARG* 1.3 84.0 + - - +
1384A ARG* 1.3 62.2 + - - +
1385A GLY 2.9 5.8 + - - -
1386A ASN* 3.3 7.0 + - - +
1387A VAL* 3.1 34.3 + - + +
1810B TRP* 5.9 0.2 + - - -
1813B ARG* 3.5 27.2 + - - -
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Residues in contact with ARG1384 (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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1374A GLU* 3.3 51.0 + - - +
1376A GLN 5.2 2.2 + - - -
1379A PHE* 3.2 38.0 + - + -
1380A SER* 3.1 19.2 + - - +
1381A MET* 3.0 20.2 + - - +
1383A ASP* 1.3 74.9 - - - +
1385A GLY* 1.3 57.6 + - - +
1387A VAL* 4.3 5.4 - - - -
1388A ALA* 3.5 20.6 + - - +
1431A THR* 5.4 1.8 + - - -
1432A GLU 4.5 1.0 + - - +
1433A SER* 3.7 30.9 - - - +
1434A VAL* 3.8 21.5 - - + +
1437A LYS* 3.8 7.9 - - - +
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Residues in contact with GLY1385 (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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1330A LEU 4.8 0.5 - - - +
1381A MET* 2.8 18.3 + - - -
1382A ARG 3.5 2.4 + - - -
1383A ASP 2.9 0.6 - - - -
1384A ARG* 1.3 80.5 - - - +
1386A ASN* 1.3 57.8 + - - +
1388A ALA 4.0 0.6 + - - -
1389A SER* 2.7 30.7 + - - -
1437A LYS* 3.3 30.1 + - - +
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Residues in contact with ASN1386 (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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1330A LEU 5.2 1.7 - - - +
1331A PHE* 4.8 20.0 - - + -
1332A PRO* 5.8 3.8 - - - +
1382A ARG* 3.5 18.1 + - - +
1383A ASP* 3.3 10.3 + - - +
1385A GLY* 1.3 77.7 - - - +
1387A VAL* 1.3 53.9 - - + +
1388A ALA 3.2 1.3 - - - -
1389A SER* 2.9 8.0 + - - -
1390A LEU* 2.7 47.8 + - + +
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Residues in contact with VAL1387 (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* 5.1 12.3 - - + -
1370A ILE* 5.7 3.6 - - + -
1373A LEU* 5.5 10.1 - - + -
1379A PHE* 6.1 4.5 - - + -
1383A ASP* 3.1 22.3 + - + +
1384A ARG* 4.7 4.9 - - - +
1386A ASN* 1.3 76.7 - - + +
1388A ALA* 1.3 60.7 + - - +
1390A LEU* 3.8 13.6 - - + +
1391A ILE* 3.0 52.5 + - + +
1434A VAL* 5.4 8.3 - - + -
1853A ILE* 5.9 3.6 - - + -
1856A TYR* 5.5 11.2 - - + -
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Residues in contact with ALA1388 (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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1384A ARG 3.5 10.5 + - - +
1385A GLY 4.2 2.2 - - - +
1386A ASN 3.2 0.4 - - - -
1387A VAL* 1.3 79.7 - - - +
1389A SER* 1.3 56.9 + - - +
1391A ILE* 4.3 2.1 - - - +
1392A MET* 2.9 30.5 + - - +
1434A VAL* 3.7 7.3 - - + +
1437A LYS* 3.5 31.6 - - + +
1438A MET* 3.4 31.6 - - + +
1441A ASN* 3.1 3.5 - - - +
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Residues in contact with SER1389 (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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1330A LEU* 3.2 36.1 + - - +
1331A PHE* 3.8 14.1 - - - -
1385A GLY 2.7 20.8 + - - -
1386A ASN 2.9 8.9 + - - -
1388A ALA* 1.3 78.4 - - - +
1390A LEU* 1.3 60.4 + - - +
1391A ILE 3.4 0.2 - - - -
1392A MET* 3.6 2.6 + - - +
1393A THR* 3.0 27.2 + - - -
1437A LYS* 3.8 7.6 + - - -
1441A ASN* 3.3 15.9 + - - -
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Residues in contact with LEU1390 (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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1331A PHE* 4.1 20.9 - - + -
1339A VAL* 6.2 1.8 - - + -
1386A ASN* 2.7 33.4 + - + +
1387A VAL* 3.8 16.4 - - + +
1389A SER* 1.3 71.3 - - - +
1391A ILE* 1.3 61.9 + - - +
1393A THR* 2.9 22.5 + - - -
1394A ALA* 3.0 13.3 + - - +
1849A ALA* 4.0 13.2 - - + +
1852A GLU* 4.2 28.7 - - + +
1853A ILE* 3.8 30.5 - - + +
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Residues in contact with ILE1391 (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* 4.6 4.9 - - + -
1366A LEU* 4.1 28.3 - - + -
1369A PHE* 5.0 5.4 - - + -
1370A ILE* 4.4 17.9 - - + -
1387A VAL* 3.0 35.3 + - + +
1388A ALA* 4.5 6.7 - - - +
1390A LEU* 1.3 75.6 - - - +
1392A MET* 1.3 59.1 + - + +
1394A ALA* 2.9 3.9 + - - +
1395A LEU* 2.8 54.0 + - + +
1434A VAL* 6.0 0.2 - - + -
1438A MET* 4.9 15.0 - - + -
1853A ILE* 3.9 21.8 - - + -
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Residues in contact with MET1392 (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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1330A LEU* 4.8 0.2 - - + -
1388A ALA 2.9 25.1 + - - +
1389A SER 3.6 5.3 + - - +
1390A LEU 3.3 0.2 - - - -
1391A ILE* 1.3 77.7 - - - +
1393A THR* 1.3 58.0 + - - +
1394A ALA 3.1 3.2 + - - -
1395A LEU* 4.4 2.9 - - - +
1396A GLN* 3.6 19.3 + - - +
1399A MET* 6.5 1.6 - - + -
1402A ALA* 4.7 18.8 - - + +
1406A LEU* 6.1 0.9 - - + -
1438A MET* 3.6 32.5 - - + +
1441A ASN* 3.6 17.5 - - + +
1442A TRP* 4.4 26.9 - - + +
1445A PHE* 3.5 51.0 - - + -
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Residues in contact with THR1393 (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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1327A MET* 6.5 0.2 - - - -
1330A LEU* 5.2 4.7 - - - -
1331A PHE* 5.1 9.0 - - - -
1339A VAL* 5.1 13.9 - - - -
1389A SER 3.0 13.7 + - - -
1390A LEU* 2.9 15.5 + - - -
1392A MET* 1.3 74.8 - - - +
1394A ALA* 1.3 55.9 + - - +
1396A GLN* 2.8 22.2 + - - +
1445A PHE* 4.8 3.3 - - - -
1844A PHE* 5.0 8.5 - - - +
1845A ASN 5.3 0.2 - - - +
1846A SER* 4.5 5.9 - - - -
1849A ALA* 3.7 21.2 - - - +
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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