Contacts of the helix formed by residues 1377 - 1392 (chain A) in PDB entry 5UAK
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 ASP1377 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1376A LEU* 1.3 76.5 - - - +
1378A PRO* 1.4 64.1 - - + +
1379A VAL* 4.1 15.4 + - - +
1380A THR* 2.6 38.2 + - - -
1381A TYR* 2.8 30.2 + - - -
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Residues in contact with PRO1378 (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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1376A LEU 4.8 0.9 - - - +
1377A ASP* 1.4 86.1 - - + +
1379A VAL* 1.3 55.5 + - + +
1381A TYR* 3.6 9.8 - - + +
1382A GLN* 2.8 35.9 + - - +
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Residues in contact with VAL1379 (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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1377A ASP* 3.0 12.2 + - - +
1378A PRO* 1.3 79.4 - - + +
1380A THR* 1.3 54.6 + - - +
1382A GLN* 3.4 7.5 + - - +
1383A ILE* 2.8 59.5 + - + +
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Residues in contact with THR1380 (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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1349A GLY* 3.5 32.3 - - - -
1376A LEU* 3.8 19.1 - - + -
1377A ASP* 2.6 39.1 + - - -
1379A VAL* 1.3 73.0 - - - +
1381A TYR* 1.3 54.8 + - - +
1383A ILE* 3.2 9.7 + - + +
1384A ILE* 2.8 45.2 + - + +
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Residues in contact with TYR1381 (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 PRO* 4.0 20.4 - - + -
1373A SER* 3.8 43.1 - - - -
1376A LEU* 4.6 9.7 - - + +
1377A ASP 2.8 17.7 + - - +
1378A PRO* 3.6 13.5 - - + +
1380A THR* 1.3 72.7 - - - +
1382A GLN* 1.3 60.7 + - - +
1384A ILE* 4.0 4.5 - - + +
1385A ARG* 3.0 67.2 + - + +
1399A LEU* 4.8 3.6 - - - +
1401A GLU* 4.4 6.1 + - - -
1406A ALA* 4.0 15.7 + - + +
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Residues in contact with GLN1382 (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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1378A PRO 2.8 21.7 + - - +
1379A VAL* 3.7 6.7 - - - +
1381A TYR* 1.3 74.5 - - + +
1383A ILE* 1.3 60.0 + - + +
1385A ARG* 4.7 2.7 - - - -
1386A ARG* 2.8 74.7 + - + +
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Residues in contact with ILE1383 (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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1353A LEU* 5.3 15.3 - - + -
1379A VAL* 2.8 45.9 + - + +
1380A THR* 3.2 9.6 + - + +
1382A GLN* 1.3 75.4 - - + +
1384A ILE* 1.3 63.0 + - + +
1386A ARG* 4.6 2.3 - - - +
1387A THR* 3.5 19.8 + - + +
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Residues in contact with ILE1384 (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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1289A ILE* 5.9 4.5 - - + -
1349A GLY 3.9 3.6 - - - +
1352A GLN* 3.8 26.7 - - + -
1353A LEU* 3.6 36.8 - - + +
1356A LEU* 5.2 5.4 - - + -
1372A PRO* 6.4 2.0 - - + -
1376A LEU* 4.6 8.5 - - + -
1380A THR* 2.8 35.5 + - + +
1381A TYR* 4.0 4.7 - - + +
1383A ILE* 1.3 73.4 - - + +
1385A ARG* 1.3 56.1 + - - +
1387A THR* 3.2 9.6 + - - +
1388A LEU* 2.8 54.4 + - + +
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Residues in contact with ARG1385 (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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1239A ARG* 3.9 19.1 - - - +
1369A LEU* 6.5 0.4 - - - -
1381A TYR* 3.0 58.8 + - + +
1382A GLN* 4.2 2.9 - - - +
1384A ILE* 1.3 78.9 - - - +
1386A ARG* 1.3 61.2 + - - +
1387A THR 3.4 0.9 + - - -
1388A LEU* 3.5 23.4 + - - +
1389A LYS* 3.6 46.7 + - - +
1399A LEU* 4.4 18.6 - - - +
1406A ALA 4.7 5.7 + - - -
1409A GLU* 3.6 33.2 - - - +
1410A CYS* 5.0 1.0 - - - -
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Residues in contact with ARG1386 (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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1382A GLN* 2.8 53.5 + - + +
1383A ILE* 4.6 3.1 - - - +
1385A ARG* 1.3 73.1 - - - +
1387A THR* 1.3 50.5 + - - +
1389A LYS* 5.5 3.6 - - - +
1390A GLN* 2.6 32.5 + - - +
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Residues in contact with THR1387 (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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1321A GLU 3.5 21.5 + - - -
1322A VAL* 3.7 20.8 + - - +
1323A GLY* 5.6 0.6 - - - -
1353A LEU* 4.7 7.0 - - + -
1356A LEU* 4.9 5.8 - - + -
1383A ILE 3.5 15.0 + - - +
1384A ILE* 3.3 15.3 - - - +
1386A ARG* 1.3 79.0 - - - +
1388A LEU* 1.3 63.6 + - - +
1389A LYS 3.4 2.5 - - - -
1390A GLN* 3.5 14.4 + - - +
1391A ALA* 3.2 22.4 + - - +
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Residues in contact with LEU1388 (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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1289A ILE* 6.4 1.6 - - + -
1356A LEU* 3.7 22.0 - - + -
1367A LEU* 5.7 0.7 - - + -
1369A LEU* 4.0 29.4 - - + -
1384A ILE* 2.8 35.7 + - + +
1385A ARG* 3.5 20.6 + - - +
1387A THR* 1.3 75.4 - - + +
1389A LYS* 1.3 54.4 + - + +
1391A ALA* 3.2 5.0 + - - +
1392A PHE* 2.8 69.0 + - + +
1397A VAL* 5.8 4.0 - - + -
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Residues in contact with LYS1389 (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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1239A ARG* 3.4 33.3 + - - +
1385A ARG* 3.6 47.0 + - - +
1386A ARG* 5.5 2.7 - - - +
1387A THR 3.4 0.4 - - - -
1388A LEU* 1.3 78.2 - - + +
1390A GLN* 1.3 62.5 + - - +
1392A PHE 3.1 4.0 - - - +
1393A ALA* 2.8 31.8 + - - +
1409A GLU* 4.0 25.1 + - + +
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Residues in contact with GLN1390 (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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1386A ARG 2.6 32.8 + - - +
1387A THR* 3.5 17.4 + - - +
1389A LYS* 1.3 78.0 + - - +
1391A ALA* 1.3 66.2 + - - +
1392A PHE 3.6 0.2 + - - -
1393A ALA* 3.8 17.0 + - - +
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Residues in contact with ALA1391 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1321A GLU 5.9 3.1 - - - +
1322A VAL* 5.7 6.1 - - + -
1356A LEU* 5.4 4.7 - - + -
1360A VAL* 5.1 11.7 - - + +
1387A THR* 3.2 22.9 + - + +
1388A LEU* 3.4 9.4 - - + +
1390A GLN* 1.3 80.0 - - - +
1392A PHE* 1.3 79.0 + - + +
1393A ALA 3.7 0.4 + - - -
1395A CYS* 5.2 1.7 - - - -
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Residues in contact with PHE1392 (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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1239A ARG* 5.4 4.3 + - - -
1356A LEU* 3.3 23.1 - - + -
1359A SER* 5.0 1.3 - - - -
1360A VAL* 3.4 40.2 - - + -
1364A ALA* 5.2 4.9 - - + -
1367A LEU* 3.4 44.4 - - + -
1369A LEU* 6.6 0.2 - - + -
1388A LEU* 2.8 35.5 + - + +
1389A LYS* 3.1 8.1 - - - +
1391A ALA* 1.3 84.6 - - + +
1393A ALA* 1.3 62.4 + - - +
1394A ASP 3.5 1.8 - - - -
1395A CYS* 3.8 37.3 - - + +
1397A VAL* 4.3 19.4 - - + +
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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