Contacts of the helix formed by residues 1347 - 1362 (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 SER1347 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1345A VAL 3.6 3.7 + - - -
1346A LEU* 1.3 76.4 - - - +
1348A HIS* 1.3 68.1 + - - +
1349A GLY* 3.9 6.8 + - - -
1350A HIS* 2.7 35.5 + - - +
1351A LYS* 3.2 23.4 + - - +
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Residues in contact with HIS1348 (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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1291A GLN 5.0 10.3 + - - -
1293A VAL* 6.3 0.4 - - - +
1347A SER* 1.3 75.9 - - - +
1349A GLY* 1.3 52.1 + - - +
1351A LYS* 2.8 23.4 + - + +
1352A GLN* 2.8 46.6 + - - +
1375A HIS* 4.4 32.8 - + + +
1376A LEU* 3.7 17.5 - - + -
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Residues in contact with GLY1349 (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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1347A SER* 3.5 5.4 + - - -
1348A HIS* 1.3 77.8 - - - +
1350A HIS* 1.3 56.7 + - - +
1352A GLN* 3.4 10.7 + - - +
1353A LEU* 3.1 34.4 + - - +
1376A LEU* 3.7 3.0 - - - +
1380A THR* 3.5 30.9 - - - +
1384A ILE* 3.9 1.9 - - - +
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Residues in contact with HIS1350 (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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1324A LEU* 4.4 7.0 - - + +
1327A VAL* 3.5 42.8 - - + +
1345A VAL 5.6 1.8 - - - -
1346A LEU* 3.9 25.9 - - + -
1347A SER* 2.7 40.4 + - - +
1348A HIS 3.2 0.4 - - - -
1349A GLY* 1.3 73.8 - - - +
1351A LYS* 1.3 61.3 + - - +
1353A LEU* 3.3 17.4 + - + +
1354A MET* 2.8 29.7 + - - +
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Residues in contact with LYS1351 (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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1293A VAL* 3.7 34.5 - - + +
1295A ILE* 3.5 34.1 - - + +
1342A GLY 4.6 1.0 + - - -
1343A GLY* 3.8 13.2 + - - -
1346A LEU* 3.6 33.8 + - + -
1347A SER 3.2 12.0 + - - +
1348A HIS* 2.8 24.1 + - + +
1350A HIS* 1.3 70.8 - - - +
1352A GLN* 1.3 56.1 + - - +
1354A MET* 4.1 6.7 - - - -
1355A CYS* 2.8 35.7 + - - +
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Residues in contact with GLN1352 (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* 3.2 40.4 - - + +
1290A PRO 4.1 9.8 + - - +
1291A GLN 5.0 3.0 + - - -
1293A VAL* 4.1 17.1 - - - +
1348A HIS* 2.8 40.8 + - - +
1349A GLY* 3.5 7.6 - - - +
1350A HIS 3.2 0.2 - - - -
1351A LYS* 1.3 76.6 - - - +
1353A LEU* 1.3 53.2 + - - +
1355A CYS* 4.5 0.2 - - - -
1356A LEU* 2.8 34.0 + - - +
1375A HIS* 6.3 0.8 - - - +
1376A LEU* 3.8 30.3 - - + +
1384A ILE* 3.8 16.2 - - + -
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Residues in contact with LEU1353 (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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1322A VAL* 3.5 26.0 - - - +
1323A GLY* 3.7 18.4 - - - +
1324A LEU* 3.4 22.3 - - + +
1327A VAL* 6.2 1.8 - - + -
1349A GLY 3.1 19.7 + - - +
1350A HIS* 3.3 17.5 + - + +
1352A GLN* 1.3 73.6 - - - +
1354A MET* 1.3 56.4 + - - +
1356A LEU* 3.4 14.4 - - + +
1357A ALA* 2.8 34.8 + - - +
1383A ILE* 5.3 13.2 - - + +
1384A ILE* 3.6 21.1 - - + -
1387A THR* 4.7 7.2 - - + -
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Residues in contact with MET1354 (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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1293A VAL* 5.7 1.1 - - + -
1300A PHE* 3.7 29.4 - - + +
1303A ASN* 3.4 34.5 - - + +
1304A LEU* 3.5 33.0 - - + +
1324A LEU* 4.1 18.1 - - + +
1328A ILE* 5.1 5.8 - - + -
1339A LEU* 5.9 0.2 - - + -
1346A LEU* 5.8 8.1 - - + -
1350A HIS 2.8 21.7 + - - +
1351A LYS* 3.7 8.7 - - - +
1353A LEU* 1.3 72.9 - - - +
1355A CYS* 1.3 58.1 + - - +
1357A ALA* 3.4 2.9 + - - +
1358A ARG* 3.0 43.3 + - - +
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Residues in contact with CYS1355 (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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275A TYR* 2.9 28.4 + - - +
1288A VAL 3.3 18.8 - - - -
1289A ILE* 3.8 20.2 - - + -
1290A PRO* 4.2 6.1 - - - -
1293A VAL* 4.1 15.8 - - + +
1351A LYS 2.8 22.4 + - - +
1352A GLN* 3.8 5.8 - - - +
1354A MET* 1.3 71.1 - - - +
1356A LEU* 1.3 56.6 + - - +
1358A ARG* 3.6 11.5 - - - +
1359A SER* 2.8 32.1 + - - -
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Residues in contact with LEU1356 (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* 4.6 8.9 - - + +
1322A VAL* 4.6 15.5 - - + +
1352A GLN 2.8 19.8 + - - +
1353A LEU* 3.4 24.7 - - + +
1354A MET 3.2 0.2 - - - -
1355A CYS* 1.3 73.7 - - - +
1357A ALA* 1.3 53.4 + - - +
1359A SER* 2.9 9.4 + - - -
1360A VAL* 2.8 43.4 + - + +
1367A LEU* 5.2 2.5 - - + -
1384A ILE* 5.2 7.2 - - + -
1387A THR* 4.9 9.9 - - + -
1388A LEU* 3.7 22.0 - - + -
1391A ALA* 5.4 4.0 - - + -
1392A PHE* 3.3 40.2 - - + -
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Residues in contact with ALA1357 (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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1304A LEU* 4.2 12.1 - - + -
1318A VAL* 4.4 9.1 - - + +
1319A ALA* 5.7 0.9 - - - -
1322A VAL* 3.8 23.3 - - + -
1324A LEU* 3.5 24.2 - - + -
1353A LEU 2.8 19.9 + - - +
1354A MET 3.8 2.5 - - - +
1356A LEU* 1.3 72.9 - - - +
1358A ARG* 1.3 57.1 + - - +
1360A VAL* 3.8 0.7 - - - +
1361A LEU* 2.9 33.4 + - - +
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Residues in contact with ARG1358 (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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275A TYR* 3.8 39.1 + - + -
277A TRP* 3.6 31.4 - - + -
1293A VAL* 5.1 5.4 - - - +
1294A PHE* 3.7 28.9 + - - +
1296A PHE* 4.6 4.0 - - - -
1303A ASN* 3.5 46.2 + - - +
1304A LEU* 4.3 22.1 - - + +
1354A MET* 3.0 32.7 + - - +
1355A CYS* 3.6 10.4 - - - +
1356A LEU 3.2 0.2 - - - -
1357A ALA* 1.3 76.4 - - - +
1359A SER* 1.3 53.5 + - - +
1361A LEU* 4.0 5.3 + - - +
1362A SER* 2.8 31.8 + - - +
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Residues in contact with SER1359 (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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275A TYR* 4.8 7.2 - - - -
1287A GLY* 4.4 14.5 - - - -
1288A VAL 4.3 12.6 + - - -
1289A ILE* 6.0 0.7 - - - +
1355A CYS* 2.8 14.5 + - - -
1356A LEU* 2.9 10.7 + - - -
1358A ARG* 1.3 76.1 - - - +
1360A VAL* 1.3 66.1 + - - +
1362A SER* 3.0 21.7 + - - -
1363A LYS 3.5 3.8 + - - -
1364A ALA* 3.9 11.4 + - - +
1367A LEU* 4.5 21.0 - - - +
1392A PHE* 5.0 2.6 - - - -
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Residues in contact with VAL1360 (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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1318A VAL* 4.1 19.5 - - + -
1321A GLU* 5.5 6.1 - - - +
1322A VAL* 4.0 19.1 - - + -
1356A LEU* 2.8 30.4 + - + +
1357A ALA 3.2 4.0 + - - +
1359A SER* 1.3 71.4 - - - +
1361A LEU* 1.3 61.9 + - - +
1363A LYS* 3.2 15.9 + - - +
1364A ALA 5.6 0.2 - - - +
1391A ALA* 5.1 8.5 - - + +
1392A PHE* 3.4 34.3 - - + -
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Residues in contact with LEU1361 (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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1304A LEU* 4.2 24.0 - - + +
1305A ASP* 5.2 0.4 - - + -
1310A TRP* 3.5 73.1 - - + +
1314A GLU* 4.5 12.6 - - + +
1315A ILE* 4.4 14.4 - - + -
1318A VAL* 4.5 24.2 - - + +
1357A ALA 2.9 16.3 + - - +
1358A ARG* 4.2 5.8 - - - +
1360A VAL* 1.3 77.3 - - - +
1362A SER* 1.3 59.4 + - - +
1363A LYS* 3.3 3.8 + - - +
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Residues in contact with SER1362 (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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275A TYR* 6.1 0.7 - - - -
1284A LYS* 4.3 13.2 - - - +
1286A PHE 5.9 1.3 - - - -
1310A TRP* 5.5 2.5 - - - +
1358A ARG* 2.8 21.3 + - - +
1359A SER* 3.0 14.0 + - - -
1361A LEU* 1.3 75.7 - - - +
1363A LYS* 1.3 75.4 + - - +
1364A ALA* 3.2 7.2 + - - -
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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