Contacts of the helix formed by residues 1398 - 1419 (chain B) 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 GLU1398 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1579A TRP* 5.2 11.2 - - + +
1361B THR* 6.2 3.4 - - + -
1395B LEU* 2.9 14.7 + - - +
1397B GLY* 1.3 79.8 - - - +
1399B MET* 1.3 58.6 + - - +
1400B GLU* 3.1 9.4 - - + +
1401B TYR* 2.9 23.7 + - + +
1402B ALA 2.8 23.9 + - - -
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Residues in contact with MET1399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1392B MET* 4.6 5.4 - - + -
1395B LEU 3.6 2.2 + - - +
1396B GLN* 3.6 25.6 + - - +
1397B GLY 3.7 0.8 - - - -
1398B GLU* 1.3 75.0 - - - +
1400B GLU* 1.3 53.8 + - - +
1402B ALA* 3.5 12.9 - - + +
1403B THR* 2.8 45.9 + - - +
1442B TRP* 3.5 35.0 - - + +
1445B PHE* 4.4 14.1 - - + -
1446B LEU* 3.6 29.6 - - + -
1833B LEU* 3.5 26.0 - - + +
1836B GLN 5.2 1.1 - - - -
1837B SER* 3.6 21.6 + - - +
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Residues in contact with GLU1400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1579A TRP* 4.1 15.0 + - - -
1651A LEU* 2.9 43.6 + - - +
1398B GLU* 4.7 4.5 - - - -
1399B MET* 1.3 82.2 - - - +
1401B TYR* 1.3 61.5 + - - +
1403B THR* 3.4 4.3 + - - -
1404B GLY* 3.2 15.8 + - - -
1830B SER* 3.9 26.9 - - - +
1833B LEU* 4.0 14.7 - - + +
1834B ALA* 3.1 33.7 - - + +
1837B SER* 5.0 1.3 + - - +
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Residues in contact with TYR1401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1360B LEU* 3.0 27.3 + - + -
1361B THR* 2.9 40.2 + - + -
1362B LYS 3.4 8.5 + - - -
1363B LYS* 3.5 18.0 - - + -
1366B LEU* 3.4 13.4 - - + +
1395B LEU* 5.2 8.5 - - + -
1398B GLU* 2.9 24.8 + - + +
1400B GLU* 1.3 76.6 - - - +
1402B ALA* 1.3 71.0 + - + +
1403B THR 3.0 2.0 - - - -
1404B GLY* 2.8 14.1 + - - -
1405B VAL* 3.0 34.7 + - + +
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Residues in contact with ALA1402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1392B MET* 4.6 15.8 - - + +
1395B LEU* 4.2 22.4 - - + +
1398B GLU 2.8 16.5 + - - +
1399B MET* 3.5 22.9 - - - +
1401B TYR* 1.3 78.3 - - - +
1403B THR* 1.3 56.7 + - - +
1405B VAL* 3.6 5.4 + - - +
1406B LEU* 3.1 29.5 + - - +
1438B MET* 4.8 4.8 - - - +
1442B TRP* 5.3 2.6 - - + -
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Residues in contact with THR1403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1399B MET* 2.8 24.3 + - - +
1400B GLU 3.6 5.2 - - - -
1402B ALA* 1.3 75.9 - - - +
1404B GLY* 1.3 64.7 + - - +
1406B LEU* 4.0 4.1 - - + +
1407B LYS* 3.1 24.7 + - + +
1442B TRP* 3.1 33.6 + - + +
1715B TYR* 3.6 37.0 + - + +
1716B MET* 6.0 0.9 - - + -
1833B LEU* 3.4 22.0 - - + +
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Residues in contact with GLY1404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1400B GLU 3.2 7.9 + - - -
1401B TYR* 2.8 9.4 + - - -
1403B THR* 1.3 80.8 - - - +
1405B VAL* 1.3 59.2 + - - +
1407B LYS* 3.9 5.6 + - - +
1408B GLN* 3.5 18.2 + - - +
1715B TYR* 5.9 1.6 - - - -
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Residues in contact with VAL1405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1363B LYS* 4.9 7.4 - - + +
1366B LEU* 4.9 9.2 - - + -
1367B LEU* 3.5 24.9 - - + -
1401B TYR* 3.0 53.4 + - + +
1402B ALA* 3.9 4.5 - - - +
1404B GLY* 1.3 73.9 - - - +
1406B LEU* 1.3 67.1 + - - +
1407B LYS 3.1 1.6 - - - -
1408B GLN* 2.8 18.7 + - - +
1409B LEU* 2.9 23.7 + - + +
1438B MET* 5.3 4.5 - - + -
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Residues in contact with LEU1406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1392B MET* 5.6 0.9 - - + -
1402B ALA 3.1 16.2 + - - +
1403B THR* 3.5 4.2 + - + +
1405B VAL* 1.3 78.6 - - - +
1407B LYS* 1.3 63.7 + - - +
1409B LEU* 3.0 17.3 + - + +
1410B LEU* 2.9 40.7 + - + +
1435B ALA 3.5 24.7 - - - +
1438B MET* 3.6 30.0 - - + +
1439B LEU* 4.2 11.9 - - + +
1442B TRP* 3.5 44.9 - - + +
1716B MET* 5.2 3.4 - - + -
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Residues in contact with LYS1407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1403B THR* 3.1 19.3 + - + +
1404B GLY* 3.9 6.7 - - - +
1406B LEU* 1.3 77.6 - - - +
1408B GLN* 1.3 57.8 + - - +
1410B LEU* 3.4 6.4 + - - -
1411B SER* 2.9 25.3 + - - -
1715B TYR* 5.0 11.0 - - + +
1716B MET* 6.0 3.1 - - + -
1719B PHE* 3.1 37.5 - - + -
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Residues in contact with GLN1408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1367B LEU* 3.8 31.2 - - + +
1404B GLY 3.5 10.5 + - - +
1405B VAL* 2.8 15.5 + - - +
1407B LYS* 1.3 77.7 - - - +
1409B LEU* 1.3 62.8 + - - +
1411B SER* 3.3 10.6 + - - -
1412B ASP* 3.2 45.5 + - - +
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Residues in contact with LEU1409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1367B LEU* 4.3 20.0 - - + +
1370B ILE* 4.8 18.8 - - + -
1374B GLU* 5.5 6.3 - - - +
1405B VAL* 2.9 21.2 + - + +
1406B LEU* 3.2 14.6 - - + +
1408B GLN* 1.3 77.4 - - - +
1410B LEU* 1.3 56.9 + - - +
1412B ASP* 3.3 4.5 + - - +
1413B LEU* 2.8 31.1 + - - +
1416B LYS* 5.0 2.8 + - - +
1434B VAL* 5.1 3.8 - - + +
1435B ALA* 3.7 20.8 - - + +
1438B MET* 3.4 39.3 - - + -
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Residues in contact with LEU1410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1406B LEU* 2.9 24.1 + - + +
1407B LYS* 3.7 7.9 - - - +
1409B LEU* 1.3 75.0 - - - +
1411B SER* 1.3 64.3 + - - +
1413B LEU* 3.1 14.8 + - + +
1414B ILE* 2.9 35.6 + - + +
1428B LEU* 5.3 5.8 - - + -
1435B ALA* 4.3 26.7 - - + +
1436B GLU* 5.0 1.6 - - + +
1439B LEU* 4.0 27.6 - - + -
1716B MET* 3.9 31.2 - - + -
1719B PHE* 3.8 17.7 - - + -
1720B LEU* 5.7 3.1 - - + -
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Residues in contact with SER1411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1407B LYS 2.9 17.2 + - - -
1408B GLN* 3.5 17.0 + - - -
1409B LEU 3.2 0.2 - - - -
1410B LEU* 1.3 78.5 - - - +
1412B ASP* 1.3 64.4 + - - +
1414B ILE* 3.5 3.9 + - - +
1415B GLU* 3.3 18.4 + - - +
1719B PHE* 4.1 2.9 - - - -
1723B GLN* 3.0 34.8 + - - -
1726B LYS* 4.8 8.8 + - - -
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Residues in contact with ASP1412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1408B GLN* 3.2 32.7 + - - +
1409B LEU* 3.9 2.7 - - - +
1411B SER* 1.3 78.0 + - - +
1413B LEU* 1.3 60.4 + - - +
1415B GLU* 3.0 10.2 + - - +
1416B LYS* 2.8 58.5 + - - +
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Residues in contact with LEU1413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1374B GLU* 6.0 2.0 - - - +
1409B LEU 2.8 19.2 + - - +
1410B LEU* 3.1 12.8 + - + +
1412B ASP* 1.3 78.2 - - - +
1414B ILE* 1.3 63.5 + - + +
1416B LYS* 3.7 15.3 + - + +
1417B ASN* 3.2 45.1 + - - +
1427B LEU* 5.4 0.4 - - + -
1428B LEU* 4.3 10.3 - - + -
1433B SER* 4.3 11.0 - - - +
1435B ALA* 4.0 19.7 - - + -
1436B GLU* 3.7 36.1 - - + +
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Residues in contact with ILE1414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1410B LEU* 2.9 23.2 + - + +
1411B SER 3.8 3.6 - - - +
1413B LEU* 1.3 77.7 - - + +
1415B GLU* 1.3 60.4 + - - +
1417B ASN* 3.1 6.5 + - - +
1418B LEU* 2.9 53.2 + - + +
1427B LEU* 4.4 13.9 - - + -
1428B LEU* 5.7 8.1 - - + -
1719B PHE* 4.9 4.5 - - + -
1720B LEU* 5.1 8.7 - - + -
1723B GLN* 3.9 34.3 - - + +
1727B HIS* 4.8 8.3 - - + +
1738B TRP* 4.0 23.3 - - + -
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Residues in contact with GLU1415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1411B SER 3.3 11.3 + - - +
1412B ASP* 3.0 16.9 + - - +
1414B ILE* 1.3 78.7 - - - +
1416B LYS* 1.3 58.5 + - + +
1418B LEU* 3.8 4.0 - - - +
1419B GLU* 2.9 40.8 + - - +
1727B HIS* 5.6 11.2 + - + +
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Residues in contact with LYS1416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1371B ARG* 6.0 5.1 - - - +
1374B GLU* 5.1 12.7 + - - -
1409B LEU* 5.0 3.0 + - - +
1412B ASP* 2.8 45.4 + - + +
1413B LEU* 3.9 16.6 - - + +
1415B GLU* 1.3 76.9 - - + +
1417B ASN* 1.3 63.6 + - - +
1419B GLU* 3.3 29.8 - - - +
1420B SER* 3.8 10.9 + - - -
1422B ASN* 4.9 0.5 + - - -
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Residues in contact with ASN1417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1413B LEU* 3.2 27.9 + - - +
1414B ILE 3.1 6.7 + - - +
1415B GLU 3.0 0.6 - - - -
1416B LYS* 1.3 85.1 - - - +
1418B LEU* 1.3 60.9 + - - +
1419B GLU 3.2 2.8 + - - -
1420B SER 3.6 4.0 + - - -
1422B ASN* 3.1 51.1 + - + +
1427B LEU* 3.4 42.7 + - + +
1436B GLU* 5.5 1.0 + - - -
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Residues in contact with LEU1418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1414B ILE* 2.9 39.9 + - + +
1415B GLU* 4.4 3.1 - - - +
1417B ASN* 1.3 75.7 - - - +
1419B GLU* 1.3 61.5 + - - +
1421B LYS* 3.8 8.0 + - - +
1422B ASN 3.7 22.0 - - - +
1424B PRO* 4.3 17.3 - - + -
1427B LEU* 4.0 17.7 - - + -
1727B HIS* 4.1 30.7 - - + +
1738B TRP* 4.5 10.3 - - + -
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Residues in contact with GLU1419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1415B GLU* 2.9 26.2 + - - +
1416B LYS* 3.3 23.4 - - - +
1418B LEU* 1.3 76.2 - - - +
1420B SER* 1.3 62.1 + - - +
1421B LYS* 3.2 6.6 + - - +
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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