Contacts of the helix formed by residues 1400 - 1415 (chain A) in PDB entry 5G04
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 LYS1400 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1360A VAL* 6.5 0.2 - - + -
1361A ASP* 3.2 28.4 + - - +
1398A PHE 3.6 3.8 + - - -
1399A VAL* 1.3 77.4 - - - +
1401A PRO* 1.4 76.9 - - + +
1402A GLU* 4.1 14.1 - - + +
1403A PHE* 3.2 42.5 + - + +
1404A LEU 3.2 9.2 + - - -
1601A TYR* 4.0 15.9 + - - -
67L GLN* 4.8 7.1 + - - +
100L ASN* 2.7 40.4 + - + -
101L ASN* 4.2 15.4 - - - +
102L PHE* 5.6 0.4 - - - -
135L PHE* 3.4 22.5 - - + +
136L MET* 5.2 1.4 - - - +
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Residues in contact with PRO1401 (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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1399A VAL 3.5 3.5 - - - +
1400A LYS* 1.4 86.3 - - + +
1402A GLU* 1.3 63.2 - - - +
1404A LEU* 3.3 16.4 + - + +
1456A THR* 5.1 6.3 - - + +
1459A GLN* 3.6 22.2 - - + +
1460A ALA* 4.2 11.7 - - + +
1463A TYR* 3.2 44.0 - - + +
71L LYS* 5.4 3.8 - - - -
100L ASN* 3.6 24.2 - - - +
135L PHE* 3.4 20.9 - - + -
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Residues in contact with GLU1402 (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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1400A LYS* 4.2 13.9 - - + -
1401A PRO* 1.3 78.8 - - - +
1403A PHE* 1.4 60.1 + - + +
1405A LEU* 3.0 29.3 + - - +
1406A LEU* 3.7 2.9 + - - +
1463A TYR* 4.0 19.4 - - + +
1590A PRO* 5.7 0.9 - - - +
1591A HIS* 3.9 32.0 + - + +
100L ASN* 5.2 3.7 - - + +
101L ASN* 3.9 11.4 - - - +
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Residues in contact with PHE1403 (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 VAL* 4.0 9.4 - - + -
1361A ASP* 3.4 33.4 - - - -
1364A CYS* 3.7 37.7 - - + -
1365A PRO* 3.7 21.8 - - + -
1368A THR* 5.3 2.0 - - + +
1399A VAL* 4.6 7.9 - - + -
1400A LYS* 3.2 37.7 + - + +
1402A GLU* 1.4 72.0 - - + +
1404A LEU* 1.3 60.1 + - - +
1405A LEU 3.2 0.2 - - - -
1406A LEU* 3.5 25.0 - - + +
1407A ARG* 2.8 33.6 + - - +
1589A TYR* 4.7 0.2 - - - -
1591A HIS* 3.9 23.3 - + - -
1601A TYR* 4.8 7.4 - + - -
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Residues in contact with LEU1404 (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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1389A ALA* 4.0 18.8 - - + -
1390A PRO* 4.4 6.5 - - + -
1396A LEU* 4.0 13.5 - - + -
1399A VAL* 3.5 24.2 - - + +
1400A LYS 3.2 8.5 + - - +
1401A PRO* 3.4 13.0 - - + +
1402A GLU 3.2 0.8 - - - -
1403A PHE* 1.3 78.2 - - - +
1405A LEU* 1.3 51.7 + - - +
1407A ARG* 3.5 20.8 - - + +
1408A THR* 2.5 39.1 + - - +
1460A ALA* 3.7 20.2 - - + +
1463A TYR* 4.5 4.5 - - + -
1464A ILE* 3.6 38.1 - - + -
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Residues in contact with LEU1405 (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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1401A PRO 3.6 2.2 + - - -
1402A GLU 3.0 11.9 + - - +
1404A LEU* 1.3 74.9 - - - +
1406A LEU* 1.3 67.0 + - - +
1408A THR* 3.1 2.2 + - - -
1409A LEU* 3.0 19.8 + - + -
1463A TYR* 3.4 44.3 + - + +
1466A ALA* 3.8 18.8 - - + -
1467A GLY* 3.2 21.2 - - - +
1470A LEU* 4.7 9.0 - - + -
1514A THR* 4.9 2.7 - - + -
1515A CYS* 4.9 1.6 - - - -
1518A VAL* 3.9 18.6 - - + -
1590A PRO* 3.7 33.4 - - + -
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Residues in contact with LEU1406 (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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1365A PRO* 3.5 41.1 - - + +
1368A THR* 3.8 11.9 - - - +
1369A LEU* 3.9 29.6 - - + -
1402A GLU 3.7 2.7 + - - +
1403A PHE* 3.4 25.0 + - + +
1405A LEU* 1.3 79.4 - - - +
1407A ARG* 1.3 54.2 - - - +
1409A LEU* 3.2 12.8 + - + +
1410A ALA* 2.8 37.4 + - + +
1589A TYR* 3.9 21.1 - - + +
1590A PRO* 4.2 17.7 - - + -
1591A HIS* 5.0 2.0 - - + +
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Residues in contact with ARG1407 (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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1329A MET* 3.7 39.9 + - - +
1330A VAL* 5.0 12.3 - - - +
1364A CYS* 4.2 8.3 - - - -
1368A THR* 4.9 7.0 + - + +
1386A TRP 4.1 16.0 + - - -
1387A LEU* 3.3 42.6 - - + +
1388A ARG 4.2 11.4 + - - -
1389A ALA* 5.0 0.9 - - - +
1390A PRO* 5.9 2.2 - - - +
1399A VAL* 4.0 34.7 - - - +
1403A PHE* 2.8 23.0 + - - +
1404A LEU* 3.5 26.0 - - + +
1406A LEU* 1.3 72.8 - - - +
1408A THR* 1.3 60.9 + - - +
1410A ALA* 3.5 2.2 + - - +
1411A ARG* 3.1 26.0 + - - +
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Residues in contact with THR1408 (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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1387A LEU 5.6 0.2 - - - -
1404A LEU* 2.5 27.8 + - - +
1405A LEU 3.1 4.4 + - - -
1407A ARG* 1.3 73.1 - - - +
1409A LEU* 1.3 65.7 + - - +
1411A ARG* 3.6 7.3 + - + +
1412A CYS* 3.0 31.7 + - - -
1429A ASN* 4.5 9.2 - - + -
1464A ILE* 3.3 46.3 + - + +
1467A GLY* 3.9 1.1 - - - -
1468A ALA* 3.5 23.1 - - + -
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Residues in contact with LEU1409 (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 LEU* 5.3 1.8 - - + -
1405A LEU* 3.0 12.5 + - + +
1406A LEU* 3.5 19.5 - - + +
1408A THR* 1.3 73.6 - - - +
1410A ALA* 1.3 70.0 + - + +
1412A CYS 2.9 12.6 + - - -
1413A LEU* 3.1 25.6 + - + +
1467A GLY* 3.5 14.6 + - - +
1470A LEU* 3.3 26.9 - - + -
1471A SER* 3.2 37.1 + - - +
1474A PHE* 3.6 17.5 - - + -
1585A LEU* 3.6 26.9 - - + -
1590A PRO* 5.3 5.4 - - + -
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Residues in contact with ALA1410 (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* 3.8 14.1 - - - +
1369A LEU* 5.4 0.9 - - + -
1372A ALA* 3.8 26.1 - - + +
1387A LEU* 3.7 23.8 - - + -
1406A LEU* 2.8 21.4 + - + +
1407A ARG* 3.8 2.2 - - - +
1409A LEU* 1.3 76.3 - - - +
1411A ARG* 1.3 64.8 + - - +
1413A LEU* 3.1 11.8 + - - +
1414A ILE* 3.2 16.7 + - - +
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Residues in contact with ARG1411 (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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1381A ARG* 5.9 1.2 - - - +
1384A ALA* 3.3 40.3 + - + +
1387A LEU* 3.9 14.3 - - + +
1388A ARG* 3.9 44.0 - - - +
1389A ALA 5.2 0.4 - - - +
1407A ARG 3.1 16.0 + - - +
1408A THR* 3.8 10.1 - - - +
1409A LEU 3.1 0.2 + - - -
1410A ALA* 1.3 78.8 - - - +
1412A CYS* 1.3 61.9 + - - +
1414A ILE* 3.1 9.1 + - - +
1415A LEU* 2.9 62.6 + - - +
1429A ASN* 3.5 27.1 + - - +
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Residues in contact with CYS1412 (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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1408A THR* 3.0 28.5 - - - -
1409A LEU 2.9 3.4 + - - -
1411A ARG* 1.3 81.2 - - - +
1413A LEU* 1.3 62.2 + - - +
1415A LEU* 3.1 31.4 - - - +
1416A TRP 3.5 0.2 + - - -
1419A ILE* 3.2 20.4 - - + +
1425A TRP* 3.4 31.0 - - + -
1429A ASN* 4.8 5.2 - - - -
1468A ALA* 4.5 7.0 - - - -
1471A SER* 3.0 25.1 - - - +
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Residues in contact with LEU1413 (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 ALA* 4.6 14.1 - - + +
1376A LEU* 4.2 10.3 - - + +
1377A LYS* 3.2 19.6 + - - +
1409A LEU* 3.1 28.5 + - + +
1410A ALA* 3.1 7.4 + - - +
1412A CYS* 1.3 79.1 - - - +
1414A ILE* 1.3 57.4 + - - +
1416A TRP* 3.4 41.2 + - + -
1419A ILE* 5.3 0.2 - - + -
1471A SER* 3.4 18.4 - - - +
1474A PHE* 3.7 21.1 - - + -
1581A ILE* 3.9 26.7 - - + -
1585A LEU* 4.0 17.5 - - + -
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Residues in contact with ILE1414 (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 LEU 3.2 27.1 - - - +
1372A ALA* 3.8 7.4 - - - +
1375A TYR* 3.1 27.8 - - + +
1377A LYS* 3.6 4.5 - - - -
1378A THR* 4.2 2.5 - - + -
1379A ASN* 3.2 26.9 + - - +
1380A ASN* 3.7 33.9 - - + +
1383A ILE* 4.2 11.7 - - + -
1384A ALA* 4.6 7.0 - - + +
1387A LEU* 3.7 30.3 - - + -
1410A ALA 3.3 9.0 - - - +
1411A ARG* 3.1 7.8 + - - +
1413A LEU* 1.3 76.8 - - - +
1415A LEU* 1.3 55.6 + - - +
1416A TRP 3.3 5.2 + - - -
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Residues in contact with LEU1415 (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 ASN* 4.2 12.6 - - + +
1380A ASN 4.8 3.6 - - - +
1381A ARG* 4.5 25.4 - - - +
1384A ALA* 3.6 29.2 - - + -
1411A ARG* 2.9 52.9 + - - +
1412A CYS* 3.1 16.9 + - + +
1414A ILE* 1.3 70.8 - - - +
1416A TRP* 1.3 65.3 + - - +
1417A ASP 3.3 2.7 - - - -
1418A ASP* 3.3 32.7 + - + +
1419A ILE* 3.8 6.1 - - - +
1425A TRP* 5.4 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