Contacts of the helix formed by residues 1359 - 1375 (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 ASN1359 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1291A ARG* 3.2 26.6 + - - +
1354A GLU* 4.2 11.9 + - - -
1358A ILE* 1.3 79.4 - - - +
1360A VAL* 1.3 61.8 + - - +
1361A ASP* 3.6 13.4 + - - +
1362A VAL* 3.5 25.4 + - - +
1363A THR* 3.2 18.7 + - - +
30L VAL* 3.5 41.8 - - + +
67L GLN* 4.8 0.9 - - - +
69L ARG* 5.3 3.8 - - + +
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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
----------------------------------------------------------
1328A TYR 3.4 18.4 - - - +
1329A MET 3.6 12.3 - - - +
1330A VAL 4.0 2.7 - - - +
1331A GLY* 3.7 24.2 - - - +
1358A ILE* 4.5 2.0 - - + -
1359A ASN* 1.3 75.4 - - - +
1361A ASP* 1.3 77.4 + - - +
1362A VAL 3.2 1.8 - - - -
1363A THR* 3.5 6.3 - - - -
1364A CYS* 2.6 49.2 + - + +
1365A PRO* 3.8 0.2 - - - +
1398A PHE 5.5 4.3 - - - +
1400A LYS* 6.5 0.2 - - + -
1403A PHE* 4.8 6.5 - - + -
69L ARG* 5.1 18.7 - - + +
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Residues in contact with ASP1361 (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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1292A GLU* 4.5 4.6 - - - +
1359A ASN* 3.2 14.3 - - - +
1360A VAL* 1.3 93.2 + - - +
1362A VAL* 1.3 60.9 + - - +
1365A PRO* 3.8 3.3 - - - +
1400A LYS* 3.2 35.8 + - - +
1403A PHE* 3.4 24.4 - - - -
1601A TYR* 4.5 13.6 - - - +
30L VAL* 5.0 0.3 - - - +
67L GLN* 3.8 36.9 - - - +
68L PHE 4.5 9.9 - - - +
69L ARG* 5.1 3.8 - - - -
135L PHE* 5.5 3.5 - - - +
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Residues in contact with VAL1362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1277A ILE 4.9 0.4 - - - +
1279A ARG 6.0 1.8 - - - +
1291A ARG* 3.6 62.1 - - + +
1292A GLU* 3.7 29.0 - - - +
1295A SER* 3.1 34.5 + - - -
1359A ASN* 3.5 13.3 + - - +
1360A VAL 3.2 0.2 - - - -
1361A ASP* 1.3 77.2 - - + +
1363A THR* 1.3 67.0 + - + +
1365A PRO* 3.3 17.2 - - - +
67L GLN* 6.0 0.7 - - - +
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Residues in contact with THR1363 (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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1277A ILE* 3.3 24.4 - - - +
1278A GLY* 3.7 15.7 - - - -
1279A ARG 5.2 0.4 - - - +
1295A SER* 3.4 10.1 + - - -
1328A TYR* 3.2 33.9 + - + -
1358A ILE* 4.0 7.0 - - + +
1359A ASN* 3.2 20.0 + - - +
1360A VAL* 3.0 2.7 + - - -
1362A VAL* 1.3 80.2 - - + +
1364A CYS* 1.3 66.4 + - - +
1365A PRO* 3.3 5.0 - - - +
1366A GLY 3.7 1.7 + - - -
1367A ALA* 3.3 21.0 + - - +
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Residues in contact with CYS1364 (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* 3.4 40.2 - - - +
1360A VAL* 2.6 39.4 + - + +
1363A THR* 1.3 74.0 + - - +
1365A PRO* 1.4 64.2 - - + +
1367A ALA* 3.4 2.4 + - - +
1368A THR* 3.1 27.1 + - - +
1403A PHE* 3.7 29.4 - - + -
1407A ARG* 4.2 7.0 - - - -
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Residues in contact with PRO1365 (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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1292A GLU* 5.0 3.6 - - + +
1296A LEU* 4.7 12.6 - - + -
1361A ASP 3.8 11.2 - - - +
1362A VAL 3.3 20.4 - - - +
1363A THR 3.3 1.3 - - - -
1364A CYS* 1.4 93.1 - - + +
1366A GLY* 1.3 63.2 + - - +
1368A THR* 2.8 21.1 + - - -
1369A LEU* 3.3 10.5 + - - +
1403A PHE* 3.7 15.0 - - + -
1406A LEU* 3.5 22.6 - - + +
1589A TYR* 3.4 27.6 - - + +
1601A TYR* 5.7 4.5 - - + -
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Residues in contact with GLY1366 (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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1277A ILE* 4.0 6.5 - - - -
1295A SER 4.3 2.7 - - - -
1296A LEU* 4.1 28.1 - - - +
1299A GLY* 4.0 12.3 - - - -
1362A VAL 5.1 0.2 + - - -
1363A THR 3.7 3.2 + - - -
1365A PRO* 1.3 80.9 - - - +
1367A ALA* 1.3 64.8 + - - +
1369A LEU* 3.0 6.2 + - - +
1370A ALA* 2.9 22.9 + - - +
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Residues in contact with ALA1367 (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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1277A ILE* 3.5 14.4 - - + +
1325A LEU* 3.8 19.8 - - - +
1328A TYR* 3.9 8.7 - - + -
1329A MET* 3.7 28.9 - - + +
1363A THR 3.3 18.3 + - - +
1364A CYS 3.5 4.9 - - - +
1366A GLY* 1.3 75.5 - - - +
1368A THR* 1.3 62.1 + - - +
1370A ALA* 3.2 4.1 + - - +
1371A LEU* 3.2 19.9 + - - +
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Residues in contact with THR1368 (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 35.6 - - + +
1364A CYS* 3.1 21.6 + - - +
1365A PRO* 2.8 20.9 + - + -
1367A ALA* 1.3 75.2 - - - +
1369A LEU* 1.3 61.8 + - - +
1371A LEU* 3.4 5.2 + - - +
1372A ALA 3.1 17.2 + - - -
1387A LEU* 4.4 12.8 - - + -
1403A PHE* 5.3 1.8 - - + +
1406A LEU* 3.8 21.7 - - + +
1407A ARG* 4.9 12.6 - - + +
1410A ALA* 3.8 16.4 - - - +
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Residues in contact with LEU1369 (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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1296A LEU* 3.5 30.3 - - + -
1299A GLY 5.1 0.4 - - - -
1300A LEU* 3.9 26.9 - - + -
1365A PRO 3.7 2.5 - - - +
1366A GLY* 3.0 10.4 + - - +
1368A THR* 1.3 79.2 + - - +
1370A ALA* 1.3 63.8 + - - +
1372A ALA* 3.3 10.0 + - + +
1373A MET* 3.3 28.3 + - - +
1406A LEU* 3.9 15.9 - - + -
1409A LEU* 5.3 1.6 - - + -
1410A ALA* 5.4 0.9 - - + -
1585A LEU* 3.7 44.9 - - + +
1589A TYR* 3.6 23.8 - - + -
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Residues in contact with ALA1370 (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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1299A GLY* 3.5 24.8 + - - +
1302A LEU* 4.7 3.4 - - + -
1303A GLY* 4.1 13.7 - - - +
1325A LEU* 3.7 22.4 - - + -
1366A GLY 2.9 9.4 + - - +
1367A ALA* 3.2 9.4 + - - +
1369A LEU* 1.3 75.3 - - - +
1371A LEU* 1.3 57.7 + - - +
1373A MET* 3.4 2.6 + - - +
1374A ILE* 2.9 40.2 + - + +
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Residues in contact with LEU1371 (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 PRO* 4.7 9.0 - - + -
1325A LEU* 3.7 35.0 - - + -
1329A MET* 3.3 31.4 - - + -
1367A ALA 3.2 5.1 + - - +
1368A THR 3.7 7.9 - - - +
1369A LEU 3.4 0.2 - - - -
1370A ALA* 1.3 78.8 - - - +
1372A ALA* 1.3 58.9 + - - +
1375A TYR* 3.4 48.3 + - + +
1383A ILE* 3.9 21.1 - - + -
1386A TRP* 3.9 20.0 - - + +
1387A LEU* 4.6 6.5 - - + -
1414A ILE* 3.2 15.4 - - - +
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Residues in contact with ALA1372 (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 3.1 7.3 + - - +
1369A LEU* 3.3 15.4 + - + +
1371A LEU* 1.3 77.4 - - - +
1373A MET* 1.3 61.6 + - + +
1375A TYR 3.5 1.7 - - - +
1376A LEU* 3.3 29.8 - - - +
1409A LEU* 6.4 0.4 - - + -
1410A ALA* 3.8 30.9 - - + +
1413A LEU* 4.6 15.7 - - + +
1414A ILE* 3.8 13.9 - - - +
1585A LEU* 4.9 5.2 - - + -
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Residues in contact with MET1373 (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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1300A LEU* 3.7 31.4 - - + +
1303A GLY* 3.3 26.7 - - - +
1304A MET* 4.1 14.1 - - + -
1307A LEU* 3.2 16.9 - - + -
1308A GLY* 2.5 33.9 + - - -
1369A LEU 3.3 16.0 + - - +
1370A ALA 3.8 0.4 - - - +
1372A ALA* 1.3 71.8 - - - +
1374A ILE* 1.3 53.6 + - - +
1375A TYR 3.2 3.2 + - - -
1376A LEU* 3.3 18.7 - - + +
1582A ALA* 3.6 36.8 - - + +
1585A LEU* 3.7 22.9 - - + -
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Residues in contact with ILE1374 (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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1302A LEU* 3.7 28.9 - - + -
1303A GLY* 4.2 8.1 - - - -
1306A CYS* 3.6 29.8 - - + -
1308A GLY* 3.2 18.9 - - - +
1309A HIS 3.6 0.3 + - - -
1310A GLY 3.3 26.4 + - - +
1313A LEU* 4.6 6.5 - - + -
1321A VAL* 4.7 13.0 - - + -
1325A LEU* 3.8 20.4 - - + -
1370A ALA* 2.9 25.9 + - + +
1373A MET* 1.3 70.6 - - - +
1375A TYR* 1.3 80.4 + - + +
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Residues in contact with TYR1375 (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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1310A GLY 3.6 9.1 + - - -
1311A SER* 3.4 33.0 + - - -
1313A LEU* 6.1 0.2 - - - +
1321A VAL* 4.5 4.3 - - + +
1322A PRO* 3.2 32.1 - - + +
1325A LEU* 5.4 0.4 - - + -
1371A LEU* 3.4 47.2 + - + +
1372A ALA 3.5 2.9 - - - -
1373A MET 3.2 0.4 - - - -
1374A ILE* 1.3 102.7 - - + +
1376A LEU* 1.3 59.7 + - - +
1378A THR* 3.4 20.7 - - + +
1380A ASN* 3.4 17.3 - - - -
1383A ILE* 3.5 25.1 - - + +
1414A ILE* 3.1 34.4 - - + +
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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