Contacts of the helix formed by residues 1365 - 1377 (chain M) in PDB entry 3HOU
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 TYR1365 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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869M GLY 4.4 10.8 - - - -
870M GLU* 2.6 42.1 + - - -
1345M ARG* 3.7 13.5 + - - -
1349M TYR* 3.4 38.1 - + - +
1362M TYR* 4.1 5.8 + - - +
1363M VAL 3.2 5.8 + - - -
1364M ASN* 1.3 73.7 + - - +
1366M ARG* 1.3 72.4 + - + +
1367M HIS 2.8 2.1 + - - -
1368M MET* 3.1 6.3 + - - +
1369M ALA* 2.8 40.7 + - + +
200Q ARG* 4.3 0.2 + - - -
202Q SER* 4.9 1.5 - - - -
203Q GLU* 3.2 48.7 - - + +
204Q THR* 4.5 14.1 - - + -
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Residues in contact with ARG1366 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865M GLN* 4.2 2.4 + - - -
868M TYR* 3.1 43.7 - - + +
869M GLY* 3.9 21.9 - - - -
871M ASP* 2.5 37.6 + - - -
873M MET* 3.2 15.1 + - - +
875M ALA* 3.7 19.0 - - - +
878M ILE* 3.6 13.3 - - - +
1364M ASN* 2.7 66.6 + - - +
1365M TYR* 1.3 85.5 - - + +
1367M HIS* 1.3 64.8 + - + +
1369M ALA* 3.4 3.9 - - - +
1370M LEU* 2.9 29.8 + - - +
204Q THR* 4.0 7.6 + - - -
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Residues in contact with HIS1367 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514M PRO 2.8 25.4 + - - -
515M GLN* 3.1 20.3 + - - -
868M TYR* 4.0 17.8 + - - -
875M ALA* 5.0 0.4 - - + -
1067M LEU* 3.9 20.2 - - + -
1068M ALA* 3.5 33.1 - - - +
1071M SER* 3.4 27.8 + - - -
1072M ILE* 4.2 4.2 - - + +
1363M VAL* 3.8 13.0 - - + -
1364M ASN* 2.9 17.1 + - + +
1365M TYR 2.8 4.4 + - - -
1366M ARG* 1.3 77.9 - - + +
1368M MET* 1.3 66.4 + - - +
1370M LEU* 3.1 6.8 + - - +
1371M LEU* 3.1 19.2 + - - +
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Residues in contact with MET1368 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1072M ILE* 4.2 20.0 - - + -
1349M TYR* 3.1 42.6 - - + +
1352M VAL* 4.4 13.2 - - + -
1353M TYR* 4.1 25.6 - - + -
1356M ILE* 3.7 25.4 - - + -
1363M VAL* 4.1 33.0 - - + +
1365M TYR* 3.1 6.6 + - - +
1367M HIS* 1.3 73.8 - - - +
1369M ALA* 1.3 62.8 + - - +
1371M LEU* 3.0 2.9 + - - +
1372M VAL* 2.8 30.1 + - + +
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Residues in contact with ALA1369 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865M GLN* 3.8 10.3 - - - +
870M GLU* 4.8 0.7 - - - +
1345M ARG* 5.0 2.7 - - - +
1349M TYR* 4.0 10.9 - - - -
1365M TYR* 2.8 51.6 + - + +
1366M ARG 3.4 5.6 - - - +
1368M MET* 1.3 77.5 - - - +
1370M LEU* 1.3 58.3 + - - +
1372M VAL* 3.2 4.0 + - - +
1373M ASP* 2.8 38.7 + - - +
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Residues in contact with LEU1370 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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845M LEU* 4.5 6.5 - - + -
848M ILE* 3.7 18.4 - - + -
856M THR* 3.8 18.6 - - + -
864M ILE* 4.4 1.8 - - + -
865M GLN* 3.3 38.1 - - + +
868M TYR* 4.7 1.6 - - + -
1064M VAL* 4.0 21.5 - - + -
1065M GLY* 5.1 1.6 - - - -
1068M ALA* 4.2 13.7 - - + -
1366M ARG 2.9 13.6 + - - +
1367M HIS 3.1 9.4 + - - +
1369M ALA* 1.3 76.1 - - - +
1371M LEU* 1.3 64.1 + - - +
1373M ASP* 3.3 2.5 + - - +
1374M VAL* 3.0 36.8 + - + +
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Residues in contact with LEU1371 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841M LEU* 3.6 29.4 - - + -
844M ALA* 6.2 1.1 - - + -
845M LEU* 4.8 20.5 - - + +
1072M ILE* 3.6 34.8 - - + -
1101M LEU* 6.2 0.4 - - + -
1105M LEU* 3.8 13.2 - - + -
1352M VAL* 5.1 13.7 - - + -
1367M HIS 3.1 5.2 + - - +
1368M MET 3.0 8.1 + - - +
1370M LEU* 1.3 75.1 - - - +
1372M VAL* 1.3 68.0 - - + +
1374M VAL* 2.9 18.2 + - + +
1375M MET* 3.0 33.7 + - + +
1384M VAL* 4.3 7.6 - - + -
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Residues in contact with VAL1372 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1345M ARG* 3.4 44.0 - - + +
1348M LEU* 3.9 21.0 - - + +
1349M TYR* 3.5 33.7 - - + +
1352M VAL* 4.4 11.0 - - + -
1368M MET 2.8 26.5 + - - +
1369M ALA* 3.4 6.5 - - - +
1371M LEU* 1.3 74.0 - - + +
1373M ASP* 1.3 62.2 + - - +
1375M MET* 3.2 12.4 + - - +
1376M THR* 3.3 15.6 + - - +
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Residues in contact with ASP1373 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864M ILE* 3.8 26.4 - - + +
865M GLN* 3.5 18.0 + - + +
870M GLU* 4.4 1.6 - - - +
1345M ARG* 2.9 39.7 + - - +
1369M ALA* 2.8 21.7 + - - +
1370M LEU* 3.5 6.3 - - - +
1372M VAL* 1.3 74.6 - - - +
1374M VAL* 1.3 59.2 + - - +
1376M THR* 2.8 8.0 + - - -
1377M THR* 2.8 36.6 + - + +
200Q ARG* 4.1 5.7 + - - -
208Q TYR* 6.0 0.3 - - - -
212Q ARG* 5.8 1.4 + - - -
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Residues in contact with VAL1374 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844M ALA* 4.2 10.1 - - + +
845M LEU* 3.8 18.6 - - + -
848M ILE* 3.4 31.0 - - + -
864M ILE* 3.7 14.1 - - + -
1370M LEU* 3.0 22.6 + - + +
1371M LEU* 2.9 9.2 + - + +
1373M ASP* 1.3 75.8 - - - +
1375M MET* 1.3 62.0 + - + +
1376M THR 3.4 0.5 + - - -
1377M THR* 3.8 13.6 + - - +
1378M GLN* 5.0 2.6 + - - +
1382M THR* 4.7 5.9 + - - +
1389M PHE* 6.1 4.3 - - + -
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Residues in contact with MET1375 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1104M ILE* 3.9 22.4 - - + +
1105M LEU* 3.9 19.7 - - - +
1107M VAL* 4.1 11.0 - - + -
1332M PHE* 5.6 0.4 - - + -
1348M LEU* 3.9 31.9 - - + -
1352M VAL* 6.0 1.6 - - - -
1371M LEU* 3.0 38.0 + - + +
1372M VAL* 3.5 9.4 - - - +
1373M ASP 3.1 0.2 - - - -
1374M VAL* 1.3 77.4 - - + +
1376M THR* 1.3 59.1 + - - +
1378M GLN* 5.4 0.4 - - - +
1379M GLY 5.6 0.2 + - - -
1380M GLY 3.3 5.2 - - - +
1381M LEU* 3.8 2.0 - - + -
1382M THR* 2.9 57.7 + - - +
1384M VAL* 4.0 10.5 - - + -
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Residues in contact with THR1376 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1341M ILE* 3.4 22.8 - - + +
1345M ARG* 3.4 33.7 - - + +
1348M LEU* 4.0 15.5 - - + -
1372M VAL 3.4 14.9 + - - +
1373M ASP* 2.8 16.2 + - - -
1375M MET* 1.3 82.6 - - - +
1377M THR* 1.3 67.2 + - - +
1378M GLN 3.2 2.5 - - - -
1379M GLY 2.8 14.5 + - - -
1380M GLY 3.5 15.3 - - - +
1381M LEU* 4.2 5.2 - - + -
212Q ARG* 3.7 9.4 + - - -
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Residues in contact with THR1377 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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863M VAL 4.1 7.1 + - - +
864M ILE* 3.9 38.8 - - + +
1373M ASP* 2.8 28.7 + - + +
1374M VAL* 3.8 11.4 + - - +
1376M THR* 1.3 72.4 + - - +
1378M GLN* 1.3 72.1 + - - +
1379M GLY 2.9 1.6 + - - -
176Q PRO* 3.7 19.9 - - + -
177Q ARG 3.0 26.1 + - - +
212Q ARG* 3.9 10.0 + - - +
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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