Contacts of the helix formed by residues 1370 - 1382 (chain B) in PDB entry 2YIN
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 ARG1370 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1341B ASP* 4.8 3.4 - - - +
1343B PHE* 3.8 4.0 - - - -
1368B TYR 3.4 4.7 + - - +
1369B GLU* 1.3 77.0 - - - +
1371B ARG* 1.3 66.1 + - - +
1372B GLU* 2.8 47.7 + - - +
1373B ASP* 3.0 31.8 + - - +
1374B PHE* 3.1 11.8 + - - +
23D TYR* 2.3 65.8 + - - +
24D THR* 4.3 6.9 + - - +
26D ASN* 2.9 31.0 + - + +
42D ALA* 5.0 2.4 - - - +
44D VAL* 4.4 16.6 - - - +
166D LYS* 4.7 13.0 - - - +
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Residues in contact with ARG1371 (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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1343B PHE* 3.7 15.8 - - + -
1370B ARG* 1.3 73.0 - - - +
1372B GLU* 1.3 69.4 + - - +
1374B PHE* 4.3 2.9 - - + -
1375B GLN* 2.9 38.6 + - - +
1408B CYS* 3.9 23.1 + - - -
1409B PHE* 3.7 26.0 - - - +
1410B THR* 3.4 22.1 + - - +
26D ASN* 3.4 31.6 + - - +
27D ALA 2.4 38.7 + - - -
28D PHE* 3.7 7.4 - - - +
29D PRO* 4.3 10.3 - - - +
162D GLN* 3.3 15.6 - - - +
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Residues in contact with GLU1372 (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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1370B ARG* 2.8 49.7 + - - +
1371B ARG* 1.3 80.0 + - - +
1373B ASP* 1.3 61.0 + - - +
1375B GLN* 4.5 3.1 - - - +
1376B MET* 3.4 35.3 + - + +
23D TYR* 4.9 1.4 - - - -
26D ASN* 3.3 10.0 - - - +
162D GLN* 5.4 11.6 + - + +
166D LYS* 3.9 33.5 - - + +
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Residues in contact with ASP1373 (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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1368B TYR 4.7 2.6 - - - +
1369B GLU* 4.5 10.3 - - + +
1370B ARG* 3.0 37.8 + - - +
1372B GLU* 1.3 75.6 - - - +
1374B PHE* 1.3 65.2 + - - +
1376B MET* 3.5 20.5 - - - +
1377B GLN* 3.5 11.1 + - - +
166D LYS* 3.8 25.9 + - - -
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Residues in contact with PHE1374 (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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1343B PHE* 3.7 30.5 - + + -
1345B VAL* 3.7 23.8 - - + -
1363B TYR* 3.5 48.7 - + + -
1364B ARG 5.6 2.7 - - - -
1369B GLU* 3.8 24.8 + - - +
1370B ARG 3.1 11.4 + - - +
1371B ARG* 3.8 6.3 - - - +
1373B ASP* 1.3 72.7 - - - +
1375B GLN* 1.3 71.4 + - - +
1376B MET 3.0 2.0 + - - -
1377B GLN* 3.0 12.0 + - + +
1378B LEU* 3.0 34.3 + - + +
1408B CYS* 4.3 8.5 - - - -
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Residues in contact with GLN1375 (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* 2.9 32.8 + - - +
1372B GLU* 4.5 3.4 - - - +
1374B PHE* 1.3 80.5 - - - +
1376B MET* 1.3 58.3 + - - +
1378B LEU* 3.2 9.5 + - + +
1379B MET* 2.9 51.9 + - + +
1387B LYS* 4.1 32.1 - - - +
1388B MET 5.9 0.4 + - - -
1406B ILE* 4.8 4.6 + - - +
1408B CYS* 3.3 40.3 + - + +
28D PHE* 6.1 0.4 - - - -
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Residues in contact with MET1376 (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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1372B GLU* 3.4 32.3 + - + +
1373B ASP* 3.5 11.7 - - - +
1374B PHE 3.0 0.6 - - - -
1375B GLN* 1.3 78.3 - - - +
1377B GLN* 1.3 63.7 + - - +
1379B MET* 3.2 8.4 + - + +
1380B THR* 2.9 26.9 + - - +
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Residues in contact with GLN1377 (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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1369B GLU* 4.6 10.7 - - - +
1373B ASP 3.5 8.3 + - - +
1374B PHE* 3.0 11.6 + - + +
1376B MET* 1.3 79.0 - - - +
1378B LEU* 1.3 57.2 + - - +
1380B THR* 3.2 12.4 - - + +
1381B GLN* 2.9 31.4 + - + +
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Residues in contact with LEU1378 (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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1198B ASP* 5.7 2.0 - - - +
1345B VAL* 3.8 31.2 - - + -
1347B TYR* 3.7 21.1 - - - +
1363B TYR* 5.0 4.9 - - + +
1374B PHE* 3.0 31.1 + - + +
1375B GLN* 3.4 11.4 - - + +
1376B MET 3.1 0.2 - - - -
1377B GLN* 1.3 75.2 - - - +
1379B MET* 1.3 66.1 + - - +
1381B GLN* 3.1 17.5 + - - +
1382B PHE* 3.0 34.8 + - + -
1406B ILE* 4.2 25.6 - - + -
1408B CYS* 4.6 7.9 - - + -
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Residues in contact with MET1379 (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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1375B GLN* 2.9 51.0 + - + +
1376B MET* 3.7 6.1 - - - +
1378B LEU* 1.3 76.4 - - - +
1380B THR* 1.3 61.6 + - - +
1382B PHE* 2.3 34.7 - - - +
1383B PRO* 3.5 5.5 - - - +
1385B ALA* 3.7 33.0 - - + +
1386B GLU 4.5 0.7 - - - -
1387B LYS* 4.0 25.8 - - + +
1406B ILE* 4.5 16.4 - - + -
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Residues in contact with THR1380 (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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1376B MET* 2.9 18.3 + - - +
1377B GLN* 3.2 15.9 - - + +
1379B MET* 1.3 79.1 - - - +
1381B GLN* 1.3 64.4 + - + +
1382B PHE 3.3 0.3 + - - -
1383B PRO* 3.8 13.5 - - - +
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Residues in contact with GLN1381 (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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1198B ASP* 3.0 35.5 + - - +
1199B ASN* 4.9 10.9 + - - -
1347B TYR* 5.5 0.8 + - - -
1377B GLN* 2.9 16.1 + - + +
1378B LEU* 3.1 20.3 + - - +
1380B THR* 1.3 81.0 - - + +
1382B PHE* 1.3 87.3 + - + +
1383B PRO* 3.6 6.6 - - - +
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Residues in contact with PHE1382 (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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1199B ASN* 6.0 1.8 - - - -
1347B TYR* 3.7 22.2 - + - -
1352B PHE* 4.2 11.2 - + - -
1353B PRO* 5.9 2.9 - - + -
1356B LEU* 3.9 25.8 - - + -
1378B LEU* 3.0 18.6 + - + +
1379B MET* 2.3 26.3 - - - +
1381B GLN* 1.3 106.3 - - + +
1383B PRO* 1.3 63.1 - - - +
1384B ASN 3.4 0.7 - - - -
1385B ALA* 3.7 24.6 + - + +
1404B GLN* 3.9 21.5 - - - +
1406B ILE* 3.8 15.3 - - + -
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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