Contacts of the helix formed by residues 1370 - 1382 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1341A ASP* 4.8 5.2 - - - +
1343A PHE* 3.9 3.6 - - - -
1368A TYR 3.4 4.9 + - - +
1369A GLU* 1.3 77.0 - - - +
1371A ARG* 1.3 65.7 + - - +
1372A GLU* 3.2 30.4 + - - +
1373A ASP* 3.2 19.9 + - - +
1374A PHE* 3.2 19.6 + - - +
23C TYR* 2.5 68.6 + - - +
24C THR* 4.3 5.5 + - - +
26C ASN* 3.0 36.1 + - - +
42C ALA* 4.9 3.0 - - - +
44C VAL* 4.1 19.5 - - - +
166C LYS* 4.6 9.6 - - - +
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Residues in contact with ARG1371 (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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1343A PHE* 3.7 16.9 - - + -
1370A ARG* 1.3 73.1 - - - +
1372A GLU* 1.3 65.9 + - - +
1374A PHE* 4.2 2.9 - - + -
1375A GLN* 2.8 46.2 + - - +
1408A CYS* 4.0 25.5 + - - -
1409A PHE* 3.7 26.0 - - - +
1410A THR* 3.7 17.9 + - - +
26C ASN* 3.2 26.6 + - - +
27C ALA 2.7 30.5 + - - -
28C PHE* 4.0 8.4 - - - +
29C PRO* 4.0 13.1 - - - +
162C GLN* 3.0 20.8 - - - +
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Residues in contact with GLU1372 (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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1370A ARG* 3.2 41.0 + - - +
1371A ARG* 1.3 82.2 + - - +
1373A ASP* 1.3 62.3 + - - +
1375A GLN* 4.0 3.5 - - - +
1376A MET* 3.1 34.5 + - + +
23C TYR* 5.5 0.7 - - - -
26C ASN* 2.8 23.1 - - - +
162C GLN* 4.0 20.6 + - + +
166C LYS* 3.5 33.1 - - + +
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Residues in contact with ASP1373 (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 TYR 5.0 2.8 - - - +
1369A GLU* 4.7 8.3 - - + +
1370A ARG* 3.2 27.8 + - - +
1372A GLU* 1.3 75.3 - - - +
1374A PHE* 1.3 62.8 + - - +
1376A MET* 3.4 16.1 + - - +
1377A GLN* 3.2 24.1 + - - +
166C LYS* 3.7 26.1 + - - +
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Residues in contact with PHE1374 (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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1343A PHE* 3.7 28.7 - + + -
1345A VAL* 3.7 22.9 - - + -
1363A TYR* 3.4 51.1 - + + -
1364A ARG 5.7 1.8 - - - -
1365A GLY* 5.9 0.2 - - - -
1369A GLU* 3.7 25.3 + - - +
1370A ARG 3.2 10.1 + - - +
1371A ARG* 3.7 6.3 - - - +
1373A ASP* 1.3 75.4 - - - +
1375A GLN* 1.3 72.7 + - - +
1377A GLN* 3.2 9.5 + - + +
1378A LEU* 2.9 37.9 + - + +
1408A CYS* 4.2 9.6 - - - -
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Residues in contact with GLN1375 (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 ARG* 2.8 40.8 + - - +
1372A GLU* 4.0 4.0 - - - +
1374A PHE* 1.3 84.3 - - - +
1376A MET* 1.3 54.2 + - - +
1378A LEU* 3.1 7.5 + - + +
1379A MET* 2.7 47.0 + - + +
1387A LYS* 4.1 38.0 - - + +
1406A ILE* 4.9 4.4 + - - +
1408A CYS* 3.5 38.3 + - + +
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Residues in contact with MET1376 (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 GLU* 3.1 29.8 + - + +
1373A ASP* 3.6 16.2 - - - +
1375A GLN* 1.3 73.6 - - - +
1377A GLN* 1.3 65.2 + - - +
1379A MET* 3.4 8.3 + - - +
1380A THR* 3.3 23.7 + - - -
166C LYS* 6.2 1.3 - - + -
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Residues in contact with GLN1377 (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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1197A LYS* 5.4 10.3 - - - +
1369A GLU* 4.4 12.6 - - - +
1373A ASP 3.2 10.8 + - - +
1374A PHE* 3.5 9.8 - - + +
1376A MET* 1.3 79.9 - - - +
1378A LEU* 1.3 60.5 + - - +
1380A THR* 3.1 21.8 - - - +
1381A GLN* 3.4 15.0 + - - +
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Residues in contact with LEU1378 (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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1345A VAL* 4.2 13.0 - - + -
1347A TYR* 3.5 28.0 - - + +
1363A TYR* 5.3 2.7 - - + +
1374A PHE* 2.9 43.1 + - + +
1375A GLN* 3.4 13.9 - - + +
1377A GLN* 1.3 73.2 - - - +
1379A MET* 1.3 64.1 + - - +
1380A THR 2.9 5.4 - - - -
1381A GLN* 3.0 26.5 + - - +
1382A PHE* 3.5 30.2 - - + -
1406A ILE* 4.5 21.5 - - + -
1408A CYS* 4.5 7.2 - - + -
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Residues in contact with MET1379 (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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1375A GLN* 2.7 41.5 + - + +
1376A MET* 3.4 8.9 + - - +
1378A LEU* 1.3 76.3 - - - +
1380A THR* 1.3 56.6 + - - +
1382A PHE 2.3 29.7 - - - +
1383A PRO* 3.6 4.0 - - - +
1385A ALA* 3.6 42.2 - - + +
1387A LYS* 4.1 26.5 - - + +
1406A ILE* 3.6 25.6 - - + -
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Residues in contact with THR1380 (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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1376A MET* 3.3 10.6 + - - +
1377A GLN* 3.1 15.7 - - + +
1378A LEU 2.9 0.4 - - - -
1379A MET* 1.3 78.3 - - - +
1381A GLN* 1.3 65.5 + - + +
1382A PHE 3.0 2.5 + - - -
1383A PRO* 3.8 14.8 - - - +
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Residues in contact with GLN1381 (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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1196A SER 5.0 14.9 + - - +
1197A LYS* 5.7 2.1 - - - +
1198A ASP* 3.9 32.5 + - - +
1347A TYR* 5.3 1.8 + - - -
1363A TYR* 6.0 0.2 + - - -
1377A GLN* 3.4 14.9 + - - +
1378A LEU* 3.0 23.0 + - - +
1380A THR* 1.3 79.1 - - + +
1382A PHE* 1.3 90.0 + - + +
1383A PRO* 3.9 4.7 - - - +
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Residues in contact with PHE1382 (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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1347A TYR* 3.8 28.9 - + - -
1352A PHE* 4.3 11.9 - + - -
1353A PRO* 6.1 2.2 - - + -
1356A LEU* 4.1 15.7 - - + -
1378A LEU* 3.5 17.7 - - + -
1379A MET* 2.3 24.1 + - - +
1381A GLN* 1.3 110.4 - - + +
1383A PRO* 1.3 63.1 - - - +
1384A ASN 3.3 1.3 - - - -
1385A ALA* 3.5 26.5 - - + +
1404A GLN* 3.7 21.8 - - - +
1406A ILE* 3.7 14.1 - - + -
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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