Contacts of the helix formed by residues 1293 - 1311 (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 MET1293 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1238A THR* 3.7 28.7 - - + +
1242A TYR* 5.4 1.1 - - + -
1288A PHE* 2.9 29.6 + - + +
1291A GLY 3.3 19.1 - - - +
1292A LYS* 1.3 83.6 - - + +
1294A TRP* 1.3 57.8 + - - +
1295A GLU* 3.3 2.9 - - - -
1296A GLU* 3.2 11.8 + - + +
1297A ALA* 2.9 27.2 + - - +
1337A ARG* 4.6 1.6 - - - +
1364A ARG* 3.9 19.3 - - - +
1433A PHE* 3.8 29.8 - - + -
1437A ASN* 4.0 2.0 - - - +
1438A TYR* 4.7 6.7 - - - -
1476A PRO* 4.0 24.5 - - + -
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Residues in contact with TRP1294 (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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1289A ASP* 3.1 34.0 + - - -
1292A LYS* 3.1 26.9 + - + -
1293A MET* 1.3 70.5 - - - +
1295A GLU* 1.3 69.0 + - - +
1297A ALA* 3.7 3.7 - - + +
1298A ILE* 2.9 31.5 + - - +
1328A PHE* 3.6 33.6 - + + -
1331A SER* 3.5 40.5 + - - -
1332A ILE* 3.8 21.1 - - + -
1335A ILE* 3.5 31.6 - - + -
1337A ARG* 3.3 43.3 - - + -
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Residues in contact with GLU1295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1294A TRP* 1.3 74.2 + - - +
1296A GLU* 1.3 58.6 + - - +
1298A ILE* 3.4 6.8 + - - +
1299A SER* 3.3 21.1 + - - -
1332A ILE* 3.7 22.5 - - + +
1337A ARG* 2.4 42.8 + - - -
1430A ILE* 4.8 4.2 - - - +
1433A PHE* 3.5 26.9 - - + +
1434A TYR* 3.8 26.3 - - - +
1438A TYR* 3.1 24.5 - - + +
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Residues in contact with GLU1296 (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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1242A TYR* 2.7 40.4 + - + +
1288A PHE* 3.8 19.6 - - + -
1293A MET* 3.2 16.4 + - + +
1295A GLU* 1.3 80.2 - - - +
1297A ALA* 1.3 59.2 + - - +
1299A SER* 2.7 30.8 + - - -
1300A LEU* 3.3 11.1 + - - +
1438A TYR* 2.9 35.6 + - + +
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Residues in contact with ALA1297 (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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1285A ILE* 4.2 11.8 - - + +
1288A PHE* 3.8 23.3 - - + -
1289A ASP 4.8 2.0 - - - +
1293A MET 2.9 15.5 + - - +
1294A TRP* 3.7 7.6 - - + +
1296A GLU* 1.3 75.8 - - - +
1298A ILE* 1.3 63.1 + - - +
1300A LEU* 3.1 8.1 + - - +
1301A CYS* 3.0 23.7 + - - -
1328A PHE* 3.7 26.7 - - + -
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Residues in contact with ILE1298 (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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1294A TRP 2.9 21.9 + - - +
1295A GLU* 3.7 6.7 - - - +
1297A ALA* 1.3 74.3 - - - +
1299A SER* 1.3 67.2 + - - +
1301A CYS* 3.0 9.3 + - - +
1302A LYS* 2.9 26.8 + - + +
1325A GLN* 3.9 18.8 - - - +
1328A PHE* 3.5 28.5 - - + -
1329A TYR* 2.6 67.3 - - + +
1332A ILE* 4.0 11.0 - - + -
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Residues in contact with SER1299 (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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1295A GLU 3.3 9.7 + - - -
1296A GLU* 2.7 31.5 + - - -
1298A ILE* 1.3 79.0 - - - +
1300A LEU* 1.3 67.6 + - - +
1302A LYS* 3.2 22.8 + - - +
1303A GLU* 3.3 19.5 + - - +
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Residues in contact with LEU1300 (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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1245A LEU* 4.4 17.0 - - + -
1281A TYR* 3.6 34.7 - - + +
1284A ILE* 3.4 35.9 - - + -
1285A ILE* 3.5 25.4 - - + -
1288A PHE* 4.1 12.1 - - + -
1296A GLU* 3.7 10.1 - - - +
1297A ALA 3.1 8.8 + - - +
1299A SER* 1.3 87.4 + - - +
1301A CYS* 1.3 62.4 + - - +
1303A GLU* 3.2 20.8 + - - +
1304A LEU* 3.3 16.6 + - - +
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Residues in contact with CYS1301 (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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1285A ILE* 3.8 20.2 - - - -
1297A ALA 3.0 16.9 + - - +
1298A ILE 3.3 9.4 - - - +
1300A LEU* 1.3 76.8 - - - +
1302A LYS* 1.3 57.3 + - - +
1304A LEU* 3.3 2.1 + - - -
1305A ALA 2.8 24.3 + - - -
1321A ASN* 3.2 26.4 + - - +
1324A GLN* 4.7 8.7 - - - -
1325A GLN* 3.3 28.0 - - + -
1328A PHE* 4.2 19.3 - - - -
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Residues in contact with LYS1302 (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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1298A ILE* 2.9 20.3 + - + +
1299A SER* 3.5 14.1 - - - +
1300A LEU 3.1 0.2 - - - -
1301A CYS* 1.3 76.2 - - - +
1303A GLU* 1.3 63.7 + - - +
1305A ALA* 3.2 5.3 + - - +
1306A GLU* 3.0 22.9 + - - +
1325A GLN* 3.7 20.8 - - - +
1329A TYR* 4.0 21.9 + - - -
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Residues in contact with GLU1303 (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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1253A TRP* 4.5 14.3 + - + +
1277A LYS* 5.7 0.2 + - - -
1281A TYR* 2.4 39.9 + - + -
1299A SER* 3.3 13.7 + - - +
1300A LEU* 3.2 15.3 + - - +
1302A LYS* 1.3 79.6 - - + +
1304A LEU* 1.3 63.8 + - - +
1306A GLU* 3.4 19.0 + - - +
1307A GLN* 3.4 17.4 + - - +
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Residues in contact with LEU1304 (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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1253A TRP* 3.5 32.1 - - + -
1278A GLU* 4.4 11.7 - - + +
1281A TYR* 3.7 23.6 - - + -
1282A GLU* 4.9 7.6 - - + +
1285A ILE* 3.7 30.1 - - + -
1300A LEU 3.3 8.2 + - - +
1301A CYS 3.5 6.1 - - - +
1303A GLU* 1.3 74.7 - - - +
1305A ALA* 1.3 65.6 + - - +
1307A GLN* 2.9 18.0 + - + +
1308A TYR* 3.0 38.3 + - + +
1321A ASN* 3.7 13.2 - - - +
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Residues in contact with ALA1305 (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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1301A CYS 2.8 20.5 + - - +
1302A LYS* 3.2 5.8 + - - +
1304A LEU* 1.3 73.1 - - - +
1306A GLU* 1.3 57.2 + - - +
1308A TYR* 4.3 3.4 - - - -
1309A GLU* 2.8 35.7 + - - +
1318A LEU* 3.5 25.6 - - + +
1321A ASN* 3.5 13.8 + - - +
1322A LEU* 4.9 3.8 - - + -
1325A GLN* 4.1 6.3 - - - +
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Residues in contact with GLU1306 (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 LYS 3.0 12.2 + - - +
1303A GLU* 3.6 14.7 - - - +
1304A LEU 3.0 0.4 + - - -
1305A ALA* 1.3 77.4 - - - +
1307A GLN* 1.3 70.0 + - - +
1309A GLU* 4.1 6.2 - - - +
1310A MET* 3.0 36.8 + - + +
1311A GLU* 3.7 7.7 + - - +
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Residues in contact with GLN1307 (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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1253A TRP* 3.5 48.1 + - + +
1274A ARG* 2.6 37.1 - - - +
1303A GLU 3.6 14.6 - - - +
1304A LEU* 2.9 8.7 + - + +
1306A GLU* 1.3 83.8 - - - +
1308A TYR* 1.3 66.0 + - + +
1311A GLU* 2.7 52.4 + - - +
1312A ILE* 2.9 15.6 + - + +
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Residues in contact with TYR1308 (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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1278A GLU* 3.6 35.4 + - + +
1282A GLU* 4.4 6.8 + - - -
1304A LEU* 3.0 42.7 + - + +
1305A ALA* 3.8 7.6 - - - +
1306A GLU 3.2 0.2 - - - -
1307A GLN* 1.3 82.1 - - + +
1309A GLU* 1.3 58.3 - - - +
1312A ILE* 3.9 20.6 - - + -
1313A PHE* 2.9 11.8 - - - -
1314A ASP* 2.9 44.2 + - + +
1315A TYR* 4.3 1.0 - - - -
1317A LEU* 3.7 51.8 - - + +
1318A LEU* 3.8 14.4 - - + -
1321A ASN* 4.5 7.9 - - + -
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Residues in contact with GLU1309 (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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1305A ALA 2.8 17.8 + - - +
1306A GLU* 4.1 5.7 - - - +
1308A TYR* 1.3 78.8 - - - +
1310A MET* 1.3 90.4 + - + +
1313A PHE* 3.1 23.4 - - - -
1315A TYR* 4.1 11.3 + - + +
1318A LEU* 3.5 22.6 - - + +
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Residues in contact with MET1310 (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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1306A GLU* 3.0 23.8 + - + +
1309A GLU* 1.3 115.9 - - + +
1311A GLU* 1.3 72.5 + - - +
1312A ILE 3.7 0.7 - - - -
1313A PHE* 3.4 23.3 - - + -
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Residues in contact with GLU1311 (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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1274A ARG* 4.1 11.8 + - - +
1306A GLU* 3.7 7.0 + - - +
1307A GLN* 2.7 57.7 + - - +
1310A MET* 1.3 83.7 - - - +
1312A ILE* 1.3 67.6 + - + +
1313A PHE* 4.3 4.7 - - - -
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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