Contacts of the helix formed by residues 1272 - 1292 (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 THR1272 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1254A SER 3.0 11.4 + - - -
1255A ASP* 2.4 40.4 + - + +
1256A GLU 3.7 7.6 - - - -
1271A GLN* 1.3 77.7 - - - +
1273A HIS* 1.3 67.1 + - - +
1274A ARG* 3.7 2.4 + - - +
1275A GLN* 2.4 48.4 + - - +
1276A LEU* 3.2 5.0 + - - +
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Residues in contact with HIS1273 (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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1250A LEU 4.4 12.6 - - - -
1251A LEU* 4.3 16.3 - - + +
1252A LYS* 2.7 66.8 + - - +
1254A SER* 3.2 13.6 + - - +
1256A GLU* 4.1 22.0 + - + +
1271A GLN 5.5 0.9 - - - -
1272A THR* 1.3 72.9 + - - +
1274A ARG* 1.3 52.5 + - - +
1276A LEU* 2.9 10.5 + - + +
1277A LYS* 2.7 35.3 + - - +
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Residues in contact with ARG1274 (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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1252A LYS 3.5 4.8 + - - -
1253A TRP* 3.0 42.2 + - + +
1254A SER* 3.2 21.1 + - - +
1255A ASP* 5.1 2.0 - - - +
1272A THR* 3.5 3.1 - - - +
1273A HIS* 1.3 77.6 - - - +
1275A GLN* 1.3 59.6 + - - +
1277A LYS* 3.9 0.9 - - - +
1278A GLU* 2.8 39.0 + - - +
1307A GLN* 2.6 38.8 - - - +
1311A GLU* 4.1 11.5 + - - +
1312A ILE* 3.8 38.0 - - + +
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Residues in contact with GLN1275 (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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1271A GLN* 3.4 28.3 - - + +
1272A THR* 2.4 64.8 + - - +
1274A ARG* 1.3 78.4 - - - +
1276A LEU* 1.3 59.5 + - - +
1278A GLU* 3.6 11.4 - - - +
1279A THR* 3.0 32.2 + - + +
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Residues in contact with LEU1276 (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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1225A TYR* 5.8 0.2 - - - +
1247A HIS* 4.7 14.4 - - + +
1251A LEU* 3.7 31.2 - - + -
1271A GLN* 3.8 31.9 - - + +
1272A THR 3.2 10.9 + - - +
1273A HIS* 2.9 10.8 + - + +
1275A GLN* 1.3 79.7 - - - +
1277A LYS* 1.3 59.2 + - - +
1279A THR* 2.4 25.8 + - - +
1280A LEU* 3.0 25.2 + - + +
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Residues in contact with LYS1277 (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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1248A THR* 3.4 20.5 + - - -
1251A LEU* 2.9 50.3 + - + +
1252A LYS* 4.1 4.3 - - - +
1253A TRP* 3.5 54.1 - - + +
1273A HIS 2.7 19.5 + - - +
1274A ARG 3.9 3.6 - - - +
1276A LEU* 1.3 73.1 - - - +
1278A GLU* 1.3 57.4 + - - +
1280A LEU* 3.2 3.0 + - - +
1281A TYR* 2.9 52.0 + - + -
1303A GLU* 5.7 0.2 + - - -
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Residues in contact with GLU1278 (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* 4.0 11.2 - - + -
1274A ARG* 2.8 25.9 + - + +
1275A GLN* 3.6 11.6 - - - +
1277A LYS* 1.3 78.6 - - - +
1279A THR* 1.3 65.3 + - + +
1281A TYR* 3.4 2.8 + - - +
1282A GLU* 3.1 37.4 + - - +
1304A LEU* 4.4 10.2 - - + +
1308A TYR* 3.6 35.7 + - + +
1312A ILE* 5.2 4.5 - - - +
1317A LEU* 4.5 9.7 - - - +
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Residues in contact with THR1279 (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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1271A GLN* 3.8 14.0 + - - +
1275A GLN* 3.0 19.1 + - + +
1276A LEU* 2.4 36.9 + - - +
1278A GLU* 1.3 80.2 - - + +
1280A LEU* 1.3 55.6 + - - +
1282A GLU* 3.3 16.1 + - - +
1283A THR* 2.6 33.1 + - - -
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Residues in contact with LEU1280 (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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1225A TYR* 4.0 15.7 - - + +
1244A LEU* 5.2 11.4 - - + +
1247A HIS* 3.6 33.0 - - + +
1248A THR* 3.7 18.6 - - + -
1251A LEU* 3.6 26.2 - - + -
1276A LEU* 3.0 23.8 + - + +
1277A LYS 3.6 7.4 - - - +
1279A THR* 1.3 78.7 + - - +
1281A TYR* 1.3 60.4 + - - +
1283A THR* 3.2 8.6 + - - +
1284A ILE* 2.9 38.2 + - + +
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Residues in contact with TYR1281 (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* 4.6 4.4 - - + +
1248A THR* 3.9 32.3 + - + -
1253A TRP* 4.1 8.7 - + - -
1277A LYS* 2.9 36.3 + - + +
1278A GLU 3.7 5.2 - - - +
1280A LEU* 1.3 76.6 - - - +
1282A GLU* 1.3 57.6 + - - +
1284A ILE* 3.8 7.4 - - + +
1285A ILE* 2.8 37.5 + - - +
1300A LEU* 3.6 33.4 - - + +
1303A GLU* 2.4 44.7 + - + -
1304A LEU* 3.7 35.2 - - + -
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Residues in contact with GLU1282 (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* 3.1 35.1 + - + +
1279A THR* 3.5 18.4 - - - +
1280A LEU 3.2 0.4 - - - -
1281A TYR* 1.3 77.3 - - - +
1283A THR* 1.3 57.6 + - - +
1285A ILE* 3.7 8.1 - - + +
1286A GLY* 3.0 22.5 + - - -
1304A LEU* 5.1 9.2 - - + -
1308A TYR* 4.4 5.9 + - - -
1317A LEU* 5.8 2.4 - - - +
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Residues in contact with THR1283 (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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1228A ARG* 5.5 1.3 - - - +
1244A LEU* 4.7 10.5 - - + -
1279A THR 2.6 18.9 + - - -
1280A LEU* 3.2 9.0 + - - +
1282A GLU* 1.3 74.6 - - - +
1284A ILE* 1.3 57.3 + - - +
1286A GLY* 2.7 21.4 + - - -
1287A TYR* 2.9 42.9 + - + +
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Residues in contact with ILE1284 (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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1241A ALA* 3.8 17.3 - - + +
1244A LEU* 3.6 31.0 - - + -
1245A LEU* 3.7 25.6 - - + +
1248A THR* 3.7 22.0 - - + -
1280A LEU* 2.9 27.8 + - + +
1281A TYR* 3.8 7.2 - - + +
1283A THR* 1.3 72.3 - - - +
1285A ILE* 1.3 65.0 + - - +
1287A TYR* 2.8 21.9 + - - +
1288A PHE* 3.0 25.6 + - + +
1300A LEU* 3.4 22.7 - - + -
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Residues in contact with ILE1285 (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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1281A TYR 2.8 29.9 + - - +
1282A GLU* 3.7 7.4 - - + +
1284A ILE* 1.3 73.3 - - - +
1286A GLY* 1.3 63.5 + - - +
1288A PHE* 3.5 6.7 + - - +
1289A ASP* 3.1 21.0 + - + +
1297A ALA* 4.2 6.6 - - + +
1300A LEU* 3.5 34.1 - - + -
1301A CYS* 3.8 17.7 - - - -
1304A LEU* 3.7 28.0 - - + -
1324A GLN* 5.6 3.1 - - + +
1328A PHE* 4.0 28.5 - - + -
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Residues in contact with GLY1286 (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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1282A GLU 3.0 10.7 + - - -
1283A THR* 2.7 10.8 + - - -
1285A ILE* 1.3 78.9 - - - +
1287A TYR* 1.3 64.9 + - - +
1289A ASP* 3.3 8.6 + - - +
1290A LYS* 3.2 23.4 + - - +
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Residues in contact with TYR1287 (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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1228A ARG* 2.7 39.0 + - - -
1232A LEU* 3.8 20.1 - - + +
1237A TYR* 3.6 29.2 - + + +
1240A ALA* 3.9 7.9 - - + -
1241A ALA* 3.5 33.4 - - + -
1244A LEU* 3.6 22.4 - - + +
1283A THR* 2.9 33.8 + - + +
1284A ILE* 2.8 10.9 + - - +
1286A GLY* 1.3 75.8 - - - +
1288A PHE* 1.3 66.5 + - - +
1290A LYS* 2.9 10.7 + - + +
1291A GLY 2.8 19.1 + - - -
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Residues in contact with PHE1288 (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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1238A THR* 3.9 7.9 - - - +
1241A ALA* 3.5 22.0 - - + -
1242A TYR* 3.8 46.7 - + - -
1245A LEU* 4.6 7.9 - - + -
1284A ILE* 3.0 33.4 + - + +
1285A ILE 3.9 0.4 - - - +
1287A TYR* 1.3 76.1 - - - +
1289A ASP* 1.3 54.0 + - - +
1291A GLY* 3.2 1.7 + - - +
1292A LYS 2.7 28.9 + - - -
1293A MET* 2.9 45.7 + - + +
1296A GLU* 3.8 23.3 - - + -
1297A ALA* 3.8 19.5 - - + -
1300A LEU* 4.1 11.2 - - + -
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Residues in contact with ASP1289 (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* 3.1 14.1 + - + +
1286A GLY* 3.3 12.6 - - - +
1287A TYR 3.0 0.2 - - - -
1288A PHE* 1.3 76.6 - - - +
1290A LYS* 1.3 65.7 + - - +
1292A LYS* 2.9 17.2 + - - +
1294A TRP* 3.1 30.5 + - - +
1297A ALA* 4.8 0.6 - - - +
1324A GLN* 5.5 1.0 - - - +
1327A LYS* 4.5 11.9 + - - -
1328A PHE* 3.1 26.0 - - + -
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Residues in contact with LYS1290 (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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1237A TYR* 3.7 53.3 + - + -
1286A GLY 3.2 10.9 + - - +
1287A TYR* 2.9 9.4 + - + +
1289A ASP* 1.3 78.6 - - + +
1291A GLY* 1.3 61.2 + - - +
1292A LYS* 3.1 14.8 + - - +
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Residues in contact with GLY1291 (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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1237A TYR* 4.0 6.2 - - - +
1238A THR* 3.5 26.8 - - - +
1287A TYR 2.8 12.7 + - - -
1288A PHE 3.5 3.6 - - - -
1290A LYS* 1.3 74.2 - - - +
1292A LYS* 1.3 69.6 - - - +
1293A MET* 3.1 17.7 + - - +
1364A ARG* 5.5 0.3 + - - -
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Residues in contact with LYS1292 (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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1288A PHE 2.7 4.2 + - - -
1289A ASP 2.9 12.5 + - - +
1290A LYS 3.4 12.9 + - - +
1291A GLY* 1.3 82.4 - - - +
1293A MET* 1.3 56.6 + - + +
1294A TRP* 3.1 34.9 + - + -
1335A ILE* 5.2 6.1 - - + -
1336A LEU 5.7 0.4 - - - -
1337A ARG* 2.7 58.6 + - + +
1338A PRO* 4.7 5.4 - - - -
1367A GLU* 3.1 32.3 + - - -
-2C GLN* 5.5 10.6 + - + +
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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