Contacts of the helix formed by residues 1314 - 1335 (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 ASP1314 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1308B TYR* 3.0 15.0 + - + +
1312B ILE* 3.0 22.5 + - + +
1313B PHE* 1.3 75.8 - - - +
1315B TYR* 1.3 57.1 + - - +
1316B GLU* 2.7 26.3 - - - +
1317B LEU* 3.2 40.9 + - + +
1318B LEU* 3.0 25.5 + - - +
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Residues in contact with TYR1315 (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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1308B TYR 4.5 1.1 - - - -
1309B GLU* 4.3 20.3 + - + +
1313B PHE* 3.5 31.5 + + + -
1314B ASP* 1.3 73.6 + - - +
1316B GLU* 1.3 66.0 + - + +
1318B LEU* 3.4 21.7 - - + +
1319B SER* 2.9 29.5 + - - -
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Residues in contact with GLU1316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1313B PHE 5.0 1.0 - - - +
1314B ASP* 2.7 25.9 - - - +
1315B TYR* 1.3 84.6 + - + +
1317B LEU* 1.3 67.0 + - + +
1319B SER* 2.7 24.0 + - - -
1320B GLN* 3.3 11.5 + - - +
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Residues in contact with LEU1317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1278B GLU* 4.9 10.3 - - - +
1282B GLU* 5.9 2.7 - - - +
1308B TYR* 3.8 38.5 - - + +
1312B ILE* 6.1 0.4 - - + -
1314B ASP* 3.2 33.0 + - + +
1316B GLU* 1.3 85.0 - - + +
1318B LEU* 1.3 56.8 + - - +
1320B GLN* 3.2 14.0 + - + +
1321B ASN* 3.0 26.5 + - - +
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Residues in contact with LEU1318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1305B ALA* 3.6 41.1 - - + +
1308B TYR* 3.8 8.9 - - + -
1309B GLU* 3.6 35.7 - - + +
1314B ASP 3.0 17.7 + - - +
1315B TYR* 3.4 23.3 - - + +
1316B GLU 3.1 0.2 - - - -
1317B LEU* 1.3 74.3 - - - +
1319B SER* 1.3 65.0 + - - +
1321B ASN* 3.0 5.8 + - + +
1322B LEU* 2.9 37.5 + - + +
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Residues in contact with SER1319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1315B TYR 2.9 12.6 + - - -
1316B GLU* 2.7 24.1 + - - -
1318B LEU* 1.3 76.9 - - - +
1320B GLN* 1.3 67.4 + - - +
1322B LEU* 3.4 11.7 + - - +
1323B ILE* 3.2 31.3 + - - +
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Residues in contact with GLN1320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1316B GLU 3.7 11.4 - - - +
1317B LEU* 3.2 18.8 + - + +
1318B LEU 3.1 0.4 - - - -
1319B SER* 1.3 85.7 + - - +
1321B ASN* 1.3 62.5 + - - +
1323B ILE* 3.4 23.7 + - - +
1324B GLN* 3.1 21.5 + - - +
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Residues in contact with ASN1321 (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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1301B CYS* 3.3 37.7 + - - +
1304B LEU* 3.8 14.7 - - - +
1305B ALA* 3.5 14.1 - - - +
1308B TYR* 4.5 7.4 - - + -
1317B LEU 3.0 12.3 + - - +
1318B LEU* 3.0 15.6 + - + +
1320B GLN* 1.3 77.6 - - - +
1322B LEU* 1.3 63.1 + - - +
1324B GLN* 3.2 8.3 + - - +
1325B GLN* 2.8 49.4 + - - +
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Residues in contact with LEU1322 (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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1305B ALA* 5.2 2.9 - - + -
1318B LEU* 2.9 35.2 + - + +
1319B SER* 3.8 11.0 - - - +
1320B GLN 3.3 0.2 - - - -
1321B ASN* 1.3 75.5 - - - +
1323B ILE* 1.3 62.1 + - + +
1325B GLN* 3.1 23.6 + - + +
1326B ALA* 2.9 27.3 + - - +
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Residues in contact with ILE1323 (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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1319B SER* 3.2 20.2 + - - +
1320B GLN* 3.7 20.6 - - - +
1321B ASN 3.3 0.2 - - - -
1322B LEU* 1.3 75.0 - - + +
1324B GLN* 1.3 67.0 + - - +
1326B ALA* 3.2 9.8 + - + +
1327B LYS* 3.1 40.3 + - + +
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Residues in contact with GLN1324 (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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1285B ILE* 5.1 6.1 - - + +
1289B ASP* 5.4 4.0 + - - -
1301B CYS* 4.4 10.5 - - - -
1320B GLN 3.1 14.3 + - - +
1321B ASN* 3.2 13.2 + - - +
1323B ILE* 1.3 77.2 - - - +
1325B GLN* 1.3 62.4 + - - +
1327B LYS* 3.4 24.4 + - - +
1328B PHE* 3.2 56.5 + - + -
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Residues in contact with GLN1325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1298B ILE* 4.0 17.9 - - + +
1301B CYS* 3.5 26.0 - - + +
1302B LYS* 3.7 29.0 - - - +
1305B ALA* 4.3 4.0 - - - +
1321B ASN* 2.8 36.9 + - - +
1322B LEU* 3.1 23.0 + - + +
1324B GLN* 1.3 74.3 - - - +
1326B ALA* 1.3 64.8 + - - +
1327B LYS 3.1 1.6 - - - -
1328B PHE* 3.2 7.5 + - - +
1329B TYR* 2.9 40.5 + - + +
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Residues in contact with ALA1326 (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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1322B LEU 2.9 13.2 + - - +
1323B ILE* 3.2 13.9 + - + +
1325B GLN* 1.3 77.3 - - - +
1327B LYS* 1.3 62.6 + - + +
1329B TYR* 4.1 5.8 - - - +
1330B GLU* 3.1 24.9 + - - +
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Residues in contact with LYS1327 (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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1323B ILE* 3.1 28.4 + - + +
1324B GLN* 3.5 27.0 + - - +
1325B GLN 3.1 0.2 - - - -
1326B ALA* 1.3 77.1 - - + +
1328B PHE* 1.3 60.0 + - + +
1330B GLU* 3.7 4.7 - - - +
1331B SER* 2.3 39.1 + - - +
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Residues in contact with PHE1328 (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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1285B ILE* 4.1 10.5 - - + -
1289B ASP* 2.8 38.6 - - + -
1294B TRP* 3.6 25.4 - + + +
1297B ALA* 3.7 27.4 - - + -
1298B ILE* 3.5 29.4 - - + -
1301B CYS* 4.5 4.0 - - - -
1324B GLN* 3.2 49.6 + - + -
1325B GLN* 3.2 3.9 + - - +
1327B LYS* 1.3 79.9 - - + +
1329B TYR* 1.3 66.2 + - - +
1331B SER* 3.6 5.8 - - - -
1332B ILE* 2.9 27.9 + - - +
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Residues in contact with TYR1329 (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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1298B ILE* 2.6 61.0 - - + +
1302B LYS* 3.9 16.6 + - - -
1325B GLN* 2.9 26.2 + - + +
1326B ALA* 4.1 5.8 - - - +
1328B PHE* 1.3 77.7 - - - +
1330B GLU* 1.3 64.0 + - - +
1332B ILE* 3.6 12.5 + - + +
1333B MET* 3.5 21.1 + - - +
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Residues in contact with GLU1330 (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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1326B ALA 3.1 20.7 + - - +
1327B LYS* 3.7 5.6 - - - +
1328B PHE 3.1 0.2 - - - -
1329B TYR* 1.3 75.1 - - - +
1331B SER* 1.3 61.9 + - - +
1333B MET* 3.0 10.9 + - - +
1334B LYS* 2.9 61.2 + - + +
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Residues in contact with SER1331 (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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1294B TRP* 3.5 34.3 - - - -
1327B LYS* 2.3 28.6 + - - +
1328B PHE* 3.6 6.0 - - - -
1330B GLU* 1.3 73.7 - - - +
1332B ILE* 1.3 68.6 + - - +
1334B LYS* 4.9 0.7 - - - +
1335B ILE* 2.7 46.2 + - - +
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Residues in contact with ILE1332 (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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1294B TRP* 3.9 15.7 - - + -
1295B GLU* 3.3 32.5 - - + +
1298B ILE* 3.9 22.7 - - + -
1328B PHE 2.9 21.9 + - - +
1329B TYR* 3.6 12.3 - - + +
1330B GLU 3.3 0.2 - - - -
1331B SER* 1.3 76.9 - - - +
1333B MET* 1.3 58.6 + - - +
1335B ILE 4.2 4.0 - - - +
1337B ARG* 3.8 21.0 + - - +
1429B GLN* 3.0 21.7 + - - +
1430B ILE* 3.2 37.5 - - + -
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Residues in contact with MET1333 (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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1329B TYR 3.7 11.9 - - - +
1330B GLU* 3.0 11.4 + - - +
1332B ILE* 1.3 76.5 - - - +
1334B LYS* 1.3 70.9 - - + +
1336B LEU* 4.5 2.1 - - - +
1427B PRO* 4.3 20.2 - - + -
1429B GLN* 3.4 34.8 + - - +
1430B ILE* 3.5 33.9 - - + -
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Residues in contact with LYS1334 (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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1330B GLU* 2.9 47.5 + - + +
1331B SER* 5.0 0.2 - - - -
1333B MET* 1.3 86.9 - - + +
1335B ILE* 1.3 68.6 + - + +
1336B LEU* 3.8 7.1 + - - +
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Residues in contact with ILE1335 (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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1292B LYS* 5.8 5.2 - - - -
1294B TRP* 3.5 31.8 - - + -
1331B SER* 2.7 41.7 + - - +
1332B ILE 4.2 3.9 - - - +
1334B LYS* 1.3 78.5 - - + +
1336B LEU* 1.3 71.9 + - - +
1337B ARG* 3.5 4.4 + - + +
1429B GLN* 5.1 0.2 + - - -
-3D PHE* 4.8 24.7 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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