Contacts of the helix formed by residues 1306 - 1315 (chain B) in PDB entry 1Y8Z
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 GLU1306 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1116B HIS* 4.5 11.9 + - + +
1176B PRO* 5.0 2.5 - - - -
1208B TRP* 3.2 19.1 - - - -
1209B LYS* 2.9 24.1 + - - -
1292B GLN* 2.9 14.9 + - - +
1294B SER* 2.7 31.6 + - - -
1296B LEU* 4.8 8.5 - - + -
1304B SER 5.3 1.8 - - - +
1305B LEU* 1.3 79.1 - - - +
1307B TYR* 1.3 66.2 + - - +
1308B THR 3.2 0.4 - - - -
1309B HIS* 2.8 34.0 + - + +
1310B LEU* 3.2 9.6 + - - +
1385B GLN* 5.0 0.4 - - - -
2001B UDP 3.4 23.8 + - - +
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Residues in contact with TYR1307 (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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1015B GLY* 3.8 9.4 - - - -
1018B LYS* 3.4 25.4 - - + -
1019B PHE* 3.2 47.6 - - + -
1022B GLU* 3.9 4.7 - - + +
1176B PRO* 3.4 26.7 - - + -
1177B PRO 2.6 32.3 + - - -
1178B MET* 3.6 26.7 - - + -
1306B GLU* 1.3 73.6 - - - +
1308B THR* 1.3 58.3 + - - +
1310B LEU* 3.2 7.1 + - + +
1311B GLU* 2.8 37.5 + - - +
2001B UDP 3.3 38.9 + - - +
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Residues in contact with THR1308 (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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1202B ILE* 3.7 26.1 + - + +
1203B GLY* 5.0 4.8 - - - +
1209B LYS* 5.1 2.8 + - - +
1275B TYR* 3.8 11.2 - - - +
1292B GLN* 2.7 38.5 + - - +
1306B GLU* 4.1 0.3 + - - +
1307B TYR* 1.3 76.2 - - - +
1309B HIS* 1.3 61.9 + - - +
1311B GLU* 3.5 6.4 + - - +
1312B LEU* 3.3 25.5 + - - +
2001B UDP 2.9 45.2 + - + +
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Residues in contact with HIS1309 (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 GLN* 3.0 45.8 + - + +
1294B SER* 4.3 6.7 - - - -
1296B LEU* 4.7 2.8 - - - +
1305B LEU* 3.7 33.0 - - + +
1306B GLU* 2.8 40.8 + - + +
1308B THR* 1.3 79.7 + - - +
1310B LEU* 1.3 64.2 + - - +
1312B LEU* 3.2 10.9 + - - +
1313B GLY 3.6 5.4 + - - -
1321B PHE* 3.4 49.3 - + + -
1322B TRP 5.5 0.2 - - - -
1325B THR* 4.4 16.1 - - + +
1381B LEU* 4.1 2.2 - - - +
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Residues in contact with LEU1310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1176B PRO 3.9 7.4 - - - +
1178B MET* 3.8 35.7 - - + -
1180B ILE* 4.4 15.9 - - + +
1305B LEU* 4.1 25.6 - - + -
1306B GLU 3.2 11.8 + - - +
1307B TYR* 3.8 9.2 - - + +
1309B HIS* 1.3 80.4 - - - +
1311B GLU* 1.3 56.8 + - - +
1312B LEU 3.3 0.2 + - - -
1313B GLY* 3.3 2.3 + - - -
1314B ALA* 2.9 30.8 + - - +
1381B LEU* 4.4 14.7 - - + +
1385B GLN* 3.6 48.5 - - + +
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Residues in contact with GLU1311 (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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1018B LYS* 3.8 10.7 - - - -
1178B MET* 3.6 21.5 - - + -
1183B VAL* 5.6 0.4 - - - -
1202B ILE* 5.0 0.7 - - + -
1277B ASN* 2.8 17.9 + - - +
1280B MET* 3.4 14.0 - - + +
1281B LEU* 3.8 21.5 - - + +
1284B MET* 5.7 0.2 - - - -
1307B TYR* 2.8 23.1 + - - +
1308B THR* 3.5 15.5 - - - +
1309B HIS 3.2 0.2 - - - -
1310B LEU* 1.3 77.0 - - - +
1312B LEU* 1.3 62.4 + - - +
1314B ALA* 4.0 1.4 - - - +
1315B CYS* 3.2 28.5 + - - +
2001B UDP 2.6 44.0 + - - -
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Residues in contact with LEU1312 (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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1202B ILE* 3.7 14.1 - - + -
1284B MET* 3.6 40.6 - - + -
1290B GLY* 3.4 30.7 - - - +
1291B TYR 3.9 1.1 - - - +
1292B GLN* 3.8 14.8 - - + +
1308B THR 3.3 11.6 + - - +
1309B HIS 3.2 5.4 + - - +
1310B LEU 3.2 0.6 - - - -
1311B GLU* 1.3 81.2 - - - +
1313B GLY* 1.3 63.4 + - - +
1314B ALA 3.3 0.2 + - - -
1315B CYS* 3.5 9.5 + - - -
1317B THR* 3.4 29.6 + - + +
1319B PRO* 4.1 9.2 - - + -
1321B PHE* 3.6 23.1 - - + -
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Residues in contact with GLY1313 (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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1180B ILE* 5.4 0.9 - - - -
1188B TRP* 3.5 20.1 - - - -
1309B HIS 3.6 4.6 + - - -
1310B LEU 3.3 3.6 + - - -
1312B LEU* 1.3 80.6 - - - +
1314B ALA* 1.3 60.0 + - - +
1316B GLY* 3.8 1.2 + - - -
1317B THR 4.7 2.3 - - - +
1319B PRO* 3.9 11.8 - - - +
1374B ARG* 4.9 0.7 - - - +
1377B ALA* 5.0 0.7 - - - -
1378B TYR* 3.6 18.1 + - - +
1381B LEU* 3.5 26.8 - - - +
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Residues in contact with ALA1314 (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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1178B MET* 3.8 7.9 - - + -
1180B ILE* 3.7 27.3 - - + +
1183B VAL* 3.7 26.5 - - + -
1184B ARG* 3.0 32.4 - - - +
1188B TRP* 3.6 1.8 - - - -
1310B LEU 2.9 18.4 + - - +
1311B GLU 4.0 1.6 - - - +
1313B GLY* 1.3 77.3 - - - +
1315B CYS* 1.3 60.0 + - - +
1316B GLY 3.3 0.7 + - - -
1378B TYR* 4.2 2.7 - - - -
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Residues in contact with CYS1315 (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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1183B VAL* 4.4 9.9 - - + -
1187B TYR* 4.3 11.4 - - + -
1188B TRP* 3.8 12.9 - - - +
1189B LYS 4.4 0.3 + - - -
1281B LEU* 3.9 20.4 - - + +
1284B MET* 3.4 39.9 - - - -
1285B SER* 3.4 29.2 - - - +
1311B GLU 3.2 20.4 + - - +
1312B LEU 3.5 7.6 - - - -
1314B ALA* 1.3 76.9 - - - +
1316B GLY* 1.3 57.0 + - - +
1317B THR 4.2 2.7 - - - -
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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