Contacts of the helix formed by residues 1306 - 1313 (chain A) in PDB entry 1Y6G
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1116A HIS* 6.2 0.9 - - - +
1176A PRO* 4.9 1.3 - - - -
1208A TRP* 3.5 10.4 - - - -
1209A LYS* 2.7 26.5 + - - -
1292A GLN* 3.7 4.7 + - - +
1294A SER* 2.4 39.2 + - - -
1296A LEU* 5.9 1.0 - - - +
1304A SER 5.6 0.9 - - - +
1305A LEU* 1.3 80.9 - - - +
1307A TYR* 1.3 60.8 + - - +
1308A THR* 3.0 6.3 - - - +
1309A HIS* 2.8 32.3 + - + +
1310A LEU* 3.1 7.2 + - - +
1403A NCO 3.4 18.6 + - - +
1404A UDP 3.0 23.4 + - - +
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Residues in contact with TYR1307 (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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1015A GLY* 3.7 13.5 - - - -
1018A LYS* 3.1 24.2 - - + -
1019A PHE* 3.2 42.5 - - + -
1022A GLU* 3.8 6.3 - - + +
1176A PRO* 2.9 45.8 - - + +
1177A PRO 2.6 26.7 + - - -
1178A MET* 3.5 23.6 - - + -
1306A GLU* 1.3 72.6 - - - +
1308A THR* 1.3 60.2 + - - +
1309A HIS 3.2 0.2 - - - -
1310A LEU* 3.8 7.1 - - + +
1311A GLU* 3.0 34.6 + - - +
1404A UDP 3.3 29.3 + - - +
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Residues in contact with THR1308 (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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1202A ILE* 2.9 48.3 - - + +
1203A GLY* 4.2 15.6 - - - +
1209A LYS* 5.1 2.2 + - - +
1275A TYR* 4.4 1.3 - - - +
1292A GLN* 2.5 30.4 + - - -
1306A GLU* 3.6 1.0 - - - +
1307A TYR* 1.3 75.1 - - - +
1309A HIS* 1.3 60.5 + - - +
1311A GLU* 3.4 10.6 + - - +
1312A LEU* 3.3 9.0 + - - +
1404A UDP 2.7 47.3 + - + +
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Residues in contact with HIS1309 (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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1292A GLN* 2.5 45.6 + - + -
1294A SER* 4.2 7.6 + - - -
1305A LEU* 3.0 37.8 - - + +
1306A GLU* 2.8 30.3 + - + +
1308A THR* 1.3 77.0 + - - +
1310A LEU* 1.3 59.6 + - - +
1311A GLU 3.0 8.7 + - - -
1312A LEU* 3.1 18.4 + - - +
1313A GLY 3.8 3.1 + - - -
1321A PHE* 3.6 48.7 - + + +
1322A TRP 5.3 0.6 + - - -
1325A THR* 4.6 14.3 - - + +
1381A LEU* 4.1 1.4 - - - +
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Residues in contact with LEU1310 (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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1176A PRO 3.7 9.6 - - - +
1178A MET* 2.9 40.5 - - + +
1180A ILE* 4.4 8.8 - - + +
1305A LEU* 3.4 31.6 - - + -
1306A GLU 3.1 11.3 + - - +
1307A TYR* 4.2 6.5 - - + +
1309A HIS* 1.3 73.3 - - - +
1311A GLU* 1.3 57.6 + - - +
1312A LEU 3.4 0.2 - - - -
1314A ALA* 3.0 17.1 + - - +
1381A LEU* 4.5 22.6 - - + +
1385A GLN* 3.1 54.1 - - + +
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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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1018A LYS* 3.9 10.2 + - - -
1178A MET* 3.7 18.3 - - + +
1183A VAL* 5.4 1.6 - - + -
1202A ILE* 5.4 1.2 - - + +
1277A ASN* 2.5 34.5 + - - +
1280A MET* 3.9 6.4 - - + +
1281A LEU* 3.3 26.5 - - + +
1307A TYR* 3.0 18.1 + - - +
1308A THR* 3.8 7.5 - - - +
1309A HIS 3.0 0.4 - - - -
1310A LEU* 1.3 76.6 - - - +
1312A LEU* 1.3 68.2 + - + +
1314A ALA* 3.6 6.0 - - + +
1315A CYS* 3.3 21.8 + - - -
1404A UDP 2.5 37.3 + - - -
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Residues in contact with LEU1312 (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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1202A ILE* 3.2 22.0 - - + -
1280A MET* 5.4 1.6 - - - -
1284A MET* 3.7 34.1 - - + -
1290A GLY* 3.4 28.9 - - - +
1292A GLN* 3.9 16.8 - - + -
1308A THR 3.3 10.1 - - - +
1309A HIS 3.1 5.5 + - - +
1311A GLU* 1.3 74.6 - - - +
1313A GLY* 1.3 65.6 + - - +
1314A ALA 2.8 4.9 + - - -
1315A CYS* 2.9 19.9 + - - -
1316A GLY 3.6 2.3 + - - -
1317A THR* 3.4 17.9 + - + +
1319A PRO* 4.4 8.7 - - + -
1321A PHE* 3.6 22.4 - - + -
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Residues in contact with GLY1313 (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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1180A ILE* 5.6 1.1 - - - -
1188A TRP* 3.4 22.0 - - - -
1309A HIS 3.8 6.3 + - - -
1312A LEU* 1.3 78.0 - - - +
1314A ALA* 1.3 58.7 + - - +
1316A GLY* 3.6 1.5 + - - -
1317A THR 4.5 2.7 - - - -
1319A PRO* 3.7 21.4 - - - +
1374A ARG 5.0 0.2 - - - +
1377A ALA* 4.5 7.4 - - - +
1378A TYR* 3.9 12.3 + - - +
1381A LEU* 3.7 18.5 - - - +
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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