Contacts of the helix formed by residues 1276 - 1285 (chain A) 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 ILE1276 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1048A SER* 3.4 28.7 - - - +
1049A SER 3.7 8.1 - - - +
1255A ASN* 3.9 13.6 + - - +
1274A CME 3.7 20.6 - - + +
1275A TYR* 1.3 73.6 - - - +
1277A ASN* 1.3 67.5 + - - +
1278A SER* 3.7 20.9 - - - +
1279A GLU* 3.0 48.6 + - - +
1280A MET 3.0 10.2 + - - -
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Residues in contact with ASN1277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1018A LYS* 4.3 10.3 + - - -
1049A SER 2.9 17.9 + - - +
1050A HIS* 4.0 16.5 + - + -
1275A TYR* 4.1 4.0 - - - -
1276A ILE* 1.3 69.4 - - - +
1278A SER* 1.3 63.9 + - - +
1280A MET* 3.1 6.3 + - - +
1281A LEU* 3.0 43.8 + - - +
1311A GLU* 2.9 18.1 + - - +
3006A UDP 2.8 51.7 + - - +
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Residues in contact with SER1278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1049A SER 4.8 0.2 + - - -
1187A TYR* 3.2 34.6 - - - -
1276A ILE* 3.3 14.3 - - - +
1277A ASN* 1.3 80.4 + - - +
1279A GLU* 1.3 67.2 + - - +
1281A LEU* 3.5 2.1 + - - -
1282A GLU* 3.3 18.9 + - - +
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Residues in contact with GLU1279 (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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1255A ASN* 4.1 12.1 + - - +
1258A ILE* 4.3 6.8 - - - +
1276A ILE* 3.0 42.1 + - + +
1278A SER* 1.3 78.2 + - - +
1280A MET* 1.3 65.1 + - - +
1282A GLU* 3.4 7.3 + - - +
1283A ARG* 3.2 48.2 + - - +
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Residues in contact with MET1280 (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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1200A ARG* 5.3 0.2 - - - -
1202A ILE* 3.9 29.6 - - + -
1232A GLU* 3.5 19.7 - - - +
1275A TYR* 3.2 37.9 - - + +
1276A ILE 3.0 5.4 + - - +
1277A ASN* 3.1 5.6 + - - +
1279A GLU* 1.3 75.0 - - - +
1281A LEU* 1.3 80.1 + - + +
1283A ARG* 3.2 13.6 + - - +
1284A MET* 2.8 41.6 + - + +
1311A GLU* 3.3 28.5 - - + +
3006A UDP 3.7 11.0 - - - +
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Residues in contact with LEU1281 (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* 6.1 0.7 - - - +
1183A VAL* 4.1 17.3 - - + -
1187A TYR* 3.5 39.5 - - + +
1277A ASN* 3.0 36.7 + - - +
1278A SER* 3.8 5.6 - - - +
1279A GLU 3.3 0.2 - - - -
1280A MET* 1.3 89.3 - - + +
1282A GLU* 1.3 57.7 + - - +
1284A MET* 3.8 2.2 - - - +
1285A SER* 3.0 30.0 + - - -
1311A GLU* 3.8 42.6 - - + +
1315A CYS* 4.0 10.6 - - + +
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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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1186A THR 5.2 0.7 - - - +
1187A TYR* 3.8 16.2 - - + -
1189A LYS* 3.0 33.1 + - - -
1278A SER 3.3 10.9 + - - +
1279A GLU* 3.6 11.0 - - - +
1280A MET 3.2 0.6 - - - -
1281A LEU* 1.3 78.0 - - - +
1283A ARG* 1.3 63.9 + - + +
1285A SER* 2.7 19.1 + - - -
1286A LYS* 3.1 46.6 + - - +
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Residues in contact with ARG1283 (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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1200A ARG* 3.8 25.9 + - - +
1232A GLU* 2.7 42.4 + - - +
1255A ASN* 5.0 0.2 + - - -
1258A ILE* 3.6 35.8 - - - +
1272A LEU* 3.6 16.1 - - - +
1275A TYR* 3.6 12.9 - - - +
1279A GLU* 3.2 33.0 + - - +
1280A MET* 3.2 14.5 + - - +
1282A GLU* 1.3 78.9 - - + +
1284A MET* 1.3 56.4 + - - +
1286A LYS* 3.3 20.4 + - - +
1287A SER* 2.7 23.3 + - - -
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Residues in contact with MET1284 (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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1200A ARG* 3.5 40.1 - - + +
1202A ILE* 3.6 24.2 - - + -
1280A MET* 2.8 26.0 + - - +
1281A LEU 3.8 1.6 - - - +
1283A ARG* 1.3 74.2 - - - +
1285A SER* 1.3 57.4 + - - +
1286A LYS 3.0 5.2 - - - -
1287A SER* 2.9 30.6 + - - +
1290A GLY* 3.7 17.3 - - - -
1311A GLU 5.6 0.2 - - - -
1312A LEU* 3.5 33.0 - - + -
1315A CYS* 3.3 23.3 - - - -
1317A THR* 3.7 10.2 - - + -
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Residues in contact with SER1285 (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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1187A TYR* 3.1 26.0 - - - -
1189A LYS* 2.9 33.3 + - - +
1194A ILE* 3.5 22.1 - - - +
1281A LEU 3.0 14.6 + - - -
1282A GLU* 2.7 20.8 + - - -
1284A MET* 1.3 74.7 - - - +
1286A LYS* 1.3 57.4 + - - +
1287A SER 3.4 0.2 - - - -
1315A CYS* 3.3 22.4 - - - +
1316A GLY 4.8 2.1 - - - +
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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