Contacts of the helix formed by residues 1179 - 1188 (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 ASP1179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1022A GLU* 2.9 19.2 + - - +
1025A ASP* 6.1 2.5 - - + +
1029A LYS* 4.9 15.6 - - - +
1178A MET* 1.3 71.1 - - - +
1180A ILE* 1.3 61.0 + - - +
1181A VAL* 3.3 12.8 + - - +
1182A LYS* 2.9 55.5 + - + +
1183A VAL* 3.4 16.8 + - - +
1386A ASP* 3.8 5.1 - - - +
1387A SER* 3.3 9.6 + - - +
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Residues in contact with ILE1180 (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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1178A MET* 2.8 34.0 + - + +
1179A ASP* 1.3 69.2 - - - +
1181A VAL* 1.3 66.4 + - - +
1183A VAL* 3.4 2.5 + - - +
1184A ARG* 3.2 21.8 + - - +
1310A LEU* 4.3 17.3 - - + +
1314A ALA* 3.6 20.0 - - + +
1378A TYR* 3.5 28.0 - - + +
1381A LEU* 3.4 35.2 - - + +
1382A TYR* 3.8 14.1 - - + -
1385A GLN 4.2 4.3 - - - +
1386A ASP* 2.9 20.1 + - - +
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Residues in contact with VAL1181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1179A ASP* 3.5 6.7 - - - +
1180A ILE* 1.3 77.0 - - - +
1182A LYS* 1.3 58.2 + - - +
1184A ARG* 3.3 3.3 + - - +
1185A SER* 2.9 41.1 + - - +
1378A TYR* 3.6 17.2 + - - +
1382A TYR* 3.5 33.7 - - + +
1386A ASP* 4.1 5.2 - - - +
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Residues in contact with LYS1182 (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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1025A ASP* 4.9 16.2 - - - +
1179A ASP* 2.9 40.4 + - + +
1180A ILE 3.3 0.2 - - - -
1181A VAL* 1.3 76.8 - - - +
1183A VAL* 1.3 63.4 + - + +
1185A SER* 3.3 7.1 + - - -
1186A THR* 2.9 37.2 + - - +
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Residues in contact with VAL1183 (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* 5.7 3.6 - - - +
1022A GLU* 5.7 0.9 - - - +
1178A MET* 3.7 26.7 - - + -
1179A ASP 3.4 13.4 + - - +
1180A ILE 3.8 1.3 - - - +
1181A VAL 3.3 0.6 - - - -
1182A LYS* 1.3 77.8 - - + +
1184A ARG* 1.3 59.0 + - - +
1186A THR* 3.1 2.7 + - - -
1187A TYR* 2.8 47.2 + - + +
1281A LEU* 4.1 21.5 - - + -
1311A GLU 4.8 0.7 - - - +
1314A ALA* 3.6 30.1 - - + -
1315A CYS* 4.1 7.2 - - + +
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Residues in contact with ARG1184 (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 3.2 4.2 + - - -
1181A VAL 3.7 6.1 - - - +
1183A VAL* 1.3 79.2 - - - +
1185A SER* 1.3 64.0 + - - +
1186A THR 3.0 0.2 + - - -
1188A TRP* 2.8 70.1 + - + +
1314A ALA 3.1 19.6 + - - +
1375A GLU* 2.8 42.4 + - - -
1378A TYR* 3.4 53.1 - - + -
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Residues in contact with SER1185 (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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1181A VAL* 2.9 27.5 + - - +
1182A LYS* 3.3 7.6 + - - -
1184A ARG* 1.3 77.5 - - - +
1186A THR* 1.3 59.8 + - - +
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Residues in contact with THR1186 (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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1182A LYS* 2.9 25.2 + - - +
1183A VAL* 3.6 3.4 - - - -
1184A ARG 3.0 0.8 - - - -
1185A SER* 1.3 82.5 - - - +
1187A TYR* 1.3 92.4 + - + +
1189A LYS* 4.9 1.9 + - - -
1282A GLU* 5.2 0.9 - - - +
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Residues in contact with TYR1187 (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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1183A VAL* 2.8 29.7 + - + +
1186A THR* 1.3 103.7 - - + +
1188A TRP* 1.3 65.7 + - - +
1189A LYS* 2.8 22.0 + - - +
1278A SER* 3.2 45.2 - - - -
1281A LEU* 3.5 32.8 - - + +
1282A GLU* 3.8 29.4 - - + -
1285A SER* 3.1 21.8 - - - -
1315A CYS* 4.1 8.3 - - + -
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Residues in contact with TRP1188 (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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1184A ARG* 2.8 62.0 + - + +
1187A TYR* 1.3 72.3 - - - +
1189A LYS* 1.3 73.5 + - - +
1313A GLY 3.5 16.6 - - - -
1314A ALA 3.5 9.6 - - - -
1315A CYS 3.7 8.2 + - - -
1316A GLY* 3.4 30.7 - - - -
1374A ARG* 3.2 56.2 - - + +
1375A GLU* 3.9 17.0 + - - -
1378A TYR* 3.8 26.9 - + + -
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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