Contacts of the helix formed by residues 180 - 192 (chain A) in PDB entry 1J59
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 ARG 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A LYS* 5.4 1.6 - - - +
169A ARG* 4.5 13.1 - - + +
170A GLN* 3.4 37.7 + - + +
173A GLY* 5.0 1.9 - - - -
178A CYS 4.1 0.2 + - - -
179A SER* 1.3 72.2 - - - +
181A GLU* 1.3 85.4 + - - +
183A VAL* 3.3 7.2 + - - +
184A GLY* 3.3 15.4 + - - -
4C T 3.3 64.6 - - + +
5C G 2.5 44.5 + - - +
5F C 4.6 2.0 - - - +
6F A 4.0 1.4 - - - +
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Residues in contact with GLU 181 (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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179A SER* 3.3 12.8 + - - -
180A ARG* 1.3 99.1 + - - +
182A THR* 1.3 67.1 + - - +
184A GLY* 3.0 11.8 + - - +
185A ARG* 3.1 30.2 + - - +
5C G 4.4 6.8 + - - +
6C T 3.3 38.7 - - + +
7F C 2.7 23.2 + - - +
8F T 3.0 27.4 - - + +
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Residues in contact with THR 182 (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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139A VAL* 3.5 36.8 - - + -
178A CYS* 3.8 5.6 - - + -
179A SER* 3.3 9.0 + - - -
181A GLU* 1.3 78.4 - - - +
183A VAL* 1.3 65.7 + - - +
185A ARG* 3.3 14.0 + - - +
186A ILE* 3.1 31.6 + - + +
8F T 5.8 0.2 - - - +
9F G 2.4 31.1 + - - +
10F T 3.5 14.7 - - + +
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Residues in contact with VAL 183 (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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143A ILE* 4.1 10.1 - - + -
169A ARG* 3.8 26.7 - - + +
172A ILE* 4.0 19.1 - - + -
173A GLY* 3.7 24.5 - - - +
178A CYS* 3.4 25.8 - - - -
179A SER 3.5 3.6 + - - +
180A ARG 3.3 8.7 + - - +
181A GLU 3.1 0.8 - - - -
182A THR* 1.3 78.3 - - - +
184A GLY* 1.3 64.1 + - - +
186A ILE* 3.1 0.5 + - - +
187A LEU* 2.8 47.9 + - + +
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Residues in contact with GLY 184 (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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169A ARG* 3.9 14.4 + - - +
180A ARG 3.3 4.9 + - - -
181A GLU 3.0 7.1 + - - -
183A VAL* 1.3 78.2 - - - +
185A ARG* 1.3 61.5 + - - +
187A LEU* 3.5 4.5 - - - +
188A LYS* 3.1 31.0 + - - +
5C G 3.6 26.9 + - - -
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Residues in contact with ARG 185 (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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181A GLU* 3.1 27.6 + - - +
182A THR* 3.7 14.2 + - - +
184A GLY* 1.3 74.5 - - - +
186A ILE* 1.3 67.3 + - + +
188A LYS* 2.9 38.0 + - - +
189A MET* 3.0 9.0 + - - +
6C T 3.4 19.1 - - + +
7C G 2.8 43.8 + - - -
8C A 4.1 5.2 - - - +
8F T 3.7 16.6 + - - +
9F G 5.1 4.8 + - - -
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Residues in contact with ILE 186 (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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139A VAL* 4.9 2.0 - - + -
140A THR* 3.2 41.7 - - + +
143A ILE* 3.7 28.0 - - + -
182A THR* 3.1 25.9 + - + +
183A VAL 3.7 4.0 - - - +
185A ARG* 1.3 80.3 - - + +
187A LEU* 1.3 65.2 + - - +
189A MET* 3.1 19.0 + - + +
190A LEU* 3.0 42.9 + - + +
10F T 5.5 3.4 - - - +
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Residues in contact with LEU 187 (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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143A ILE* 4.3 15.9 - - + -
147A LEU* 5.0 5.6 - - + -
169A ARG* 3.8 43.5 - - + +
172A ILE* 4.3 16.2 - - + -
183A VAL* 2.8 34.2 + - + +
184A GLY 3.5 5.8 - - - +
186A ILE* 1.3 79.1 - - - +
188A LYS* 1.3 60.9 + - - +
190A LEU* 3.6 5.6 + - + -
191A GLU* 3.2 20.4 + - - +
196A ILE* 3.6 25.3 - - + +
198A ALA* 4.5 12.3 - - + -
202A THR* 5.0 8.1 - - + +
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Residues in contact with LYS 188 (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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184A GLY 3.1 19.4 + - - +
185A ARG* 2.9 32.8 + - - +
187A LEU* 1.3 73.2 - - - +
189A MET* 1.3 63.7 + - - +
191A GLU* 2.9 22.7 + - - +
192A ASP* 2.9 25.0 + - - +
5C G 3.7 24.8 + - - +
6C T 3.0 28.0 + - - +
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Residues in contact with MET 189 (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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140A THR* 5.7 5.6 - - + -
185A ARG 3.0 7.3 + - - +
186A ILE* 3.3 26.2 - - + +
188A LYS* 1.3 77.9 - - - +
190A LEU* 1.3 62.4 + - + +
192A ASP* 3.1 17.2 + - + +
193A GLN* 3.0 36.0 + - + +
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Residues in contact with LEU 190 (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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140A THR* 4.2 12.6 - - + +
143A ILE* 5.1 9.6 - - + -
144A ALA* 5.5 12.8 - - + +
147A LEU* 5.4 6.3 - - + -
186A ILE* 3.0 46.8 + - + +
187A LEU* 3.7 10.8 - - - +
189A MET* 1.3 75.0 - - + +
191A GLU* 1.3 59.8 + - - +
193A GLN* 3.4 11.3 + - - +
194A ASN 3.2 2.8 + - - -
195A LEU* 2.8 57.2 + - + +
196A ILE* 3.8 22.0 - - + -
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Residues in contact with GLU 191 (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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187A LEU 3.2 10.3 + - - +
188A LYS* 2.9 16.6 + - - +
190A LEU* 1.3 76.4 - - - +
192A ASP* 1.3 59.2 + - - +
194A ASN* 2.5 31.7 + - - +
196A ILE* 3.3 25.1 - - + +
197A SER* 3.4 8.1 - - - -
198A ALA* 3.2 38.2 + - - +
207A GLY 5.3 2.1 - - - +
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Residues in contact with ASP 192 (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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188A LYS* 2.9 25.6 + - - +
189A MET* 3.3 16.0 - - + +
191A GLU* 1.3 76.6 - - - +
193A GLN* 1.3 60.4 + - + +
194A ASN* 3.3 13.2 + - - +
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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