Contacts of the helix formed by residues 190 - 201 (chain A) in PDB entry 2J6U
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 GLY 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A GLY 3.7 0.2 - - - -
189A ILE* 1.3 76.5 - - - +
191A ASN* 1.3 56.5 + - - -
194A ALA* 2.7 34.1 + - - +
1003A CA 4.3 2.7 - - - -
12P T 2.9 36.4 + - - -
13P C 3.6 13.2 - - - -
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Residues in contact with ASN 191 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A GLY* 1.3 70.9 - - - -
192A ILE* 1.3 68.4 + - + +
194A ALA* 3.3 8.4 + - - +
195A GLU* 3.0 29.5 + - + +
12P T 3.9 2.8 + - - +
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Residues in contact with ILE 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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190A GLY 3.3 1.2 - - - -
191A ASN* 1.3 81.8 - - + +
193A THR* 1.3 64.2 + - - +
195A GLU* 3.3 6.4 + - + +
196A LYS* 3.1 38.3 + - - +
11P T 3.6 44.0 - - + +
12P T 3.4 18.1 + - - +
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Residues in contact with THR 193 (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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189A ILE* 3.7 31.0 - - + -
190A GLY 3.7 3.1 - - - -
192A ILE* 1.3 72.4 - - - +
194A ALA* 1.3 66.6 + - - +
195A GLU 3.1 0.2 + - - -
196A LYS* 3.2 10.6 + - - +
197A LEU* 3.0 34.5 + - + +
220A ILE* 4.3 14.3 - - + +
224A LYS* 4.1 24.1 + - + -
11P T 3.6 6.9 + - - -
12P T 2.6 28.3 + - - -
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Residues in contact with ALA 194 (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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183A ILE* 5.1 5.6 - - + +
184A ALA* 4.2 24.0 - - + -
189A ILE* 3.9 10.7 - - + +
190A GLY 2.7 22.5 + - - +
191A ASN* 3.4 11.4 - - - +
192A ILE 3.3 0.2 - - - -
193A THR* 1.3 73.4 - - - +
195A GLU* 1.3 58.9 + - + +
197A LEU* 3.5 5.9 + - - +
198A LYS* 3.0 28.9 + - - +
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Residues in contact with GLU 195 (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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191A ASN* 3.0 17.9 + - + +
192A ILE* 3.5 10.1 - - + +
194A ALA* 1.3 73.0 - - + +
196A LYS* 1.3 69.3 + - + +
197A LEU 2.9 1.3 - - - -
198A LYS* 2.7 30.4 + - - +
199A LYS* 3.0 34.4 + - - +
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Residues in contact with LYS 196 (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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192A ILE* 3.1 30.8 + - + +
193A THR* 3.7 10.1 + - - +
195A GLU* 1.3 79.6 - - + +
197A LEU* 1.3 60.8 + - - +
199A LYS* 3.9 6.3 + - - +
200A LEU* 3.4 15.6 + - - +
219A MET* 3.0 58.4 + - + +
220A ILE* 4.0 15.7 - - + +
10P A 5.1 0.4 + - - -
11P T 3.6 23.0 + - - -
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Residues in contact with LEU 197 (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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183A ILE* 3.8 21.1 - - + -
189A ILE* 4.4 5.2 - - + -
193A THR* 3.0 30.5 + - + +
194A ALA* 3.6 5.2 - - - +
195A GLU 2.9 1.0 - - - -
196A LYS* 1.3 78.1 - - - +
198A LYS* 1.3 66.4 + - - +
200A LEU* 3.1 4.9 + - + +
201A GLY 3.0 5.2 + - - -
202A ILE* 2.9 52.8 + - + +
208A THR* 5.4 0.4 - - + -
216A LEU* 4.0 13.7 - - + -
220A ILE* 3.9 31.4 - - + -
228A LEU* 3.8 25.1 - - + -
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Residues in contact with LYS 198 (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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182A ASP* 5.2 10.3 + - - -
183A ILE* 5.8 3.2 - - + +
194A ALA 3.0 15.0 + - - +
195A GLU* 2.7 28.6 + - - +
197A LEU* 1.3 70.0 - - - +
199A LYS* 1.3 65.8 - - + +
201A GLY* 2.8 16.6 + - - -
202A ILE 3.8 6.3 + - - +
203A ASN* 2.8 42.4 + - - +
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Residues in contact with LYS 199 (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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195A GLU* 3.0 32.7 + - - +
196A LYS* 4.0 11.4 - - - +
198A LYS* 1.3 80.7 - - + +
200A LEU* 1.3 60.5 + - - +
201A GLY 3.4 0.3 + - - -
219A MET* 5.0 7.9 - - + -
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Residues in contact with LEU 200 (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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196A LYS 3.4 14.2 + - - +
197A LEU* 3.1 9.1 + - + +
198A LYS 3.1 0.8 - - - -
199A LYS* 1.3 79.0 - - - +
201A GLY* 1.3 59.1 + - - +
202A ILE* 3.4 20.1 - - + +
211A ILE* 3.9 17.4 - - + +
215A LYS* 3.6 37.5 + - + +
216A LEU* 3.7 30.7 - - + -
219A MET* 3.4 42.4 - - + -
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Residues in contact with GLY 201 (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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198A LYS 2.8 12.5 + - - -
199A LYS 3.2 1.2 + - - -
200A LEU* 1.3 80.7 - - - +
202A ILE* 1.3 61.6 + - - +
203A ASN* 3.4 13.1 + - - +
207A ASP* 3.9 13.2 - - - +
211A ILE* 5.5 3.5 - - - +
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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