Contacts of the helix formed by residues 189 - 200 (chain A) in PDB entry 3HVK
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 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A GLN* 4.2 31.1 + - - +
185A HIS* 3.7 19.2 + - + +
186A TRP* 2.9 20.2 + - + +
188A ASP* 1.3 99.1 - - - +
190A TYR* 1.3 65.2 + - - +
191A LEU 3.3 2.2 - - - -
192A PRO* 3.5 27.2 - - - +
193A ASP* 3.0 32.7 + - - +
267A 719 3.7 26.2 - - - -
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Residues in contact with TYR 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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183A LEU* 3.2 36.3 + - + +
184A ASP* 3.5 1.2 - - - -
185A HIS* 3.6 39.9 - + - -
186A TRP 3.5 8.1 - - - -
187A LYS* 2.9 32.6 + - + +
189A ARG* 1.3 77.3 - - - +
191A LEU* 1.3 59.1 + - - +
193A ASP* 4.0 0.2 - - - -
194A THR* 2.8 34.1 + - - -
211A ALA* 3.8 20.6 - - + -
212A ASP 2.7 30.0 + - - -
219A THR* 3.7 34.5 - - + +
222A PHE* 3.8 13.5 - + + -
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Residues in contact with LEU 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 LYS 4.9 0.8 + - - -
188A ASP 4.9 0.2 + - - -
190A TYR* 1.3 77.3 - - - +
192A PRO* 1.4 73.7 - - + +
194A THR* 3.1 6.8 + - - -
195A LEU* 3.0 48.2 + - + +
221A ASP* 3.7 41.6 + - + +
222A PHE* 4.0 18.7 - - + +
225A TYR* 3.6 41.1 - - + -
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Residues in contact with PRO 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 ASP 3.3 25.8 - - - +
189A ARG* 3.5 36.3 - - - +
191A LEU* 1.4 94.8 - - + +
193A ASP* 1.3 57.9 + - - +
195A LEU* 3.4 10.8 + - + +
196A LEU* 3.0 27.4 + - - +
221A ASP* 4.7 3.6 - - - +
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Residues in contact with ASP 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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108A LEU* 3.9 18.0 - - + +
162A SER* 2.6 35.8 + - - -
163A GLN* 4.4 5.5 + - - -
166A ILE* 4.1 8.8 - - + +
183A LEU* 5.6 0.2 - - + -
185A HIS* 2.7 19.5 + - - +
189A ARG* 3.0 34.2 + - - +
190A TYR 4.2 1.6 - - - +
192A PRO* 1.3 74.4 - - - +
194A THR* 1.3 61.4 + - - +
196A LEU* 3.7 10.6 - - - +
197A LEU* 2.9 35.7 + - - +
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Residues in contact with THR 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 LEU* 3.7 9.4 - - - +
190A TYR 2.8 22.2 + - - -
191A LEU* 3.6 11.7 - - + -
193A ASP* 1.3 75.0 - - - +
195A LEU* 1.3 68.1 + - + +
197A LEU* 3.4 12.0 + - + +
198A GLU* 3.1 22.4 + - + +
203A LEU* 4.3 4.8 - - + +
209A LEU* 3.7 24.7 - - + +
222A PHE* 3.4 20.9 - - + -
225A TYR* 5.5 0.9 - - + -
226A VAL* 5.2 1.8 - - + -
232A PHE* 3.9 20.0 - - + -
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Residues in contact with LEU 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 LEU* 3.0 35.0 + - + +
192A PRO* 3.7 7.9 - - + +
194A THR* 1.3 79.5 - - + +
196A LEU* 1.3 55.5 + - - +
198A GLU* 3.4 8.8 + - + +
199A LYS* 3.0 27.6 + - - +
225A TYR* 3.8 37.7 - - + +
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Residues in contact with LEU 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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163A GLN* 3.9 37.5 - - + +
166A ILE* 3.9 25.8 - - + -
167A PRO* 4.3 7.4 - - + -
192A PRO 3.0 17.2 + - - +
193A ASP* 3.2 9.8 + - - +
195A LEU* 1.3 74.9 - - - +
197A LEU* 1.3 64.3 + - - +
199A LYS* 3.1 32.9 + - + +
200A CYS* 2.9 36.3 + - - -
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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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106A LEU* 3.8 14.6 - - + -
108A LEU* 4.8 4.9 - - + -
166A ILE* 3.9 19.5 - - + -
178A LEU* 3.8 25.1 - - + -
181A VAL* 4.1 31.6 - - + -
183A LEU* 6.0 1.3 - - + -
193A ASP 2.9 25.3 + - - +
194A THR* 3.6 10.8 - - + +
196A LEU* 1.3 76.3 - - - +
198A GLU* 1.3 63.4 + - - +
200A CYS 3.4 0.7 + - - -
201A GLY 3.3 2.8 + - - -
202A LEU* 3.1 42.4 + - + +
203A LEU* 3.9 18.8 - - + -
209A LEU* 5.2 3.4 - - + -
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Residues in contact with GLU 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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194A THR* 3.1 13.5 + - + +
195A LEU* 3.7 10.5 - - + +
197A LEU* 1.3 77.0 - - - +
199A LYS* 1.3 69.1 + - - +
201A GLY* 3.0 15.2 + - - -
202A LEU 5.0 0.2 - - - +
203A LEU* 3.9 16.3 - - + +
255A TYR* 3.4 35.0 + - + +
258A PRO* 4.8 11.3 - - - +
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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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167A PRO* 6.0 1.4 - - - +
195A LEU 3.0 17.2 + - - +
196A LEU* 3.1 30.5 + - + +
198A GLU* 1.3 83.0 + - - +
200A CYS* 1.3 70.7 + - - +
201A GLY* 3.3 1.4 + - - -
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Residues in contact with CYS 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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166A ILE* 4.1 6.1 - - - +
167A PRO* 4.0 27.4 - - + -
170A LYS* 3.3 18.6 - - + +
196A LEU* 2.9 37.6 + - - +
197A LEU 3.9 0.2 - - - +
198A GLU 3.1 0.2 - - - -
199A LYS* 1.3 86.9 - - - +
201A GLY* 1.3 59.7 + - - +
202A LEU* 3.3 20.8 + - + +
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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