Contacts of the helix formed by residues 190 - 208 (chain A) in PDB entry 3HA3
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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187A ALA 2.9 14.5 + - - -
188A ALA 3.2 2.8 + - - -
189A ARG* 1.3 81.9 - - - +
191A LYS* 1.3 61.2 + - - -
192A LYS 3.3 2.7 - - - -
193A LEU* 3.3 4.0 + - - -
194A SER* 2.9 28.3 + - - -
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Residues in contact with LYS 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 ALA* 5.0 11.9 - - + +
190A GLY* 1.3 70.4 - - - -
192A LYS* 1.3 68.2 + - - +
194A SER* 3.1 6.6 + - - -
195A PHE* 3.0 56.6 + - + -
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Residues in contact with LYS 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 0.6 - - - -
191A LYS* 1.3 80.3 - - - +
193A LEU* 1.3 62.3 + - - +
195A PHE* 4.2 5.0 - - - +
196A GLU* 3.2 36.7 + - + +
199A ARG* 5.3 0.5 + - - -
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Residues in contact with LEU 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 ARG* 4.2 16.2 - - + +
190A GLY* 3.3 8.3 + - - +
191A LYS 3.1 0.4 - - - -
192A LYS* 1.3 80.8 - - - +
194A SER* 1.3 57.8 + - - +
196A GLU* 3.4 26.0 + - - +
197A THR* 2.9 40.2 + - - +
280A HIS* 5.6 2.0 - - - +
281A TYR* 4.4 6.3 - - + -
284A ASP* 3.6 24.2 - - - +
286A MET* 3.6 35.4 - - + -
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Residues in contact with SER 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 PRO* 4.6 3.1 + - - +
186A MET* 3.3 41.0 + - - +
187A ALA* 4.1 5.5 + - - +
190A GLY 2.9 17.2 + - - -
191A LYS* 3.1 8.5 + - - -
193A LEU* 1.3 77.9 - - - +
195A PHE* 1.4 60.9 + - - +
197A THR* 3.7 1.9 + - - -
198A ALA* 3.1 27.0 + - - +
286A MET* 4.3 8.3 - - - +
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Residues in contact with PHE 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 LYS* 3.0 51.2 + - + +
192A LYS* 4.3 3.8 - - - +
194A SER* 1.4 75.2 - - - +
196A GLU* 1.3 66.1 + - - +
198A ALA* 3.6 7.3 - - + +
199A ARG* 3.0 55.9 + - - +
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Residues in contact with GLU 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 LYS* 3.2 33.5 + - + +
193A LEU* 3.6 23.7 - - - +
195A PHE* 1.3 80.2 - - - +
197A THR* 1.3 61.1 + - - +
199A ARG* 3.3 15.7 + - - +
200A PHE* 3.0 21.0 + - - +
280A HIS* 4.3 9.2 + - - -
281A TYR* 2.5 31.8 + - - +
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Residues in contact with THR 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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186A MET* 4.1 12.6 - - - -
193A LEU 2.9 21.7 + - - -
194A SER 3.9 4.3 - - - -
196A GLU* 1.3 75.1 - - - +
198A ALA* 1.3 58.1 + - - +
200A PHE* 3.1 4.4 + - + +
201A ILE* 2.9 48.6 + - + +
281A TYR* 3.6 21.3 - - + -
286A MET* 3.4 46.0 - - + +
287A LEU* 4.7 3.1 - - + -
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Residues in contact with ALA 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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186A MET* 4.7 14.7 - - + +
194A SER 3.1 18.1 + - - +
195A PHE* 3.6 11.2 - - + +
196A GLU 3.3 0.2 - - - -
197A THR* 1.3 75.4 - - - +
199A ARG* 1.3 57.2 + - + +
201A ILE* 3.3 8.5 + - - +
202A LYS* 3.0 27.1 + - - +
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Residues in contact with ARG 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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192A LYS 5.3 0.4 + - - -
195A PHE* 3.0 51.8 + - - +
196A GLU* 3.6 15.5 - - - +
198A ALA* 1.3 72.0 - - + +
200A PHE* 1.3 66.7 + - - +
202A LYS* 3.3 8.1 + - - +
203A PHE* 3.1 20.8 + - - +
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Residues in contact with PHE 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 GLU 3.0 11.4 + - - +
197A THR* 3.1 7.4 + - + +
199A ARG* 1.3 76.7 - - - +
201A ILE* 1.3 68.8 + - + +
203A PHE* 3.0 35.0 + + - +
204A ILE* 3.0 43.5 + - + +
273A LYS* 3.7 17.9 - - + -
274A TYR* 3.8 9.2 - - - -
277A GLY* 3.4 16.2 - - - -
278A CYS* 3.3 35.4 - - - -
281A TYR* 3.5 35.4 - + + +
287A LEU* 4.6 4.7 - - + -
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Residues in contact with ILE 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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180A SER* 3.6 30.1 - - - +
186A MET* 5.1 7.0 - - + -
197A THR* 2.9 37.4 + - + +
198A ALA* 3.7 8.7 - - - +
200A PHE* 1.3 79.2 - - + +
202A LYS* 1.3 62.6 + - - +
204A ILE* 3.2 11.7 + - + +
205A VAL* 3.1 29.0 + - + +
214A LEU* 4.2 25.1 - - + +
287A LEU* 3.9 17.9 - - + -
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Residues in contact with LYS 202 (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 ALA 3.0 13.8 + - - +
199A ARG* 3.6 11.9 - - - +
200A PHE 3.3 0.2 - - - -
201A ILE* 1.3 76.1 - - - +
203A PHE* 1.3 60.9 + - - +
205A VAL* 3.5 8.6 + - + +
206A THR* 2.6 41.9 + - - +
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Residues in contact with PHE 203 (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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199A ARG 3.1 12.2 + - - +
200A PHE* 3.0 31.9 + + - +
202A LYS* 1.3 77.0 - - - +
204A ILE* 1.3 66.1 + - + +
206A THR* 3.1 4.1 + - - -
207A GLU* 2.9 62.6 + - + +
208A ILE* 3.9 15.0 + - + -
270A ARG* 3.5 25.8 - - + -
273A LYS* 3.7 46.2 - - + +
274A TYR* 3.9 18.2 - + - -
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Residues in contact with ILE 204 (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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200A PHE* 3.0 50.6 + - + +
201A ILE* 3.4 14.4 - - + +
203A PHE* 1.3 74.4 - - + +
205A VAL* 1.3 65.1 + - + +
206A THR 3.0 1.6 + - - -
208A ILE* 2.9 34.6 + - + +
209A PHE* 2.9 35.7 + - + -
214A LEU* 4.6 22.4 - - + -
274A TYR* 3.9 19.5 - - + +
278A CYS* 4.0 13.2 - - - -
287A LEU* 4.9 4.0 - - + -
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Residues in contact with VAL 205 (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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201A ILE* 3.1 17.9 + - + +
202A LYS* 4.1 11.7 - - + +
204A ILE* 1.3 85.7 - - + +
206A THR* 1.3 57.8 + - - +
209A PHE* 3.0 22.4 - - + +
211A GLY* 3.3 14.9 + - - -
212A GLY* 3.4 35.2 + - - +
213A ARG* 3.8 15.3 - - + +
214A LEU* 4.2 13.9 - - + +
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Residues in contact with THR 206 (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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25A TYR* 3.7 15.1 - - + +
202A LYS* 2.6 36.8 + - - +
203A PHE* 3.8 3.6 - - - -
204A ILE 3.1 0.2 - - - -
205A VAL* 1.3 81.4 + - - +
207A GLU* 1.3 72.3 + - + +
208A ILE 3.8 0.2 - - - -
210A PRO* 3.6 23.2 - - - +
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Residues in contact with GLU 207 (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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25A TYR* 3.5 59.9 + - + +
203A PHE* 2.9 43.4 + - + +
206A THR* 1.3 85.6 - - + +
208A ILE* 1.3 64.3 + - - +
209A PHE 3.8 0.2 - - - -
210A PRO* 4.5 0.7 - - - -
270A ARG* 3.2 33.2 + - - +
271A TYR* 4.5 1.9 + - - -
273A LYS* 5.2 2.1 + - - -
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Residues in contact with ILE 208 (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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25A TYR 5.3 1.9 - - - +
42A TYR* 4.0 11.7 - - - +
203A PHE* 4.0 12.8 - - + -
204A ILE* 2.9 16.8 + - - +
207A GLU* 1.3 80.3 - - - +
209A PHE* 1.3 92.2 + - + +
210A PRO* 3.6 6.5 - - - +
270A ARG* 3.8 29.6 - - + +
271A TYR* 3.7 27.0 + - + +
274A TYR* 3.6 45.8 - - + -
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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