Contacts of the helix formed by residues 198 - 220 (chain B) in PDB entry 1VYH
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 THR 198 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A GLN* 3.7 20.9 - - - +
56B TYR* 4.0 3.8 - - - -
188B CYS 4.0 4.3 - - - +
189B HIS* 3.0 25.5 + - - +
190B ASP 3.2 22.0 + - - -
191B MET 3.8 2.5 - - - +
192B PHE* 3.8 14.4 - - + +
197B LEU* 1.3 75.2 - - - +
199B GLY* 1.3 66.7 + - - +
200B GLY 3.2 4.8 + - - -
201B GLY 2.8 18.7 + - - -
202B TYR* 3.0 22.2 + - - -
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Residues in contact with GLY 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLN* 4.2 2.0 - - - +
56B TYR* 3.4 34.3 - - - -
58B ILE* 4.4 9.1 - - - +
198B THR* 1.3 74.5 - - - +
200B GLY* 1.3 63.1 - - - +
202B TYR* 3.4 3.3 + - - +
203B ALA* 3.3 19.5 + - - +
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Residues in contact with GLY 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B HIS 4.9 3.4 - - - -
190B ASP* 5.1 3.8 - - - -
198B THR* 3.1 7.4 + - - -
199B GLY* 1.3 74.0 - - - +
201B GLY* 1.3 63.1 + - - +
203B ALA* 3.2 20.4 + - - +
204B LYS* 3.4 10.6 + - - +
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Residues in contact with GLY 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B PHE* 3.8 13.8 - - - -
189B HIS 4.7 1.4 + - - -
190B ASP* 4.0 7.1 + - - +
197B LEU* 3.9 24.5 - - - -
198B THR* 2.8 19.9 + - - -
200B GLY* 1.3 71.0 - - - +
202B TYR* 1.3 63.8 + - - +
204B LYS* 2.8 22.8 + - - +
205B ILE* 3.3 3.8 + - - +
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Residues in contact with TYR 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B MET* 2.7 43.7 + - - +
52B LEU* 3.4 14.5 - - + +
53B MET* 3.6 32.8 - - + -
56B TYR* 3.9 27.1 - + + -
58B ILE* 4.5 8.7 - - + -
101B TRP* 4.1 10.3 - + - -
196B HIS* 5.6 0.9 - - - -
197B LEU* 3.5 45.3 + - + +
198B THR 3.0 24.6 + - - +
199B GLY* 3.9 4.7 - - - +
201B GLY* 1.3 73.1 - - - +
203B ALA* 1.3 51.5 + - - +
205B ILE* 2.8 7.4 + - + +
206B CYS* 2.5 47.8 + - - -
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Residues in contact with ALA 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ILE* 4.1 19.7 - - + +
199B GLY 3.3 9.7 + - - +
200B GLY* 3.2 15.1 + - - +
201B GLY 3.0 0.6 + - - -
202B TYR* 1.3 77.1 - - - +
204B LYS* 1.3 61.5 + - - +
207B LYS* 3.3 27.4 + - - +
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Residues in contact with LYS 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B THR* 3.8 6.4 - - - +
177B GLY* 3.6 26.7 + - - -
178B GLY* 3.6 19.8 + - - +
179B PHE* 4.1 15.5 - - + -
181B HIS* 6.2 1.0 - - - -
190B ASP* 3.6 30.2 + - - -
200B GLY 3.4 8.4 + - - +
201B GLY 2.8 13.5 + - - +
203B ALA* 1.3 80.3 - - - +
205B ILE* 1.3 57.7 + - + +
207B LYS* 5.3 0.4 - - - -
208B PRO* 3.4 19.6 - - - +
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Residues in contact with ILE 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B MET* 4.6 5.6 - - + -
101B TRP* 4.3 23.6 - - + -
137B LEU* 4.9 10.7 - - + +
140B LEU* 4.4 9.9 - - + -
173B LEU* 5.6 0.2 - - - +
175B THR* 3.8 34.4 + - + +
177B GLY 5.0 2.7 - - - +
179B PHE* 3.6 26.0 - - + -
197B LEU* 4.0 22.7 - - + -
201B GLY 3.3 1.7 + - - +
202B TYR* 2.8 11.5 + - + +
204B LYS* 1.3 83.0 - - + +
206B CYS* 1.3 69.9 + - - +
207B LYS 3.5 0.2 - - - -
208B PRO* 3.1 18.6 - - - +
209B LEU* 3.4 11.0 + - + +
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Residues in contact with CYS 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B MET* 3.5 45.1 - - - -
58B ILE* 3.1 35.2 - - + -
62B LEU* 4.1 6.1 - - + -
63B PHE* 4.0 9.4 - - + -
202B TYR* 2.5 28.5 + - - +
205B ILE* 1.3 73.4 - - - +
207B LYS* 1.3 57.9 + - - +
209B LEU* 3.0 6.3 + - - -
210B HIS* 2.7 37.4 + - - +
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Residues in contact with LYS 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ILE* 5.0 0.2 - - - +
62B LEU* 4.8 6.1 - - - +
203B ALA* 3.3 16.9 + - - +
204B LYS 4.9 0.7 - - - +
206B CYS* 1.3 80.0 - - - +
208B PRO* 1.3 67.9 - - + +
210B HIS* 3.5 7.0 + - - +
211B GLU* 3.0 36.6 + - - +
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Residues in contact with PRO 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B LEU* 4.4 13.3 - - + +
175B THR* 3.6 18.4 - - + -
204B LYS 3.4 18.4 - - - +
205B ILE 3.1 19.3 - - - +
207B LYS* 1.3 95.0 - - + +
209B LEU* 1.3 57.2 + - - +
211B GLU* 3.3 14.6 - - + +
212B LEU* 2.9 29.5 + - - +
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Residues in contact with LEU 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B PHE* 3.8 27.1 - - + -
53B MET* 4.2 9.4 - - + -
63B PHE* 4.2 9.2 - - + -
99B VAL* 4.4 4.0 - - + -
135B ILE* 4.2 19.3 - - + -
137B LEU* 3.7 43.3 - - + -
173B LEU* 4.1 14.3 - - + +
205B ILE* 3.5 12.6 - - + +
206B CYS* 3.0 9.1 + - - +
208B PRO* 1.3 77.9 - - - +
210B HIS* 1.3 64.9 + - - +
212B LEU* 3.1 4.2 + - - +
213B ILE* 2.9 40.6 + - + +
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Residues in contact with HIS 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU* 3.7 52.5 + - + +
63B PHE* 3.7 18.3 - + + -
66B LEU* 4.2 8.0 - - + +
206B CYS 2.7 20.4 + - - +
207B LYS* 3.7 5.0 + - - +
209B LEU* 1.3 71.3 - - - +
211B GLU* 1.3 68.0 + - - +
213B ILE* 3.1 5.0 + - - +
214B MET* 2.9 65.6 + - + +
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Residues in contact with GLU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B LYS* 3.0 27.4 + - - +
208B PRO* 3.3 18.7 - - - +
210B HIS* 1.3 87.0 - - - +
212B LEU* 1.3 61.5 + - - +
214B MET* 3.7 6.2 - - - +
215B GLN* 3.4 24.7 + - - +
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Residues in contact with LEU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B ILE* 3.7 36.3 - - + -
171B GLN* 4.0 27.8 - - + +
173B LEU* 4.3 20.4 - - + -
208B PRO 2.9 13.9 + - - +
209B LEU* 3.1 9.2 + - - +
211B GLU* 1.3 74.1 - - - +
213B ILE* 1.3 69.3 + - - +
215B GLN* 2.8 47.5 + - + +
216B LEU* 3.0 15.8 + - + +
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Residues in contact with ILE 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B VAL* 4.1 23.1 - - + -
44B PHE* 4.3 13.2 - - + -
63B PHE* 3.9 22.2 - - + -
66B LEU* 4.7 5.8 - - + -
97B VAL* 4.3 6.3 - - + -
99B VAL* 4.3 7.2 - - + -
135B ILE* 3.7 20.9 - - + -
209B LEU* 2.9 32.8 + - + +
210B HIS* 3.6 4.5 - - - +
212B LEU* 1.3 72.9 - - - +
214B MET* 1.3 65.2 + - - +
216B LEU* 2.7 21.5 + - - +
217B LEU* 2.8 36.4 + - + +
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Residues in contact with MET 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B LEU* 4.7 20.6 - - + -
210B HIS* 2.9 59.5 + - + +
211B GLU* 3.7 7.9 - - - +
213B ILE* 1.3 74.5 - - - +
215B GLN* 1.3 62.2 + - - +
217B LEU* 3.4 11.8 + - + +
218B GLU* 3.0 27.8 + - + +
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Residues in contact with GLN 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B GLU* 3.4 17.4 + - - +
212B LEU* 2.8 35.1 + - + +
214B MET* 1.3 76.8 - - - +
216B LEU* 1.3 65.8 + - + +
218B GLU* 3.0 19.3 + - - +
219B GLU* 3.2 10.4 + - - +
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Residues in contact with LEU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B LYS* 6.1 0.2 - - - +
97B VAL* 4.0 15.9 - - + +
133B LYS* 3.5 52.0 - - + +
134B ILE 5.7 0.7 - - - +
135B ILE* 4.0 23.6 - - + -
171B GLN* 4.3 17.5 - - - +
212B LEU* 3.0 30.9 + - + +
213B ILE 2.7 11.9 + - - +
215B GLN* 1.3 83.0 - - + +
217B LEU* 1.3 61.0 + - - +
219B GLU* 3.1 18.4 - - + +
220B THR 4.2 2.3 + - - +
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Residues in contact with LEU 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ASP* 4.8 9.2 - - + +
42B VAL* 4.3 9.4 - - + -
66B LEU* 3.9 34.1 - - + +
96B LYS* 4.0 26.3 - - + +
97B VAL* 3.5 28.7 - - + -
213B ILE* 2.8 31.1 + - + +
214B MET* 3.7 13.9 - - + +
216B LEU* 1.3 68.2 - - - +
218B GLU* 1.3 58.5 + - - +
219B GLU 3.0 10.5 + - - -
220B THR 3.5 20.5 + - - +
221B PRO* 4.6 4.3 - - - +
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Residues in contact with GLU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B MET* 3.0 18.7 + - + +
215B GLN* 3.0 8.3 + - - +
217B LEU* 1.3 73.6 - - - +
219B GLU* 1.3 61.4 + - - +
220B THR* 4.9 0.2 - - - -
221B PRO* 5.6 3.9 - - - +
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Residues in contact with GLU 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B LYS* 4.4 17.3 - - + +
215B GLN 3.2 6.8 + - - +
216B LEU* 3.1 22.0 - - + +
217B LEU 3.0 2.0 - - - -
218B GLU* 1.3 80.4 - - - +
220B THR* 1.3 71.4 + - - +
221B PRO* 4.6 1.4 - - - +
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Residues in contact with THR 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B LYS* 4.1 18.2 - - - +
133B LYS* 6.0 1.9 - - - +
216B LEU 4.2 2.1 + - - +
217B LEU* 3.5 11.3 + - - +
219B GLU* 1.3 87.4 + - - +
221B PRO* 1.3 71.3 - - + +
222B GLU* 3.9 2.2 - - + +
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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
------------------------------------------------------------
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