Contacts of the helix formed by residues 198 - 220 (chain R) 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 R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55Q GLN* 3.4 27.6 - - - +
56R TYR* 3.8 5.4 - - - -
188R CYS 3.9 2.2 - - - +
189R HIS* 2.9 32.1 + - - +
190R ASP 3.2 8.4 + - - -
192R PHE* 3.7 26.7 - - + +
197R LEU* 1.3 75.3 - - - +
199R GLY* 1.3 64.8 + - - +
200R GLY 3.4 4.0 + - - -
201R GLY 3.1 12.5 + - - -
202R TYR* 3.0 23.0 + - - -
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Residues in contact with GLY 199 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55Q GLN* 4.6 2.0 + - - +
56R TYR* 3.8 32.1 - - - -
58R ILE* 4.5 8.2 - - - +
198R THR* 1.3 75.5 - - - +
200R GLY* 1.3 62.6 + - - +
202R TYR* 3.3 3.6 + - - +
203R ALA* 3.2 19.8 + - - +
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Residues in contact with GLY 200 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189R HIS 5.0 3.6 - - - -
190R ASP* 4.5 4.9 - - - -
198R THR* 3.2 6.7 + - - -
199R GLY* 1.3 74.7 - - - +
201R GLY* 1.3 63.3 + - - +
203R ALA* 3.1 22.2 + - - +
204R LYS* 3.4 7.8 + - - +
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Residues in contact with GLY 201 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179R PHE* 3.9 8.6 - - - -
190R ASP* 4.0 19.1 + - - -
197R LEU* 3.9 22.9 - - - -
198R THR* 3.1 15.2 + - - -
200R GLY* 1.3 74.3 - - - +
202R TYR* 1.3 63.0 + - - +
204R LYS* 2.8 19.4 + - - +
205R ILE* 3.3 7.3 + - - +
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Residues in contact with TYR 202 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49R MET* 2.7 39.1 + - - +
52R LEU* 3.2 20.3 - - + +
53R MET* 3.7 39.9 - - + -
56R TYR* 3.3 39.7 - + + -
58R ILE* 4.6 7.9 - - + -
101R TRP* 4.4 3.1 - + - -
196R HIS* 5.7 0.9 - - - -
197R LEU* 3.6 38.1 + - + +
198R THR 3.0 18.4 + - - +
199R GLY 3.8 4.7 - - - +
201R GLY* 1.3 74.1 - - - +
203R ALA* 1.3 51.5 + - - +
205R ILE* 2.9 7.0 + - + -
206R CYS* 2.6 47.7 + - - +
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Residues in contact with ALA 203 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58R ILE* 3.9 19.6 - - + +
199R GLY 3.2 10.8 + - - +
200R GLY* 3.1 17.9 + - - +
201R GLY 3.1 0.2 - - - -
202R TYR* 1.3 76.9 - - - +
204R LYS* 1.3 59.2 - - - +
207R LYS* 3.3 27.9 + - - +
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Residues in contact with LYS 204 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175R THR* 3.8 8.6 - - - +
177R GLY* 3.8 23.0 + - - -
178R GLY* 3.5 27.2 + - - +
179R PHE* 4.1 18.6 - - + -
181R HIS* 5.5 3.2 + - - -
190R ASP* 4.4 17.5 + - - +
200R GLY 3.4 5.5 + - - +
201R GLY 2.8 11.0 + - - +
203R ALA* 1.3 77.9 - - + +
205R ILE* 1.3 59.7 + - - +
207R LYS* 5.5 0.7 - - - -
208R PRO* 3.3 20.3 - - - +
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Residues in contact with ILE 205 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53R MET* 4.2 16.2 - - + -
101R TRP* 4.0 11.2 - - + -
137R LEU* 3.8 24.7 - - + -
140R LEU* 3.7 29.6 - - + -
175R THR* 3.8 25.9 + - + +
179R PHE* 3.9 17.5 - - + -
197R LEU* 4.0 15.3 - - + -
201R GLY 3.3 9.4 + - - +
202R TYR* 2.9 11.0 + - - +
204R LYS* 1.3 79.2 - - - +
206R CYS* 1.3 60.9 + - - +
208R PRO* 3.1 18.5 - - - +
209R LEU* 3.4 12.2 + - + +
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Residues in contact with CYS 206 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53R MET* 3.8 27.8 - - - -
58R ILE* 3.3 36.1 - - + -
62R LEU* 3.8 6.3 - - + -
63R PHE* 3.7 21.0 - - + -
202R TYR* 2.6 28.1 + - - +
205R ILE* 1.3 73.1 - - - +
207R LYS* 1.3 59.3 - - - +
209R LEU* 3.0 7.0 + - - -
210R HIS* 2.7 37.6 + - - +
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Residues in contact with LYS 207 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58R ILE* 4.9 0.6 - - - +
62R LEU* 4.5 5.3 - - - +
203R ALA 3.3 14.4 + - - +
204R LYS* 5.0 0.4 - - - +
206R CYS* 1.3 79.4 - - - +
208R PRO* 1.3 69.2 - - + +
210R HIS* 3.7 5.6 + - - +
211R GLU* 3.0 35.4 + - - +
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Residues in contact with PRO 208 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173R LEU* 4.4 13.3 - - + +
175R THR* 3.7 20.0 - - + +
204R LYS 3.3 21.8 - - - +
205R ILE 3.1 17.0 - - - +
207R LYS* 1.3 98.5 - - + +
209R LEU* 1.3 56.7 + - - +
211R GLU* 3.3 9.3 + - + +
212R LEU* 2.9 29.3 + - - +
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Residues in contact with LEU 209 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44R PHE* 3.8 27.8 - - + -
53R MET* 4.4 15.5 - - + -
63R PHE* 4.0 16.2 - - + -
99R VAL* 4.1 8.1 - - + -
135R ILE* 4.0 17.7 - - + -
137R LEU* 3.8 27.8 - - + -
173R LEU* 4.0 13.1 - - + +
205R ILE* 3.4 17.0 - - + +
206R CYS* 3.0 4.1 + - - +
208R PRO* 1.3 78.6 - - - +
210R HIS* 1.3 62.6 + - - +
212R LEU* 3.1 5.0 + - - +
213R ILE* 2.9 40.4 + - + +
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Residues in contact with HIS 210 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62R LEU* 3.5 53.0 + - + +
63R PHE* 3.7 16.6 - + + -
66R LEU* 4.0 13.0 - - + +
206R CYS 2.7 20.0 + - - +
207R LYS* 3.7 4.6 + - - +
209R LEU* 1.3 72.0 - - - +
211R GLU* 1.3 68.9 + - - +
213R ILE* 3.1 6.3 + - - +
214R MET* 2.9 54.8 + - + +
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Residues in contact with GLU 211 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207R LYS* 3.0 28.2 + - - +
208R PRO* 3.6 8.1 - - + +
210R HIS* 1.3 85.1 + - - +
212R LEU* 1.3 62.8 + - - +
214R MET* 3.8 5.1 + - - +
215R GLN* 3.4 33.4 + - - +
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Residues in contact with LEU 212 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135R ILE* 3.8 26.9 - - + -
171R GLN* 3.4 33.4 - - + +
173R LEU* 4.3 31.4 - - + -
208R PRO 2.9 13.8 + - - +
209R LEU* 3.5 8.7 - - - +
210R HIS 3.1 0.2 - - - -
211R GLU* 1.3 75.5 + - - +
213R ILE* 1.3 67.8 + - - +
215R GLN* 3.0 34.1 + - + +
216R LEU* 3.0 18.4 + - + +
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Residues in contact with ILE 213 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42R VAL* 4.0 22.9 - - + -
44R PHE* 4.4 9.9 - - + -
63R PHE* 4.7 5.4 - - + -
66R LEU* 4.6 9.6 - - + -
97R VAL* 4.0 12.8 - - + -
99R VAL* 4.0 11.4 - - + -
135R ILE* 3.6 20.4 - - + -
209R LEU* 2.9 48.9 + - + +
210R HIS* 3.7 7.2 - - - +
212R LEU* 1.3 73.2 - - - +
214R MET* 1.3 52.1 + - - +
216R LEU* 2.8 14.3 + - - +
217R LEU* 2.7 52.0 + - + +
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Residues in contact with MET 214 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66R LEU* 4.5 23.8 - - + -
210R HIS* 2.9 50.3 + - + +
211R GLU* 3.9 7.0 - - - +
213R ILE* 1.3 75.6 - - - +
215R GLN* 1.3 61.6 + - - +
217R LEU* 3.8 16.2 - - + +
218R GLU* 3.0 25.3 + - + +
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Residues in contact with GLN 215 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211R GLU* 3.4 21.8 + - - +
212R LEU* 3.0 28.8 + - + +
214R MET* 1.3 76.5 - - - +
216R LEU* 1.3 64.1 + - + +
218R GLU* 3.0 19.8 + - - +
219R GLU* 3.1 10.9 + - - +
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Residues in contact with LEU 216 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96R LYS* 6.1 0.3 - - - +
97R VAL* 3.8 15.5 - - + +
133R LYS* 3.3 62.6 - - + +
134R ILE 5.5 0.7 - - - +
135R ILE* 4.0 32.3 - - + -
171R GLN* 4.6 18.4 - - + +
212R LEU* 3.0 17.8 + - + +
213R ILE 2.8 13.8 + - - +
215R GLN* 1.3 75.8 - - + +
217R LEU* 1.3 60.0 + - - +
219R GLU* 3.3 17.0 - - + +
220R THR 4.3 2.1 + - - +
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Residues in contact with LEU 217 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41R ASP* 4.5 14.4 - - + +
42R VAL* 4.7 7.0 - - + -
66R LEU* 4.2 26.7 - - + +
96R LYS* 3.8 38.8 - - + -
97R VAL* 4.4 8.5 - - + -
213R ILE* 2.7 32.0 + - + +
214R MET* 3.8 18.4 - - + +
216R LEU* 1.3 69.6 - - - +
218R GLU* 1.3 57.7 + - - +
219R GLU 3.0 9.2 + - - -
220R THR 3.5 21.2 + - - +
221R PRO* 4.5 4.9 - - - +
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Residues in contact with GLU 218 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214R MET* 3.0 19.0 + - + +
215R GLN* 3.0 9.1 + - - +
217R LEU* 1.3 74.4 - - - +
219R GLU* 1.3 60.9 + - - +
220R THR 3.7 0.4 - - - -
221R PRO* 5.6 4.3 - - - +
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Residues in contact with GLU 219 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133R LYS* 3.7 23.6 - - + +
215R GLN 3.1 7.9 + - - +
216R LEU* 3.3 15.7 - - + +
217R LEU 3.0 3.0 - - - -
218R GLU* 1.3 80.1 - - - +
220R THR* 1.3 66.9 + - - +
221R PRO* 4.6 2.0 - - - +
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Residues in contact with THR 220 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96R LYS* 4.7 14.4 - - - +
133R LYS* 5.7 1.6 + - - +
216R LEU 4.3 2.3 + - - +
217R LEU* 3.5 11.3 + - - +
219R GLU* 1.3 86.3 + - - +
221R PRO* 1.3 70.7 - - + +
222R GLU* 3.9 8.3 - - + +
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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
------------------------------------------------------------
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