Contacts of the helix formed by residues 213 - 233 (chain V) in PDB entry 1UW9
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 213 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B VAL 5.3 5.3 + - - -
152B PRO 5.6 0.7 - - - +
285B ARG* 3.7 46.3 - - - +
109O GLU* 5.4 0.6 - - - +
110O GLU* 2.8 43.8 + - - -
208V SER* 3.5 14.7 + - - +
209V GLN* 3.4 29.9 + - - +
210V PRO* 3.6 20.5 + - - +
212V MET* 1.3 78.6 - - - +
214V TRP* 1.3 66.1 + - + +
215V ARG* 3.4 2.9 - - + +
216V ASP* 3.3 24.7 + - - +
217V ARG 3.3 16.3 + - - -
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Residues in contact with TRP 214 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ARG* 6.4 0.6 - - - +
286B ASP* 5.2 10.5 + - - -
207V ASN 3.4 18.6 - - - +
208V SER* 3.0 28.3 + - - -
212V MET 3.9 0.2 + - - -
213V ARG* 1.3 72.3 - - + +
215V ARG* 1.3 92.0 + - + +
217V ARG* 3.1 19.8 + - - +
218V PHE* 2.9 51.5 + + + -
249V GLU* 3.9 5.5 + - - -
252V LYS* 3.8 29.6 - - + +
253V ARG* 3.4 54.2 - - + +
256V SMC 3.6 35.9 - - + -
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Residues in contact with ARG 215 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LYS* 5.1 1.9 - - - +
258B LYS* 4.6 3.2 - - - +
285B ARG* 3.7 15.7 - - - +
286B ASP* 3.0 33.0 + - - +
287B ASN* 3.4 21.6 + - - +
288B GLY* 3.6 19.6 - - - +
63C VAL* 3.8 36.4 + - - +
65C CYS 4.9 2.2 + - - -
213V ARG* 3.4 2.0 - - + +
214V TRP* 1.3 111.1 - - + +
216V ASP* 1.3 67.8 + - - +
218V PHE* 3.8 1.5 - - - +
219V LEU* 3.2 54.9 + - + +
256V SMC 3.8 19.7 - - - +
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Residues in contact with ASP 216 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B PRO 4.9 3.9 - - - +
153B HIS* 3.4 12.5 + - - -
157B VAL* 3.4 33.0 - - + +
161B LYS* 3.0 32.8 + - - +
285B ARG* 6.0 1.5 - - - -
182V ALA* 3.6 18.8 - - + -
213V ARG* 3.3 25.9 + - - +
214V TRP 3.3 0.6 - - - -
215V ARG* 1.3 77.1 - - - +
217V ARG* 1.3 63.1 + - - +
219V LEU* 3.3 3.3 + - - +
220V PHE* 3.1 30.1 + - + -
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Residues in contact with ARG 217 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182V ALA* 3.6 10.2 - - - +
185V TYR* 3.7 14.4 - - + -
202V ASP* 2.8 40.6 + - - -
206V VAL* 3.4 20.2 + - - +
207V ASN* 2.8 33.1 + - - +
209V GLN* 5.5 0.2 + - - -
212V MET* 3.6 38.6 + - - +
213V ARG 3.3 3.5 + - - +
214V TRP* 3.1 19.4 + - - +
216V ASP* 1.3 77.7 - - - +
218V PHE* 1.3 78.7 + - - +
220V PHE* 3.3 0.9 + - - +
221V VAL* 2.8 49.1 + - + +
240V LEU* 4.7 1.5 - - + +
241V ASN 4.1 4.4 + - - -
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Residues in contact with PHE 218 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214V TRP* 2.9 55.0 + + + +
215V ARG* 3.8 6.1 - - - +
216V ASP 3.4 0.2 - - - -
217V ARG* 1.3 99.8 - - - +
219V LEU* 1.3 54.9 + - - +
221V VAL* 3.9 0.9 - - - +
222V THR* 2.7 38.1 + - - -
240V LEU* 3.6 49.1 - - + +
241V ASN 3.4 21.8 - - - -
242V ALA* 5.1 0.4 - - - -
253V ARG* 3.3 27.6 - - + -
256V SMC 3.8 14.8 - - + -
257V ALA* 4.3 7.2 - - + -
260V LEU* 4.1 12.1 - - + -
265V ILE* 5.3 0.7 - - + -
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Residues in contact with LEU 219 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LYS* 4.4 18.4 - - - +
288B GLY 5.7 0.2 - - - +
63C VAL 4.9 3.1 - - - +
65C CYS 3.5 24.0 - - - +
66C LEU 4.0 16.2 - - - +
67C TYR* 4.0 22.9 - - + +
71C ARG* 5.1 3.1 + - - +
215V ARG* 3.2 46.1 + - - +
216V ASP* 3.6 8.7 - - - +
217V ARG 3.1 0.6 - - - -
218V PHE* 1.3 75.5 - - + +
220V PHE* 1.3 68.7 + - + +
222V THR* 3.2 8.5 + - - -
223V GLU* 3.1 18.4 + - - +
256V SMC 4.6 2.7 - - + -
260V LEU* 4.2 24.2 - - + -
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Residues in contact with PHE 220 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B VAL* 5.2 3.4 - - + -
160B ASP* 3.6 44.9 - - + -
161B LYS* 3.7 22.9 - - + -
71C ARG* 4.3 26.0 - - + +
72C TYR* 3.4 37.4 - + - +
182V ALA* 3.6 19.5 - - + +
183V LYS* 3.5 30.7 - - + -
186V GLY* 4.2 2.5 - - - -
216V ASP* 3.1 24.4 + - + +
217V ARG 4.1 0.9 - - - +
219V LEU* 1.3 79.4 - - + +
221V VAL* 1.3 62.8 + - - +
223V GLU* 3.2 7.3 + - - +
224V ALA* 3.0 18.4 + - - +
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Residues in contact with VAL 221 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185V TYR* 4.2 16.2 - - + -
186V GLY* 4.4 7.0 - - - +
189V VAL* 4.2 13.2 - - + -
217V ARG* 2.8 37.0 + - + +
218V PHE 4.0 0.2 - - - +
220V PHE* 1.3 76.2 - - - +
222V THR* 1.3 58.0 + - - +
224V ALA* 3.1 8.7 + - - +
225V ILE* 2.8 35.2 + - + +
238V HIS* 3.5 42.8 - - + +
240V LEU* 3.8 13.5 - - + -
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Residues in contact with THR 222 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C PHE* 4.0 12.6 - - + -
67C TYR* 4.0 10.8 - - + -
218V PHE 2.7 22.3 + - - -
219V LEU* 3.4 7.6 - - - -
221V VAL* 1.3 76.7 - - - +
223V GLU* 1.3 62.4 + - - +
225V ILE* 3.3 10.5 + - - +
226V TYR* 3.1 50.8 + - + -
240V LEU* 4.8 2.6 - - - +
260V LEU* 3.5 19.1 - - + +
262V VAL* 3.5 18.3 - - + +
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Residues in contact with GLU 223 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C TYR* 3.3 24.5 + - + +
68C TYR 3.1 17.5 - - - +
69C ASP* 4.3 6.4 - - - +
70C ASN 3.5 5.8 + - - +
71C ARG* 2.9 42.8 + - - +
72C TYR* 3.0 44.5 + - + +
1141C EDO 6.3 0.2 - - - -
219V LEU 3.1 10.1 + - - +
220V PHE* 3.2 10.6 + - - +
222V THR* 1.3 75.1 - - - +
224V ALA* 1.3 58.1 + - - +
226V TYR* 3.9 1.4 - - - +
227V LYS* 3.0 32.0 + - + +
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Residues in contact with ALA 224 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C TYR* 4.4 4.4 - - + -
186V GLY 3.1 28.5 - - - +
189V VAL* 3.8 9.0 - - + -
190V TYR* 3.5 23.6 - - + +
193V LEU* 4.6 2.0 - - - -
220V PHE 3.0 11.4 + - - +
221V VAL 3.1 8.5 + - - +
223V GLU* 1.3 74.5 - - - +
225V ILE* 1.3 64.8 + - - +
227V LYS* 3.8 3.1 - - - +
228V ALA* 3.0 26.3 + - - +
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Residues in contact with ILE 225 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193V LEU* 3.9 14.6 - - + +
221V VAL* 2.8 30.9 + - + +
222V THR* 3.3 4.2 + - - +
224V ALA* 1.3 73.9 - - - +
226V TYR* 1.3 75.8 + - + +
228V ALA* 3.4 0.7 + - - -
229V GLN* 2.9 30.6 + - - +
236V LYS* 3.4 31.5 - - + +
237V GLY* 4.3 1.6 - - - -
238V HIS* 3.8 40.4 - - + +
240V LEU* 5.3 1.3 - - + -
262V VAL* 4.0 27.8 - - + -
263V PRO* 4.7 3.6 - - + -
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Residues in contact with TYR 226 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C SER* 3.5 34.8 - - - +
59C ARG* 2.9 40.7 + - - -
60C PHE* 3.9 9.2 - + - -
67C TYR* 3.8 3.4 - - - +
69C ASP* 4.6 0.2 - - - +
1141C EDO 3.5 6.8 - - - -
222V THR* 3.1 37.9 + - + +
223V GLU 4.1 1.8 - - - +
225V ILE* 1.3 90.7 - - + +
227V LYS* 1.3 64.9 + - - +
229V GLN* 3.8 17.9 - - - +
230V ALA* 3.0 25.6 + - - +
260V LEU 2.7 23.6 + - - -
261V GLY 3.2 11.9 + - - -
262V VAL* 3.6 8.6 + - + -
263V PRO* 5.8 1.1 - - + -
54W ASN* 5.8 2.2 - - - -
68W TYR* 5.4 3.1 - + - -
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Residues in contact with LYS 227 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ALA* 5.8 1.2 - - - +
49C LYS* 4.1 32.1 - - - +
70C ASN* 4.6 6.6 + - - +
72C TYR* 3.4 40.0 + - + +
73C TRP* 4.4 6.3 - - - +
74C THR* 4.6 1.9 + - - -
1141C EDO 3.6 20.9 + - - +
190V TYR* 3.4 44.1 + - + -
223V GLU* 3.0 23.6 + - + +
224V ALA* 3.8 4.3 - - - +
226V TYR* 1.3 76.6 - - - +
228V ALA* 1.3 55.7 + - - +
230V ALA* 3.3 3.5 + - - +
231V GLU* 2.9 34.3 + - - +
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Residues in contact with ALA 228 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190V TYR* 4.0 12.3 - - + -
193V LEU* 3.5 33.9 - - + -
194V ARG* 3.7 14.4 - - - +
224V ALA 3.0 16.5 + - - +
225V ILE 3.9 2.2 - - - +
227V LYS* 1.3 76.5 - - - +
229V GLN* 1.3 57.1 + - - +
231V GLU* 3.7 5.3 - - - +
232V THR* 2.9 37.6 + - - +
236V LYS* 4.1 3.8 - - + -
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Residues in contact with GLN 229 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ARG* 6.0 0.2 - - - -
225V ILE* 2.9 21.7 + - - +
226V TYR* 3.8 16.9 - - - +
228V ALA* 1.3 77.2 - - - +
230V ALA* 1.3 57.2 + - - +
233V GLY* 2.8 30.7 + - - -
234V GLU 3.3 21.7 + - - +
235V VAL* 3.4 13.0 - - - +
236V LYS* 3.0 37.1 + - + +
52W VAL* 3.5 24.6 - - + +
54W ASN* 4.9 5.2 + - - +
68W TYR* 3.5 23.1 + - - -
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Residues in contact with ALA 230 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C LYS* 4.2 9.4 - - - +
1141C EDO 3.8 25.8 - - - +
226V TYR 3.0 18.7 + - - +
227V LYS 3.8 2.9 - - - +
229V GLN* 1.3 78.0 - - - +
231V GLU* 1.3 62.5 + - - +
233V GLY* 4.0 0.9 + - - -
10W LYS* 3.2 24.4 + - - -
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Residues in contact with GLU 231 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C LYS* 6.1 2.0 - - - +
190V TYR* 2.6 29.4 + - - -
194V ARG* 2.9 44.5 + - - +
227V LYS* 2.9 21.5 + - + +
228V ALA* 3.7 5.2 - - - +
230V ALA* 1.3 79.5 - - - +
232V THR* 1.3 62.0 + - + +
4W TRP* 5.2 0.3 - - - -
5W THR 4.3 1.0 - - - +
6W PRO* 3.2 36.6 - - + +
9W ASN* 4.2 7.2 + - + +
10W LYS* 3.9 22.8 + - - +
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Residues in contact with THR 232 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194V ARG* 3.5 35.7 - - - +
228V ALA 2.9 20.6 + - - +
231V GLU* 1.3 81.8 - - + +
233V GLY* 1.3 63.1 + - - +
234V GLU* 3.2 17.0 + - - -
236V LYS* 3.2 23.6 - - - +
9W ASN 4.6 4.0 - - - +
10W LYS* 3.6 3.5 - - - +
11W MET* 2.8 41.1 + - + +
17W TYR* 4.8 5.2 - - - +
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Residues in contact with GLY 233 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229V GLN 2.8 14.3 + - - -
230V ALA 4.0 2.5 + - - -
231V GLU 3.6 2.0 - - - -
232V THR* 1.3 76.8 - - - +
234V GLU* 1.3 61.1 + - - +
10W LYS* 4.0 6.9 - - - +
11W MET 4.6 1.5 - - - +
13W GLU* 6.0 0.3 - - - +
51W TYR* 3.8 33.9 - - - -
52W VAL* 4.8 15.1 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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