Contacts of the helix formed by residues 170 - 192 (chain R) in PDB entry 3A68
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 TYR 170 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56R GLU* 4.2 6.3 - - - -
94R HIS* 2.7 53.8 + + + -
97R LYS* 3.4 20.7 - - + +
98R LEU* 3.3 24.6 + - + +
147R LEU* 3.7 35.7 - - + +
165R PHE* 3.7 30.1 - + - -
166R VAL* 3.0 19.3 + - + +
168R THR 3.5 0.4 - - - -
169R GLU* 1.3 93.9 - - + +
171R LEU* 1.3 62.2 + - - +
172R GLY 3.5 2.0 - - - -
173R GLU* 3.4 5.0 + - - +
174R GLN* 2.8 32.9 + - - +
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Residues in contact with LEU 171 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C VAL* 3.5 32.3 - - + -
161C GLN* 3.7 19.6 - - + +
164C ASP* 5.6 0.9 - - + +
144R ASN* 4.4 10.2 - - - +
147R LEU* 3.8 31.0 - - + -
148R LEU* 3.9 23.8 - - + -
151R HIS* 4.3 8.1 - - + -
166R VAL* 3.2 18.6 + - + +
167R GLU* 3.4 23.1 + - + +
170R TYR* 1.3 77.6 - - - +
172R GLY* 1.3 63.6 + - - +
174R GLN* 3.3 4.5 + - - +
175R VAL* 3.1 26.3 + - - +
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Residues in contact with GLY 172 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C GLN* 3.6 24.5 - - - +
164C ASP* 5.4 1.5 + - - -
167R GLU 3.9 5.7 + - - -
171R LEU* 1.3 78.3 - - - +
173R GLU* 1.3 67.5 + - - +
175R VAL* 3.2 5.4 + - - +
176R GLU* 3.1 29.8 + - - +
215R CA 4.6 4.9 - - - -
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Residues in contact with GLU 173 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94R HIS* 5.8 8.5 - - + +
168R THR 3.5 2.4 - - - +
169R GLU* 3.3 30.9 - - - +
170R TYR* 3.6 6.0 + - - +
171R LEU 3.3 0.2 - - - -
172R GLY* 1.3 78.1 + - - +
174R GLN* 1.3 57.2 + - - +
176R GLU* 3.3 15.0 + - - +
177R ALA* 2.9 28.6 + - - +
215R CA 2.6 29.8 - - - -
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Residues in contact with GLN 174 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94R HIS* 5.3 3.8 - - - -
140R GLU* 2.7 53.1 + - - +
143R THR* 3.6 12.4 - - - +
144R ASN* 3.5 35.0 - - + +
147R LEU* 4.0 17.7 - - + +
170R TYR* 2.8 19.1 + - - +
171R LEU 3.6 5.6 - - - +
172R GLY 3.3 0.2 - - - -
173R GLU* 1.3 76.5 - - - +
175R VAL* 1.3 62.6 + - - +
177R ALA* 3.3 4.5 + - - +
178R ILE* 2.9 30.4 + - + +
214R CA 4.1 10.7 - - - -
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Residues in contact with VAL 175 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C TYR* 5.2 2.2 - - + -
104C LYS* 4.0 31.4 - - + +
105C ARG* 3.8 30.3 - - + +
161C GLN* 3.7 27.1 - - + +
144R ASN* 5.1 11.9 - - - +
171R LEU 3.1 16.2 + - - +
172R GLY* 3.2 9.6 + - - +
174R GLN* 1.3 76.0 - - - +
176R GLU* 1.3 61.8 + - + +
178R ILE* 3.4 8.6 + - + +
179R LYS* 3.1 22.0 + - - +
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Residues in contact with GLU 176 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C LYS* 3.2 39.5 + - + +
172R GLY 3.1 19.7 + - - +
173R GLU* 3.7 15.4 - - - +
175R VAL* 1.3 74.4 - - + +
177R ALA* 1.3 59.8 + - - +
179R LYS* 3.3 5.9 + - - +
180R ARG* 3.0 29.8 + - - +
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Residues in contact with ALA 177 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90R GLU* 5.9 3.1 - - - +
140R GLU* 4.1 22.2 - - + +
173R GLU 2.9 16.1 + - - +
174R GLN* 3.3 8.7 + - - +
176R GLU* 1.3 76.2 - - - +
178R ILE* 1.3 63.1 + - - +
180R ARG* 3.4 9.4 + - - +
181R ILE* 3.1 33.2 + - + +
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Residues in contact with ILE 178 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ALA* 3.6 35.2 - - + +
39C GLN* 3.5 24.7 - - + +
104C LYS 5.7 0.4 - - - +
137R LEU* 3.8 15.8 - - + +
140R GLU* 3.9 34.8 - - + +
141R LYS* 4.1 7.9 - - + +
144R ASN* 3.8 16.4 - - + +
174R GLN* 2.9 22.6 + - + +
175R VAL* 3.7 8.3 - - + +
177R ALA* 1.3 76.1 - - - +
179R LYS* 1.3 61.0 + - - +
181R ILE* 3.5 0.6 + - - -
182R SER* 2.8 28.8 + - - -
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Residues in contact with LYS 179 (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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37C ALA* 4.3 3.6 - - + -
100C GLU 5.2 0.4 + - - -
103C ASN* 3.8 16.4 - - - +
104C LYS* 4.0 34.0 - - + +
71O ASP* 3.0 47.6 + - - -
73O ASP* 3.9 18.6 - - + +
175R VAL 3.1 15.7 + - - +
176R GLU* 3.3 6.5 + - - +
178R ILE* 1.3 77.3 - - - +
180R ARG* 1.3 64.0 + - - +
182R SER* 3.3 5.5 + - - -
183R GLU* 2.9 53.6 + - - +
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Residues in contact with ARG 180 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83R PHE* 3.6 30.4 - - - -
86R GLU* 5.4 4.9 + - - -
87R SER* 5.6 0.6 + - - -
90R GLU* 4.8 10.9 + - - -
176R GLU 3.0 17.3 + - - +
177R ALA* 3.5 9.9 - - - +
179R LYS* 1.3 78.4 - - - +
181R ILE* 1.3 64.5 + - + +
183R GLU* 3.3 16.2 + - - +
184R TYR* 2.9 56.6 + - + +
204R LEU* 5.3 1.2 - - - +
207R GLU* 4.3 5.9 + - - -
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Residues in contact with ILE 181 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63R TYR* 4.2 8.7 - - + +
83R PHE* 4.3 24.2 - - + -
133R MET* 3.5 39.3 - - - +
136R ALA* 4.2 9.4 - - + +
137R LEU* 3.8 16.2 - - + +
140R GLU* 3.5 34.1 - - + -
177R ALA* 3.1 16.1 + - + +
178R ILE 4.2 1.8 - - - +
180R ARG* 1.3 76.0 - - + +
182R SER* 1.3 66.7 + - - +
184R TYR* 3.0 8.7 + - + +
185R VAL* 2.9 21.6 + - - +
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Residues in contact with SER 182 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LEU* 3.4 20.8 - - - +
37C ALA* 3.3 23.0 + - - -
73O ASP* 3.6 27.6 - - - -
137R LEU* 3.5 15.4 - - - +
178R ILE 2.8 23.5 + - - -
179R LYS 3.5 4.9 - - - -
181R ILE* 1.3 75.5 - - - +
183R GLU* 1.3 57.7 + - - +
185R VAL* 3.2 2.0 + - - -
186R ALA* 2.9 25.6 + - - +
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Residues in contact with GLU 183 (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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71O ASP* 4.5 3.5 - - - +
72O ARG 5.1 0.5 - - - +
73O ASP* 3.7 24.5 - - + +
76O ALA* 3.9 11.2 - - + +
78O ARG* 4.7 21.5 - - - +
179R LYS* 2.9 50.4 + - - +
180R ARG* 3.5 15.9 - - - +
182R SER* 1.3 76.2 - - - +
184R TYR* 1.3 58.7 + - + +
186R ALA* 3.4 1.6 + - - +
187R GLN* 3.0 46.6 + - - +
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Residues in contact with TYR 184 (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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83R PHE* 3.8 24.7 - + - -
133R MET* 3.6 31.4 - - + -
180R ARG* 2.9 48.4 + - + +
181R ILE* 3.0 12.8 + - - +
183R GLU* 1.3 75.7 - - + +
185R VAL* 1.3 59.9 + - - +
187R GLN* 3.3 12.1 + - - +
188R LEU* 2.9 35.9 + - - +
200R PHE* 3.7 27.3 - + + -
203R MET* 4.9 0.9 - - + -
204R LEU* 3.4 17.1 - - + +
207R GLU* 2.6 36.1 + - - -
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Residues in contact with VAL 185 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C VAL* 5.2 0.4 - - + -
36C LEU* 3.9 16.6 - - + -
130R LEU* 3.8 13.4 - - + +
133R MET* 3.7 35.4 - - + +
134R GLU* 4.0 12.6 - - + +
137R LEU* 4.4 11.9 - - + -
181R ILE 2.9 17.4 + - - +
182R SER 3.5 7.0 - - - +
184R TYR* 1.3 74.8 - - - +
186R ALA* 1.3 64.1 + - - +
188R LEU* 3.3 3.4 + - - +
189R ARG* 3.0 50.6 + - - +
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Residues in contact with ALA 186 (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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36C LEU* 4.0 6.5 - - + +
73O ASP 3.4 25.6 - - - +
74O ASN* 3.8 22.2 - - - +
75O VAL 4.7 2.0 - - - +
76O ALA* 3.8 8.5 - - + -
182R SER 2.9 9.3 + - - +
183R GLU 3.7 3.6 - - - +
184R TYR 3.3 0.2 - - - -
185R VAL* 1.3 77.7 - - - +
187R GLN* 1.3 56.2 + - - +
189R ARG* 3.3 10.2 + - - +
190R ARG* 3.0 28.4 + - - +
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Residues in contact with GLN 187 (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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76O ALA* 3.8 23.8 - - + +
78O ARG* 3.0 34.6 + - - +
198O TRP* 2.9 34.4 + - + +
183R GLU* 3.0 38.3 + - - +
184R TYR* 3.8 18.4 - - - +
186R ALA* 1.3 73.0 - - - +
188R LEU* 1.3 66.2 + - - +
190R ARG* 3.1 8.4 + - - +
191R VAL* 3.0 30.2 + - - +
200R PHE* 3.8 13.0 - - + -
203R MET* 3.7 6.6 - - - +
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Residues in contact with LEU 188 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80R LEU* 5.4 0.4 - - + -
129R ALA* 3.7 35.9 - - + +
130R LEU* 3.9 17.3 - - + +
133R MET* 3.6 34.3 - - + -
184R TYR 2.9 17.9 + - - +
185R VAL 3.7 3.6 - - - +
187R GLN* 1.3 75.4 - - - +
189R ARG* 1.3 63.8 + - - +
191R VAL* 3.6 3.8 - - + +
192R GLY* 3.3 22.2 + - - -
197R VAL* 4.1 21.0 - - + +
200R PHE* 3.5 39.7 - - + -
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Residues in contact with ARG 189 (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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28C VAL* 3.7 16.4 - - - +
29C PRO 3.0 28.8 + - - -
30C THR* 4.0 22.6 + - - +
31C VAL 5.2 2.6 + - - -
32C PRO* 5.9 1.8 - - - +
36C LEU* 3.6 14.5 - - - +
130R LEU* 3.8 19.4 - - + +
134R GLU* 2.9 29.1 + - - -
185R VAL* 3.0 31.7 + - - +
186R ALA* 3.6 9.0 - - - +
187R GLN 3.2 0.2 - - - -
188R LEU* 1.3 76.5 - - - +
190R ARG* 1.3 62.3 + - - +
192R GLY* 3.9 6.4 + - - -
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Residues in contact with ARG 190 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74O ASN 5.1 1.8 + - - -
75O VAL* 3.2 27.3 + - - +
76O ALA 5.3 0.8 + - - -
77O LEU* 3.6 25.8 - - - +
128O ASP* 3.3 37.8 + - - -
194O GLY* 3.3 47.6 - - - +
197O VAL* 3.9 11.0 - - - +
198O TRP* 4.1 18.1 - - + +
186R ALA 3.0 14.4 + - - +
187R GLN* 3.1 10.4 + - - +
189R ARG* 1.3 80.3 - - - +
191R VAL* 1.3 62.6 + - + +
192R GLY* 3.6 0.3 + - - -
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Residues in contact with VAL 191 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195O HIS* 3.8 23.6 + - + +
198O TRP* 3.5 50.9 - - + -
187R GLN 3.0 18.5 + - - +
188R LEU* 3.6 12.8 - - + +
190R ARG* 1.3 76.8 - - - +
192R GLY* 1.3 68.0 + - - +
193R LYS 4.8 0.5 - - - +
196R GLY* 3.5 40.6 + - - +
197R VAL* 3.9 4.5 - - - +
200R PHE* 4.4 5.8 - - + -
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Residues in contact with GLY 192 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188R LEU 3.3 13.8 + - - -
189R ARG 3.9 5.3 + - - -
190R ARG 3.4 3.0 - - - -
191R VAL* 1.3 82.2 - - - +
193R LYS* 1.3 67.9 + - - +
196R GLY* 3.6 0.3 - - - -
197R VAL* 3.1 23.8 + - - +
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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
------------------------------------------------------------
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