Contacts of the helix formed by residues 170 - 192 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56J GLU* 4.3 6.1 - - - -
94J HIS* 2.7 52.6 + + + -
97J LYS* 3.3 22.7 - - - +
98J LEU* 3.2 24.4 - - + +
147J LEU* 3.8 35.1 - - + +
150J LEU* 6.5 0.2 - - + -
165J PHE* 3.7 33.0 - + - -
166J VAL* 3.0 20.4 + - + +
168J THR 3.5 0.6 - - - -
169J GLU* 1.3 93.6 - - + +
171J LEU* 1.3 57.9 + - - +
172J GLY 3.5 2.2 - - - -
173J GLU* 3.4 4.8 + - - +
174J GLN* 2.9 32.8 + - - +
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Residues in contact with LEU 171 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144J ASN* 4.4 9.7 - - - +
147J LEU* 3.8 29.8 - - + -
148J LEU* 3.9 23.6 - - + -
151J HIS* 4.3 6.5 - - + -
166J VAL* 3.2 20.4 + - + +
167J GLU* 3.4 22.7 + - + +
170J TYR* 1.3 77.0 - - - +
172J GLY* 1.3 62.8 + - - +
174J GLN* 3.3 4.5 + - - +
175J VAL* 3.1 26.9 + - - +
160N VAL* 3.5 33.0 - - + -
161N GLN* 3.7 20.1 - - + +
164N ASP* 5.6 0.9 - - + +
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Residues in contact with GLY 172 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167J GLU 3.9 5.9 + - - -
170J TYR 3.5 0.2 - - - -
171J LEU* 1.3 78.3 - - - +
173J GLU* 1.3 67.3 + - - +
175J VAL* 3.2 5.0 + - - +
176J GLU* 3.0 30.1 + - - +
215J CA 4.6 4.7 - - - -
161N GLN* 3.6 23.4 - - - +
164N ASP* 5.4 1.3 + - - -
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Residues in contact with GLU 173 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94J HIS* 5.9 9.9 - - + +
168J THR 3.5 3.1 - - - +
169J GLU* 3.3 30.6 - - - +
170J TYR* 3.5 8.0 + - - +
171J LEU 3.3 0.2 - - - -
172J GLY* 1.3 77.1 + - - +
174J GLN* 1.3 58.3 + - - +
176J GLU* 3.3 14.3 + - - +
177J ALA* 2.9 29.0 + - - +
215J CA 2.6 29.1 - - - -
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Residues in contact with GLN 174 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94J HIS* 5.4 4.0 - - - -
140J GLU* 2.6 55.0 + - - +
143J THR* 3.8 9.1 - - - -
144J ASN* 3.6 34.5 - - + +
147J LEU* 3.9 17.4 - - + +
170J TYR* 2.9 19.2 + - - +
171J LEU 3.6 6.1 - - - +
172J GLY 3.2 0.4 - - - -
173J GLU* 1.3 74.4 - - - +
175J VAL* 1.3 64.8 + - - +
177J ALA* 3.2 6.0 + - - +
178J ILE* 3.0 31.0 + - + +
214J CA 4.1 10.9 - - - -
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Residues in contact with VAL 175 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144J ASN* 5.2 11.4 - - - +
171J LEU 3.1 15.4 + - - +
172J GLY 3.2 8.9 + - - +
174J GLN* 1.3 76.6 - - - +
176J GLU* 1.3 63.0 + - + +
178J ILE* 3.3 8.8 + - + +
179J LYS* 3.1 21.8 + - - +
101N TYR* 5.2 2.2 - - + -
104N LYS* 3.9 34.8 - - + +
105N ARG* 3.8 26.7 - - + +
161N GLN* 3.6 30.3 - - + +
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Residues in contact with GLU 176 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172J GLY 3.0 19.0 + - - +
173J GLU* 3.7 15.5 - - - +
174J GLN 3.2 0.4 - - - -
175J VAL* 1.3 78.0 - - + +
177J ALA* 1.3 62.4 + - - +
179J LYS* 3.3 6.5 + - - +
180J ARG* 3.0 24.3 + - - +
104N LYS* 3.5 37.7 + - + +
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Residues in contact with ALA 177 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140J GLU* 4.3 21.5 - - - +
173J GLU 2.9 17.1 + - - +
174J GLN* 3.2 9.4 + - - +
176J GLU* 1.3 75.6 - - - +
178J ILE* 1.3 63.0 + - - +
180J ARG* 3.4 10.1 + - - +
181J ILE* 3.1 32.8 + - + +
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Residues in contact with ILE 178 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137J LEU* 3.8 17.2 - - + +
140J GLU* 3.9 28.7 - - + +
141J LYS* 4.2 7.2 - - + +
144J ASN* 3.8 24.0 - - + +
174J GLN* 3.0 23.5 + - + +
175J VAL* 3.8 7.0 - - + +
177J ALA* 1.3 73.5 - - - +
179J LYS* 1.3 60.1 + - - +
181J ILE* 3.4 0.6 + - - -
182J SER* 2.8 33.1 + - - -
37N ALA* 3.6 35.2 - - + +
39N GLN* 3.6 24.0 - - + +
104N LYS 5.7 0.2 - - - +
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Residues in contact with LYS 179 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175J VAL 3.1 16.0 + - - +
176J GLU* 3.3 6.0 + - - +
178J ILE* 1.3 77.4 - - - +
180J ARG* 1.3 63.6 + - - +
182J SER* 3.2 5.6 + - - -
183J GLU* 2.9 52.5 + - - +
37N ALA* 4.3 3.8 - - + +
100N GLU 5.4 0.4 + - - -
103N ASN* 3.8 22.3 - - - +
104N LYS* 4.0 29.3 - - + +
71R ASP* 2.9 46.9 + - - -
73R ASP* 3.9 19.1 - - + +
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Residues in contact with ARG 180 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83J PHE* 3.6 30.1 - - - -
86J GLU* 5.7 2.8 + - - -
87J SER* 5.4 1.0 + - - -
90J GLU* 5.1 8.5 + - - -
176J GLU 3.0 16.6 + - - +
177J ALA* 3.5 9.9 - - - +
178J ILE 3.3 0.2 - - - -
179J LYS* 1.3 78.4 - - - +
181J ILE* 1.3 64.5 + - - +
183J GLU* 3.3 14.3 + - - +
184J TYR* 2.9 55.8 + - + +
204J LEU* 5.3 1.2 - - - +
207J GLU* 4.4 4.9 + - - -
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Residues in contact with ILE 181 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63J TYR* 4.1 9.4 - - - +
83J PHE* 4.4 23.6 - - + -
133J MET* 3.4 36.3 - - + +
136J ALA* 4.1 9.0 - - + +
137J LEU* 3.6 18.4 - - + +
140J GLU* 3.4 34.3 - - + -
177J ALA* 3.1 17.1 + - + +
178J ILE 4.1 2.0 - - - +
180J ARG* 1.3 75.4 - - + +
182J SER* 1.3 66.7 + - - +
184J TYR* 3.1 9.6 + - + +
185J VAL* 2.9 21.1 + - - +
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Residues in contact with SER 182 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137J LEU* 3.5 13.7 - - - +
178J ILE 2.8 22.6 + - - -
179J LYS 3.4 5.2 - - - -
181J ILE* 1.3 78.2 - - - +
183J GLU* 1.3 57.0 + - - +
185J VAL* 3.3 4.7 + - - -
186J ALA* 3.0 25.5 + - - +
36N LEU* 3.5 18.3 - - - +
37N ALA* 3.3 22.8 + - - -
73R ASP* 3.5 28.5 - - - -
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Residues in contact with GLU 183 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179J LYS* 2.9 50.1 + - - +
180J ARG* 3.5 15.8 - - - +
181J ILE 3.2 0.2 - - - -
182J SER* 1.3 76.1 - - - +
184J TYR* 1.3 58.2 + - + +
186J ALA* 3.4 2.1 + - - +
187J GLN* 2.9 46.0 + - - +
71R ASP* 4.5 2.8 - - - +
72R ARG 5.1 0.5 - - - +
73R ASP* 3.7 24.9 - - - +
76R ALA* 3.9 10.9 - - + +
78R ARG* 4.8 20.0 - - - +
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Residues in contact with TYR 184 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83J PHE* 3.7 25.4 - + - -
133J MET* 3.6 34.1 - - + -
180J ARG* 2.9 46.4 + - + +
181J ILE* 3.1 12.1 + - - +
183J GLU* 1.3 77.0 - - + +
185J VAL* 1.3 59.1 + - - +
187J GLN* 3.3 15.0 + - - +
188J LEU* 2.9 34.1 + - - +
200J PHE* 3.7 22.8 - + + -
203J MET* 4.9 1.1 - - + -
204J LEU* 3.4 17.5 - - + +
207J GLU* 2.6 35.5 + - - -
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Residues in contact with VAL 185 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130J LEU* 3.9 13.0 - - + -
133J MET* 3.7 35.9 - - + +
134J GLU* 4.0 13.2 - - + +
137J LEU* 4.5 10.3 - - + -
181J ILE 2.9 19.1 + - - +
182J SER* 3.5 7.6 - - - +
184J TYR* 1.3 76.2 - - - +
186J ALA* 1.3 64.5 + - - +
188J LEU* 3.4 2.3 + - - +
189J ARG* 3.0 52.5 + - - +
28N VAL* 5.3 0.9 - - + -
36N LEU* 3.9 13.2 - - + -
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Residues in contact with ALA 186 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182J SER 3.0 10.4 + - - +
183J GLU 3.7 3.4 - - - +
185J VAL* 1.3 78.6 - - - +
187J GLN* 1.3 57.4 + - - +
189J ARG* 3.3 9.8 + - - +
190J ARG* 3.0 28.6 + - - +
36N LEU* 4.2 7.0 - - + -
73R ASP 3.4 25.1 - - - +
74R ASN* 3.8 21.8 - - - +
75R VAL 4.8 1.8 - - - +
76R ALA* 3.8 8.3 - - + -
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Residues in contact with GLN 187 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183J GLU* 2.9 36.8 + - - +
184J TYR* 3.8 18.2 - - - +
186J ALA* 1.3 76.9 - - - +
188J LEU* 1.3 61.9 + - - +
190J ARG* 3.1 7.9 + - - +
191J VAL* 3.0 30.3 + - - +
200J PHE* 3.8 13.4 - - + -
203J MET* 3.7 6.3 - - - +
76R ALA* 3.9 20.8 - - + +
78R ARG* 3.0 36.0 + - - +
198R TRP* 2.8 35.3 + - + +
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Residues in contact with LEU 188 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80J LEU* 5.5 0.2 - - + -
129J ALA* 3.7 44.9 - - + +
130J LEU* 4.0 18.7 - - + +
133J MET* 3.8 20.4 - - + -
184J TYR 2.9 21.4 + - - +
185J VAL 3.7 3.8 - - - +
187J GLN* 1.3 75.8 - - - +
189J ARG* 1.3 62.7 + - - +
191J VAL* 3.6 5.2 - - + +
192J GLY* 3.3 21.7 + - - -
197J VAL* 4.1 20.7 - - + +
200J PHE* 3.5 41.7 - - + -
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Residues in contact with ARG 189 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126J LYS* 5.2 1.8 - - - +
130J LEU* 4.0 20.2 - - + +
134J GLU* 2.7 32.5 + - - -
185J VAL* 3.0 27.5 + - - +
186J ALA* 3.6 10.8 - - - +
187J GLN 3.2 0.2 - - - -
188J LEU* 1.3 79.1 - - - +
190J ARG* 1.3 61.1 + - - +
191J VAL 3.6 0.2 + - - -
192J GLY* 3.8 6.8 + - - -
28N VAL* 3.7 10.5 - - - +
29N PRO 3.0 29.3 + - - -
30N THR* 4.0 23.1 + - - +
31N VAL 5.1 2.6 + - - -
32N PRO* 6.0 1.4 - - - +
36N LEU* 3.4 15.9 - - - +
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Residues in contact with ARG 190 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186J ALA 3.0 15.0 + - - +
187J GLN* 3.1 9.3 + - - +
189J ARG* 1.3 78.7 - - - +
191J VAL* 1.3 62.9 + - + +
192J GLY* 3.6 0.3 + - - -
74R ASN 5.1 1.4 + - - -
75R VAL* 3.2 27.5 + - - +
76R ALA 5.3 0.6 + - - -
77R LEU* 3.7 26.3 - - - +
128R ASP* 3.1 38.8 + - - -
194R GLY* 3.2 47.8 - - - +
197R VAL* 3.9 10.8 - - - +
198R TRP* 4.1 19.5 - - + +
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Residues in contact with VAL 191 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187J GLN 3.0 21.4 + - - +
188J LEU* 3.6 12.8 - - + +
190J ARG* 1.3 77.8 - - - +
192J GLY* 1.3 67.6 + - - +
193J LYS 4.9 0.3 - - - +
196J GLY* 3.5 36.6 + - - +
197J VAL* 3.9 4.7 - - + +
200J PHE* 4.3 5.6 - - + -
195R HIS* 3.6 27.0 + - + +
198R TRP* 3.5 51.1 - - + -
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Residues in contact with GLY 192 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188J LEU 3.3 14.3 + - - -
189J ARG 3.8 4.9 + - - -
190J ARG 3.4 2.8 - - - -
191J VAL* 1.3 79.9 - - - +
193J LYS* 1.3 64.3 + - - -
196J GLY* 3.5 0.5 - - - -
197J VAL* 3.0 30.8 + - - +
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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