Contacts of the helix formed by residues 170 - 192 (chain N) in PDB entry 3A9Q
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 N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56N GLU* 4.3 6.1 - - - -
94N HIS* 2.6 54.6 + + + -
97N LYS* 3.3 23.0 - - - +
98N LEU* 3.2 23.8 + - + +
147N LEU* 3.8 34.5 - - + +
150N LEU* 6.6 0.2 - - + -
165N PHE* 3.6 33.9 - + - -
166N VAL* 2.9 19.9 + - + +
168N THR 3.6 0.2 - - - -
169N GLU* 1.3 92.6 - - + +
171N LEU* 1.3 60.0 + - - +
172N GLY 3.4 2.0 - - - -
173N ALA* 3.4 5.6 + - - +
174N GLN* 2.9 31.8 + - - +
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Residues in contact with LEU 171 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144N ASN* 4.2 10.0 - - - +
147N LEU* 3.8 30.7 - - + -
148N LEU* 4.1 24.0 - - + -
151N HIS* 4.1 9.9 - - + -
166N VAL* 3.0 18.5 + - + +
167N GLU* 3.6 19.6 + - + +
170N TYR* 1.3 75.7 - - - +
172N GLY* 1.3 61.2 + - - +
174N GLN* 3.4 3.6 + - - +
175N VAL* 3.2 27.0 + - - +
160Q VAL* 3.6 31.4 - - + -
161Q GLN* 3.7 19.9 - - + +
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Residues in contact with GLY 172 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167N GLU 3.7 8.4 + - - -
168N THR 5.4 1.5 + - - -
170N TYR 3.4 0.8 - - - +
171N LEU* 1.3 75.4 - - - +
173N ALA* 1.3 66.2 + - - +
175N VAL* 3.1 13.2 + - - +
176N GLU* 3.1 19.5 + - - +
161Q GLN* 3.7 22.7 - - - +
164Q ASP* 5.7 0.6 + - - -
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Residues in contact with ALA 173 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94N HIS* 5.6 10.3 - - + +
168N THR 5.8 1.2 + - - -
169N GLU 4.3 14.3 - - - +
170N TYR* 3.4 8.6 + - - +
172N GLY* 1.3 75.9 - - - +
174N GLN* 1.3 57.1 + - - +
176N GLU* 3.2 10.2 + - - +
177N ALA* 2.9 28.7 + - - +
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Residues in contact with GLN 174 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94N HIS* 5.9 0.5 - - - -
140N GLU* 2.7 56.1 + - - +
143N THR* 3.7 17.3 - - - +
144N ASN* 3.3 38.1 - - + +
147N LEU* 3.7 11.0 - - + +
170N TYR 2.9 18.5 + - - +
171N LEU 3.6 6.1 - - - +
172N GLY 3.2 0.2 - - - -
173N ALA* 1.3 77.8 - - - +
175N VAL* 1.3 61.6 + - - +
177N ALA* 3.3 3.7 + - - +
178N ILE* 3.0 26.5 + - + +
215N CA 4.1 7.1 - - - -
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Residues in contact with VAL 175 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144N ASN* 5.2 11.2 - - - +
171N LEU 3.2 15.3 + - - +
172N GLY 3.1 9.7 + - - +
174N GLN* 1.3 76.0 - - - +
176N GLU* 1.3 59.9 + - + +
178N ILE* 3.4 8.2 + - + +
179N LYS* 3.0 26.0 + - - +
101Q TYR* 5.2 2.2 - - + -
104Q LYS* 3.9 31.4 - - + +
105Q ARG* 3.7 36.3 - - - +
161Q GLN* 3.7 21.5 - - + +
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Residues in contact with GLU 176 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172N GLY 3.1 18.6 + - - +
173N ALA* 3.2 8.9 + - - +
175N VAL* 1.3 77.2 - - + +
177N ALA* 1.3 59.7 + - - +
179N LYS* 3.3 6.5 + - - +
180N ARG* 2.9 29.3 + - - +
104Q LYS* 2.7 45.8 + - - +
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Residues in contact with ALA 177 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140N GLU* 4.0 24.2 - - + +
173N ALA 2.9 17.6 + - - +
174N GLN* 3.7 6.7 - - - +
176N GLU* 1.3 75.8 - - - +
178N ILE* 1.3 63.9 + - - +
180N ARG* 3.2 11.6 + - - +
181N ILE* 3.0 32.6 + - + +
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Residues in contact with ILE 178 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137N LEU* 3.8 15.4 - - + +
140N GLU* 3.9 18.8 - - + +
141N LYS* 4.1 8.3 - - + +
144N ASN* 3.8 23.6 - - + +
174N GLN* 3.0 30.9 + - - +
175N VAL* 3.8 7.0 - - + +
177N ALA* 1.3 73.7 - - - +
179N LYS* 1.3 65.5 + - - +
181N ILE* 5.0 0.2 - - - -
182N SER* 2.8 29.8 + - - -
37Q ALA* 3.5 34.1 - - + +
39Q GLN* 3.5 24.9 - - + +
104Q LYS 5.8 0.4 - - - +
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Residues in contact with LYS 179 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175N VAL 3.0 17.3 + - - +
176N GLU* 3.9 7.0 - - - +
178N ILE* 1.3 76.4 - - - +
180N ARG* 1.3 63.3 - - - +
182N SER* 3.3 1.0 + - - -
183N GLU* 3.0 47.0 + - - +
37Q ALA* 4.2 8.2 - - + +
100Q GLU 5.2 0.4 + - - -
103Q ASN* 3.8 22.0 - - - +
104Q LYS* 4.0 29.6 - - + +
71U ASP* 2.9 48.5 + - - -
73U ASP* 4.0 17.9 - - + +
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Residues in contact with ARG 180 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83N PHE* 3.5 30.6 - - - -
86N GLU* 5.5 4.0 + - - -
87N SER* 5.3 1.6 + - - -
90N GLU* 4.6 16.2 + - - -
176N GLU 2.9 17.7 + - - +
177N ALA* 3.4 10.8 - - - +
178N ILE 3.2 0.2 - - - -
179N LYS* 1.3 77.8 - - - +
181N ILE* 1.3 63.8 + - + +
183N GLU* 3.3 16.4 + - - +
184N TYR* 2.8 51.4 + - + +
207N GLU* 3.2 26.4 + - - +
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Residues in contact with ILE 181 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63N TYR* 4.2 9.0 - - + +
83N PHE* 4.2 26.0 - - + -
133N MET* 3.5 35.7 - - - +
136N ALA* 4.3 7.2 - - + -
137N LEU* 3.7 19.3 - - + +
140N GLU* 3.6 33.4 - - + -
177N ALA* 3.0 19.7 + - + +
178N ILE 4.3 1.6 - - - +
180N ARG* 1.3 76.4 - - + +
182N SER* 1.3 67.4 + - - +
184N TYR* 3.0 10.1 + - + +
185N VAL* 2.9 20.7 + - - +
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Residues in contact with SER 182 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137N LEU* 3.3 20.7 - - - +
178N ILE 2.8 22.7 + - - -
179N LYS 3.6 4.5 - - - -
181N ILE* 1.3 76.7 - - - +
183N GLU* 1.3 56.3 + - - +
185N VAL* 3.2 5.1 + - - +
186N ALA* 2.9 25.1 + - - +
36Q LEU* 3.5 12.8 - - - +
37Q ALA* 3.2 24.9 + - - -
73U ASP* 3.6 24.2 - - - -
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Residues in contact with GLU 183 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179N LYS* 3.0 49.7 + - - +
180N ARG* 3.5 14.4 - - - +
182N SER* 1.3 74.4 - - - +
184N TYR* 1.3 66.5 + - + +
186N ALA* 3.4 1.2 + - - +
187N GLN* 3.0 41.5 + - - +
71U ASP* 4.5 3.6 - - - +
72U ARG 5.1 0.7 - - - +
73U ASP* 3.7 25.5 - - + +
76U ALA* 4.1 9.9 - - + -
78U ARG* 4.7 22.1 - - - +
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Residues in contact with TYR 184 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83N PHE* 3.8 25.4 - + - -
133N MET* 3.7 32.1 - - + -
180N ARG* 2.8 47.7 + - + -
181N ILE* 3.0 13.1 + - - +
183N GLU* 1.3 77.7 - - + +
185N VAL* 1.3 63.0 + - - +
187N GLN* 3.3 12.4 + - - +
188N LEU* 2.9 29.8 + - - +
200N PHE* 3.7 25.7 - + + -
203N MET* 4.8 5.2 - - + -
204N LEU* 3.4 17.0 - - + +
207N GLU* 2.5 31.0 + - - -
78U ARG* 6.1 2.2 - - - -
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Residues in contact with VAL 185 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130N LEU* 4.0 12.7 - - + +
133N MET* 3.7 35.9 - - + +
134N GLU* 3.9 10.3 - - + +
137N LEU* 4.4 11.7 - - + -
181N ILE 2.9 16.3 + - - +
182N SER 3.5 7.6 - - - +
184N TYR* 1.3 75.7 - - - +
186N ALA* 1.3 63.6 + - - +
188N LEU* 3.2 3.5 + - - +
189N ARG* 3.0 52.9 + - - +
28Q VAL* 5.3 0.9 - - + -
36Q LEU* 3.7 16.6 - - + -
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Residues in contact with ALA 186 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182N SER 2.9 9.1 + - - +
183N GLU 3.7 0.2 - - - +
184N TYR 3.3 0.2 - - - -
185N VAL* 1.3 77.7 - - - +
187N GLN* 1.3 61.4 + - - +
189N ARG* 3.4 8.7 + - - +
190N ARG* 3.0 23.8 + - - +
36Q LEU* 4.0 6.7 - - + +
73U ASP 3.4 26.0 - - - +
74U ASN* 3.8 19.3 - - - +
75U VAL 4.7 1.8 - - - +
76U ALA* 3.7 14.4 - - + -
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Residues in contact with GLN 187 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183N GLU* 3.0 39.7 + - - +
184N TYR* 3.8 16.8 - - - +
186N ALA* 1.3 74.9 - - - +
188N LEU* 1.3 64.1 + - - +
190N ARG* 3.0 8.0 + - - +
191N VAL* 2.9 29.5 + - - +
200N PHE* 3.8 12.5 - - + -
203N MET* 3.8 5.0 - - - +
76U ALA* 3.8 20.6 - - + +
78U ARG* 2.9 37.9 + - - +
198U TRP* 2.8 35.6 + - + +
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Residues in contact with LEU 188 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80N LEU* 5.6 0.7 - - + -
129N ALA* 3.8 34.5 - - + +
130N LEU* 4.0 16.9 - - + +
133N MET* 3.6 33.9 - - + -
184N TYR 2.9 18.9 + - - +
185N VAL* 3.2 4.2 + - - +
187N GLN* 1.3 77.2 - - - +
189N ARG* 1.3 61.3 + - - +
191N VAL* 3.5 5.0 + - + +
192N GLY* 3.2 22.3 + - - -
197N VAL* 4.1 21.1 - - + +
200N PHE* 3.5 40.2 - - + -
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Residues in contact with ARG 189 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126N LYS* 5.4 1.2 - - - +
130N LEU* 4.0 19.4 - - + +
134N GLU* 2.7 30.1 + - - -
185N VAL* 3.0 28.8 + - - +
186N ALA* 3.6 10.8 - - - +
188N LEU* 1.3 77.7 - - - +
190N ARG* 1.3 61.8 + - - +
192N GLY* 3.8 7.5 + - - -
28Q VAL* 3.5 16.4 - - - +
29Q PRO 3.0 30.7 + - - -
30Q THR* 4.2 18.1 + - - +
31Q VAL 5.7 0.8 + - - -
32Q PRO* 6.2 1.0 - - - +
36Q LEU* 3.6 14.1 - - - +
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Residues in contact with ARG 190 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186N ALA 3.0 12.9 + - - +
187N GLN* 3.0 11.7 + - - +
189N ARG* 1.3 79.3 - - - +
191N VAL* 1.3 63.0 + - + +
192N GLY* 4.6 0.5 - - - -
74U ASN 5.2 1.6 + - - -
75U VAL* 3.3 26.3 + - - +
76U ALA 5.3 0.4 + - - -
77U LEU* 3.7 22.9 - - - +
128U ASP* 3.2 36.8 + - - -
194U GLY* 3.3 42.1 - - - +
197U VAL* 3.8 15.6 - - - +
198U TRP* 4.0 19.1 - - + +
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Residues in contact with VAL 191 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187N GLN 2.9 22.5 + - - +
188N LEU* 3.6 12.3 - - + +
190N ARG* 1.3 76.4 - - - +
192N GLY* 1.3 67.4 + - - +
193N LYS 4.8 0.7 - - - +
196N GLY* 3.4 39.2 + - - +
197N VAL* 3.8 4.3 - - - +
200N PHE* 4.4 5.8 - - + -
195U HIS* 3.7 25.8 + - + +
198U TRP* 3.5 49.4 - - + -
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Residues in contact with GLY 192 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188N LEU 3.2 14.3 + - - -
189N ARG 3.8 5.6 + - - -
190N ARG 3.3 3.4 - - - -
191N VAL* 1.3 81.3 - - - +
193N LYS* 1.3 68.3 + - - +
196N GLY* 3.6 0.5 - - - -
197N 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) + - + + + + + -
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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