Contacts of the helix formed by residues 166 - 188 (chain A) in PDB entry 2B7O
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 PRO 166 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TRP* 3.3 45.0 - - + -
44A GLN* 3.4 48.0 - - + +
45A ALA* 4.0 5.6 - - - +
48A MSE 3.1 24.0 - - + +
164A HIS 4.0 0.2 - - - +
165A ASP* 1.4 83.0 - - - +
167A SER* 1.3 53.8 + - - -
168A ARG 3.0 4.9 - - - -
169A LEU* 3.0 28.5 + - + +
0B ALA* 3.7 5.6 - - + -
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Residues in contact with SER 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE* 4.2 1.8 - - - -
48A MSE 2.4 29.8 - - - +
165A ASP* 2.8 26.5 + - - +
166A PRO* 1.3 72.8 - - - +
168A ARG* 1.3 65.1 + - - +
170A VAL* 3.2 5.4 + - - +
171A ARG* 3.2 17.1 + - - +
-1B GLY* 3.8 3.0 - - - -
0B ALA* 3.5 7.1 - - - +
4B THR 3.3 26.5 + - - -
5B VAL* 3.8 12.4 - - - +
6B ASP* 4.9 2.3 + - - -
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Residues in contact with ARG 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PHE* 3.8 15.9 - - + -
150A ASP* 2.8 44.6 + - - +
151A MSE 3.2 16.6 - - - +
152A ILE 3.4 24.5 - - - -
153A ASN* 3.5 19.8 + - - +
154A GLY* 3.4 20.4 - - - +
161A ALA* 4.6 4.8 + - - +
163A GLU 5.2 0.8 + - - -
165A ASP* 2.9 20.4 + - + +
167A SER* 1.3 81.0 + - - +
169A LEU* 1.3 57.4 + - - +
170A VAL 3.3 0.2 - - - -
171A ARG* 3.8 24.1 - - + +
172A ALA* 2.8 30.5 + - - +
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Residues in contact with LEU 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TRP* 3.6 38.4 - - + -
45A ALA* 4.7 5.4 - - - +
48A MSE 3.9 17.9 - - + -
49A ARG* 4.8 4.0 - - + +
52A LEU* 3.6 23.2 - - + +
151A MSE 3.9 11.2 + - + -
166A PRO* 3.0 21.2 + - + +
168A ARG* 1.3 76.2 - - - +
170A VAL* 1.3 58.6 + - - +
172A ALA* 3.4 3.3 + - - +
173A TYR* 3.0 21.8 + - - +
251A VAL* 3.9 7.6 - - + -
253A ASP* 4.0 20.4 - - + +
254A TYR* 3.7 29.6 - - + +
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Residues in contact with VAL 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE* 4.5 6.7 - - + -
48A MSE 3.6 30.3 - - + +
51A VAL* 3.9 29.2 - - + -
52A LEU* 4.0 18.2 - - + -
167A SER 3.2 7.3 + - - +
169A LEU* 1.3 74.4 - - - +
171A ARG* 1.3 66.3 + - - +
173A TYR* 3.2 3.9 + - + +
174A ALA* 3.0 22.5 + - - +
1001A CE1 4.2 40.4 - - + -
5B VAL* 4.3 5.8 - - + -
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Residues in contact with ARG 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PHE* 3.4 36.7 - - + +
92A MSE 5.3 0.6 - - - +
167A SER 3.2 9.2 + - - +
168A ARG* 3.9 28.1 - - - +
170A VAL* 1.3 81.1 - - - +
172A ALA* 1.4 57.7 + - - +
174A ALA* 3.5 1.2 + - - +
175A ASN* 2.8 39.8 + - - +
1001A CE1 2.8 54.1 + - + -
5B VAL* 3.6 29.1 - - + +
6B ASP 3.6 15.7 + - - -
7B ILE* 3.9 16.6 - - - +
8B PRO* 4.2 11.5 - - - +
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Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PHE* 3.5 19.7 - - + -
131A TYR* 3.9 9.2 - - + -
151A MSE 3.7 34.3 - - + -
168A ARG 2.8 20.6 + - - +
169A LEU 3.6 4.9 - - - +
170A VAL 3.2 0.2 - - - -
171A ARG* 1.4 73.2 - - - +
173A TYR* 1.3 55.3 + - - +
175A ASN* 3.3 3.3 + - - +
176A ALA* 2.8 37.2 + - - +
254A TYR* 4.4 1.6 - - + -
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Residues in contact with TYR 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.6 28.3 - - + -
55A VAL* 3.4 24.5 - - + -
56A PRO* 2.6 34.8 + - - +
58A VAL* 4.0 15.7 - - + -
169A LEU 3.0 10.6 + - - +
170A VAL* 3.2 9.2 + - - +
172A ALA* 1.3 76.7 - - - +
174A ALA* 1.3 62.5 + - - +
176A ALA* 3.2 1.2 + - - +
177A SER* 2.9 51.2 + - - -
254A TYR* 3.7 14.7 - - + -
258A MSE 4.1 13.9 - - - -
1001A CE1 3.8 25.8 - - + -
178B ALA* 3.4 16.3 - - + +
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Residues in contact with ALA 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A VAL 3.0 16.3 + - - +
171A ARG 3.8 3.1 - - - +
173A TYR* 1.3 83.9 - - + +
175A ASN* 1.3 57.5 + - - +
177A SER* 3.6 5.3 - - - -
178A ALA* 3.1 29.3 + - - +
1001A CE1 3.7 38.4 - - + -
173B TYR* 5.8 1.6 - - + -
174B ALA* 4.2 17.6 - - + +
177B SER* 5.0 2.3 + - - -
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Residues in contact with ASN 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PHE* 3.5 19.5 - - + -
94A ASN* 3.0 31.0 + - - +
131A TYR* 3.4 17.0 - - - +
171A ARG* 2.8 30.2 + - - +
172A ALA 3.7 2.9 - - - +
174A ALA* 1.3 75.8 - - - +
176A ALA* 1.3 59.6 + - - +
178A ALA* 3.4 3.3 + - - +
179A ALA* 3.0 25.5 + - - +
1001A CE1 2.8 56.0 + - - +
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Residues in contact with ALA 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A VAL* 4.3 9.4 - - + -
128A ALA* 3.2 41.1 - - - +
129A GLY* 4.1 3.4 - - - +
131A TYR* 4.2 2.6 - - + -
172A ALA 2.8 20.5 + - - +
173A TYR 3.6 4.0 - - - +
175A ASN* 1.3 71.9 - - - +
177A SER* 1.3 58.3 + - - +
179A ALA 3.3 0.7 + - - -
180A MSE 2.9 31.5 + - - +
254A TYR* 4.0 14.6 - - - +
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Residues in contact with SER 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PRO 4.7 0.9 + - - -
57A PRO 4.8 0.7 + - - -
58A VAL* 4.2 8.0 - - - +
173A TYR* 2.9 43.9 + - - -
174A ALA* 3.6 7.0 - - - -
176A ALA* 1.3 77.5 - - - +
178A ALA* 1.3 57.0 + - - -
180A MSE 3.9 4.2 - - - +
181A ASN* 2.9 29.3 + - - +
174B ALA 5.7 0.7 - - - -
177B SER* 4.8 2.0 - - - -
178B ALA* 3.9 21.5 - - - -
181B ASN* 3.8 15.6 + - - +
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Residues in contact with ALA 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A ALA 3.1 15.3 + - - +
175A ASN* 3.9 6.7 - - - +
177A SER* 1.3 76.7 - - - +
179A ALA* 1.3 63.8 + - - +
181A ASN* 3.5 4.4 + - - +
182A LEU 3.2 16.1 + - - -
56B PRO* 3.6 23.6 - - + +
57B PRO 5.1 0.2 - - - +
173B TYR* 3.2 30.5 - - + +
177B SER* 4.0 18.2 - - - +
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Residues in contact with ALA 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLU* 4.7 2.5 - - - +
94A ASN* 3.4 20.8 - - - +
99A ILE* 3.7 19.8 - - + +
127A ILE* 4.9 3.8 - - + -
128A ALA* 4.3 16.4 - - + +
131A TYR* 5.3 0.2 - - - +
175A ASN 3.0 17.7 + - - +
176A ALA 3.7 3.8 - - - +
178A ALA* 1.3 75.6 - - - +
180A MSE 1.3 60.1 + - - +
182A LEU* 3.1 3.8 + - - +
183A VAL* 2.8 33.8 + - - +
56B PRO* 4.6 0.2 - - - -
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Residues in contact with MSE 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A VAL* 3.5 30.3 - - + +
59A THR* 4.5 0.2 - - - -
127A ILE* 5.5 0.4 - - - -
128A ALA* 4.1 4.9 - - + +
176A ALA 2.9 18.1 + - - +
177A SER 3.9 2.7 - - - +
179A ALA* 1.3 77.4 - - - +
181A ASN* 1.3 62.4 + - - +
183A VAL* 3.6 34.7 - - + -
184A ARG* 3.0 49.7 + - + +
243A ILE 3.8 14.6 - - - +
244A TYR 5.3 0.2 - - - -
245A ALA* 3.7 29.2 - - + -
277A HIS* 4.1 18.8 - - + -
181B ASN* 3.3 16.2 - - - +
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Residues in contact with ASN 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A SER 2.9 18.7 + - - +
178A ALA* 3.5 7.2 + - - +
180A MSE 1.3 77.6 - - - +
182A LEU* 1.3 59.9 + - - +
184A ARG* 3.4 1.6 + - - +
185A ALA* 3.1 18.7 + - - +
57B PRO 3.4 16.8 + - - -
58B VAL* 2.9 29.3 + - - +
177B SER* 4.0 10.2 - - - +
180B MSE 3.2 12.9 - - - +
181B ASN* 3.2 24.6 + - + -
184B ARG* 2.7 35.7 + - - +
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Residues in contact with LEU 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A GLU* 3.6 41.3 - - + +
99A ILE* 3.9 24.2 - - + -
178A ALA 3.2 11.4 + - - +
179A ALA* 3.1 8.8 + - - +
181A ASN* 1.3 81.0 - - - +
183A VAL* 1.3 58.3 + - - +
185A ALA* 3.2 3.5 + - + -
186A LEU* 2.8 48.1 + - + +
56B PRO* 4.1 12.8 - - + -
57B PRO* 4.2 15.5 - - + +
60B VAL* 3.7 29.6 - - + -
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Residues in contact with VAL 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ILE* 4.2 6.5 - - + +
103A VAL* 4.1 12.6 - - + -
125A ALA* 6.1 0.2 - - + -
127A ILE* 4.2 33.4 - - + -
179A ALA 2.8 31.7 + - - +
180A MSE 3.3 26.4 + - + -
182A LEU* 1.3 72.4 - - - +
184A ARG* 1.3 60.8 + - - +
186A LEU* 4.5 6.3 - - - +
187A THR* 2.9 32.9 + - + +
243A ILE* 4.0 29.8 - - + +
244A TYR 6.2 0.2 - - - -
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Residues in contact with ARG 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A VAL 3.0 23.6 + - - -
59A THR* 3.7 5.5 - - - +
63A GLU* 2.6 44.0 + - - -
180A MSE 3.0 30.7 + - + +
181A ASN 3.7 3.8 - - - +
183A VAL* 1.3 76.0 - - - +
185A ALA* 1.3 62.6 + - - +
187A THR* 3.2 15.8 + - - -
188A SER* 3.1 18.3 + - - -
277A HIS* 4.4 3.4 + - - -
181B ASN* 2.8 27.8 + - - -
184B ARG* 3.7 33.8 - - + +
185B ALA* 3.7 17.0 - - - +
188B SER* 5.3 2.2 + - - -
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Residues in contact with ALA 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ASN* 3.1 10.9 + - - +
182A LEU* 3.2 10.1 + - + +
184A ARG* 1.3 75.3 - - - +
186A LEU* 1.3 63.6 + - - +
188A SER* 3.4 4.4 + - - -
189A SER* 3.2 20.7 + - - -
60B VAL* 3.9 23.6 - - + +
63B GLU* 3.3 27.5 - - - +
184B ARG* 3.6 21.0 - - - +
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Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLU* 4.6 11.4 - - - +
99A ILE* 4.3 1.6 - - + -
100A ARG* 3.7 38.4 - - + +
103A VAL* 4.1 20.9 - - + -
182A LEU* 2.8 49.4 + - + +
183A VAL* 4.0 3.6 - - - +
185A ALA* 1.3 72.5 - - - +
187A THR* 1.3 58.9 + - - +
189A SER* 2.7 33.1 + - - +
191A LEU* 3.5 31.9 - - + +
192A ALA 4.1 1.2 + - - -
60B VAL* 4.7 9.9 - - + -
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Residues in contact with THR 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A VAL* 4.5 7.9 - - + -
107A LEU* 5.3 2.2 - - + -
183A VAL* 2.9 21.1 + - + +
184A ARG* 3.2 10.9 + - - -
186A LEU* 1.3 77.7 - - - +
188A SER* 1.3 58.5 + - - +
189A SER 3.4 0.2 - - - -
192A ALA* 3.3 23.7 - - - +
240A THR* 3.6 13.6 - - - +
241A ALA* 3.5 26.3 + - + +
243A ILE* 3.5 44.0 + - + +
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Residues in contact with SER 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ARG 3.1 16.9 + - - -
185A ALA* 3.7 6.3 + - - -
186A LEU 3.3 0.2 - - - -
187A THR* 1.3 76.0 - - - +
189A SER* 1.3 59.3 + - - +
240A THR* 3.8 19.5 - - - -
63B GLU* 5.1 4.0 + - - +
66B ARG* 5.1 9.5 + - - -
184B ARG* 5.4 1.7 + - - -
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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