Contacts of the helix formed by residues 167 - 188 (chain B) 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 SER 167 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ASP 4.0 5.6 - - - -
7A ILE* 4.1 5.4 - - - +
8A PRO* 3.1 22.7 - - - +
48B MSE 3.6 26.7 - - - +
165B ASP* 2.8 20.8 + - - -
166B PRO* 1.3 77.9 - - - +
168B ARG* 1.3 59.3 + - - +
169B LEU 3.1 1.1 - - - -
170B VAL* 3.1 15.1 + - - +
171B ARG* 3.0 33.4 + - - +
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Residues in contact with ARG 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ASP* 4.5 2.8 + - - -
91B PHE* 3.7 15.4 - - + -
150B ASP* 2.7 48.4 + - - +
151B MSE 3.1 20.6 - - - +
152B ILE 3.4 25.1 - - - -
153B ASN* 3.5 14.0 + - - +
154B GLY* 3.5 21.2 - - - +
161B ALA* 4.9 2.6 + - - +
165B ASP* 2.9 20.1 + - + +
167B SER* 1.3 74.8 + - - +
169B LEU* 1.3 57.8 + - - +
170B VAL 3.3 0.2 - - - -
171B ARG* 3.4 41.0 - - - +
172B ALA* 2.9 30.8 + - - +
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Residues in contact with LEU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TRP* 3.7 36.6 - - + -
45B ALA* 4.4 8.1 - - - +
48B MSE 3.7 20.9 - - + -
49B ARG* 4.9 4.7 - - + +
52B LEU* 3.7 17.6 - - + +
151B MSE 4.2 7.9 - - + -
166B PRO* 3.0 20.7 + - + +
168B ARG* 1.3 77.0 - - - +
170B VAL* 1.3 57.7 + - - +
172B ALA* 3.6 2.4 - - - +
173B TYR* 3.2 20.4 + - - +
251B VAL* 3.9 8.3 - - + -
253B ASP* 4.2 12.3 - - + -
254B TYR* 3.6 43.1 - - + +
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Residues in contact with VAL 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 3.9 21.5 - - + -
1001A CE1 3.7 33.0 - - + -
7B ILE* 4.7 0.2 - - + -
48B MSE 3.9 34.5 - - + +
51B VAL* 4.1 17.7 - - + -
52B LEU* 3.9 22.4 - - + -
167B SER 3.1 8.3 + - - +
169B LEU* 1.3 76.5 - - - +
171B ARG* 1.3 59.0 + - - +
172B ALA 3.2 0.2 - - - -
173B TYR* 3.4 3.6 + - - +
174B ALA* 3.0 25.6 + - - +
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Residues in contact with ARG 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 3.6 20.4 - - + -
8A PRO* 3.5 33.9 + - - +
10A ASP* 2.5 40.7 + - - +
1001A CE1 4.1 10.1 - - + -
91B PHE* 3.7 15.6 - - + -
165B ASP* 3.0 16.6 + - - -
167B SER* 3.0 40.6 + - - +
168B ARG* 3.4 37.2 - - - +
170B VAL* 1.3 72.3 - - - +
172B ALA* 1.3 60.6 + - - +
174B ALA* 3.9 5.5 - - - +
175B ASN* 2.7 40.7 + - - +
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Residues in contact with ALA 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B PHE* 3.7 15.6 - - + -
131B TYR* 3.9 9.6 - - + -
151B MSE 3.8 37.7 - - + -
168B ARG 2.9 22.1 + - - +
169B LEU 3.6 4.9 - - - +
171B ARG* 1.3 73.6 - - - +
173B TYR* 1.3 59.1 + - - +
175B ASN* 3.3 2.9 + - - +
176B ALA* 2.9 30.7 + - - +
254B TYR* 4.3 2.5 - - + -
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Residues in contact with TYR 173 (chain B).
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* 5.8 1.6 - - + -
178A ALA* 3.2 25.3 - - + +
1001A CE1 4.7 11.9 - - + -
52B LEU* 3.7 22.7 - - + -
55B VAL* 3.3 33.4 - - + +
56B PRO* 2.6 30.6 + - - +
58B VAL* 4.3 8.5 - - + -
169B LEU 3.2 12.9 + - - +
170B VAL 3.4 8.3 + - - +
172B ALA* 1.3 79.0 - - - +
174B ALA* 1.3 63.3 + - + +
176B ALA* 4.1 0.4 - - - -
177B SER* 2.9 50.5 + - - -
254B TYR* 3.6 16.9 + - + +
258B MSE 3.9 22.9 - - + -
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Residues in contact with ALA 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ALA* 4.2 10.6 - - + +
177A SER* 5.7 0.7 - - - -
1001A CE1 3.9 51.2 - - + +
170B VAL 3.0 16.9 + - - +
171B ARG 3.9 2.5 - - - +
173B TYR* 1.3 80.2 - - - +
175B ASN* 1.3 63.9 + - - +
177B SER* 3.4 6.4 + - - -
178B ALA* 3.2 23.7 + - - +
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Residues in contact with ASN 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ASP* 5.2 2.0 + - - -
12A LEU* 5.6 0.9 - - - +
1001A CE1 3.5 29.4 - - - +
91B PHE* 3.6 32.5 - - + +
94B ASN* 2.9 45.8 + - - +
131B TYR* 3.4 17.7 - - + +
171B ARG* 2.7 33.7 + - - +
172B ALA 3.8 3.1 - - - +
174B ALA* 1.3 75.7 - - - +
176B ALA* 1.3 57.4 + - - +
178B ALA* 3.4 0.7 + - - +
179B ALA* 3.0 21.8 + - - +
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Residues in contact with ALA 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B VAL* 4.3 9.4 - - + -
128B ALA* 3.4 43.4 - - - +
129B GLY* 4.2 2.9 - - - +
131B TYR* 4.5 1.8 - - - -
172B ALA 2.9 18.8 + - - +
173B TYR 3.1 4.9 + - - +
175B ASN* 1.3 76.4 - - - +
177B SER* 1.3 57.9 + - - +
179B ALA 3.3 0.9 + - - -
180B MSE 2.9 25.4 + - - +
254B TYR* 3.9 15.0 - - - +
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Residues in contact with SER 177 (chain B).
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 5.0 2.1 + - - -
177A SER* 4.3 2.7 - - - +
178A ALA* 4.0 24.4 + - - +
181A ASN* 4.0 13.7 - - - +
56B PRO 5.5 0.4 - - - -
57B PRO 5.5 0.4 - - - -
58B VAL* 4.5 5.8 - - - +
173B TYR* 2.9 38.1 + - - -
174B ALA* 3.4 8.5 + - - -
176B ALA* 1.3 77.4 - - - +
178B ALA* 1.3 57.2 + - - +
180B MSE 3.9 6.9 - - - +
181B ASN* 2.9 30.8 + - - +
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Residues in contact with ALA 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PRO* 3.9 15.2 - - + +
57A PRO 5.0 0.5 - - - +
173A TYR* 3.4 26.0 - - + +
177A SER* 3.9 16.1 - - - +
1001A CE1 3.7 13.7 - - + -
174B ALA 3.2 19.4 + - - +
175B ASN 3.7 3.8 - - - +
177B SER* 1.3 77.4 + - - +
179B ALA* 1.3 62.8 + - - +
181B ASN* 3.6 4.7 + - - +
182B LEU* 3.2 21.5 + - - +
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Residues in contact with ALA 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B GLU* 4.6 4.7 - - - +
94B ASN* 3.4 25.5 - - - +
99B ILE* 3.6 20.4 - - + +
127B ILE* 4.9 4.0 - - + -
128B ALA* 4.5 15.0 - - + +
175B ASN 3.0 12.3 + - - +
176B ALA 3.8 3.1 - - - +
178B ALA* 1.3 76.4 - - - +
180B MSE 1.3 60.0 + - - +
182B LEU* 3.3 2.6 + - - +
183B VAL* 2.8 34.1 + - - +
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Residues in contact with MSE 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A ASN* 3.2 18.2 - - - +
58B VAL* 3.4 32.1 - - + +
127B ILE* 5.4 0.9 - - + -
128B ALA* 4.0 7.7 - - + +
176B ALA 2.9 17.2 + - - +
177B SER 3.9 2.7 - - - +
179B ALA* 1.3 72.1 - - - +
181B ASN* 1.3 66.3 + - - +
183B VAL* 3.1 33.3 + - + +
184B ARG* 2.9 55.4 + - + +
243B ILE 3.9 15.0 - - - +
245B ALA* 3.6 28.7 - - + +
277B HIS* 4.2 13.0 - - + -
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Residues in contact with ASN 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A PRO 3.6 15.6 + - - -
58A VAL* 3.0 28.7 + - - +
177A SER* 3.8 17.3 + - - +
180A MSE 3.3 6.6 - - - +
181A ASN* 3.2 30.4 + - + +
184A ARG* 2.8 28.6 + - - +
177B SER 2.9 19.0 + - - +
178B ALA* 3.6 5.8 - - - +
180B MSE 1.3 78.9 - - - +
182B LEU* 1.3 59.9 + - - +
184B ARG* 3.4 4.0 + - - +
185B ALA* 3.1 18.2 + - - +
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Residues in contact with LEU 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PRO* 4.2 11.4 - - + -
57A PRO* 4.1 16.2 - - + +
60A VAL* 3.8 29.2 - - + -
96B GLU* 3.7 38.4 - - + +
99B ILE* 3.7 27.4 - - + -
178B ALA 3.2 11.4 + - - +
179B ALA 3.7 7.2 - - - +
181B ASN* 1.3 77.9 - - - +
183B VAL* 1.3 68.0 + - - +
185B ALA* 3.2 2.8 + - + -
186B LEU* 2.9 40.0 + - + +
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Residues in contact with VAL 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ILE* 4.0 17.0 - - + -
103B VAL* 4.1 11.0 - - + -
127B ILE* 4.2 27.4 - - + -
179B ALA 2.8 32.1 + - - +
180B MSE 3.1 26.2 + - + +
182B LEU* 1.3 72.4 - - - +
184B ARG* 1.3 60.2 + - - +
186B LEU* 3.5 6.4 + - - +
187B THR* 3.0 31.6 + - + +
243B ILE* 4.2 30.1 - - + +
244B TYR 6.3 0.2 - - - -
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Residues in contact with ARG 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A ASN* 2.7 27.1 + - - +
184A ARG* 3.7 34.0 - - + +
185A ALA* 3.6 17.1 - - - +
188A SER* 5.4 2.0 + - - -
58B VAL 3.0 24.0 + - - -
59B THR* 3.8 6.7 - - - +
63B GLU* 2.6 44.6 + - - -
180B MSE 2.9 34.8 + - + +
181B ASN 3.6 6.3 - - - +
183B VAL* 1.3 73.9 - - - +
185B ALA* 1.3 64.9 + - - +
187B THR* 3.3 16.0 + - - -
188B SER* 3.2 17.5 + - - -
277B HIS* 5.2 0.8 + - - -
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Residues in contact with ALA 185 (chain B).
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 5.6 0.2 - - - +
59A THR 5.5 0.2 - - - -
60A VAL* 3.9 25.4 - - + +
63A GLU* 3.4 25.9 - - - +
184A ARG* 3.7 18.0 - - - +
181B ASN* 3.1 10.1 + - - +
182B LEU* 3.6 9.6 - - - +
184B ARG* 1.3 78.1 - - - +
186B LEU* 1.3 62.7 + - - +
188B SER* 3.4 5.6 + - - -
189B SER* 3.3 21.4 + - - -
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Residues in contact with LEU 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A VAL* 4.9 9.0 - - + -
96B GLU* 4.6 4.5 - - - +
99B ILE* 4.3 1.6 - - + -
100B ARG* 3.8 44.0 - - + +
103B VAL* 4.2 21.1 - - + -
107B LEU* 5.7 0.2 - - - +
182B LEU* 2.9 46.2 + - + +
183B VAL 3.9 3.4 - - - +
185B ALA* 1.3 77.5 - - - +
187B THR* 1.3 61.5 + - - +
189B SER* 2.9 27.4 + - - +
191B LEU* 3.5 31.5 - - + +
192B ALA* 4.2 1.4 + - - +
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Residues in contact with THR 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B VAL* 4.5 6.1 - - + -
107B LEU* 5.4 1.8 - - + -
183B VAL* 3.0 22.1 + - + +
184B ARG* 3.3 12.1 + - - -
185B ALA 3.3 0.2 - - - -
186B LEU* 1.3 78.9 - - - +
188B SER* 1.3 57.9 + - - +
189B SER 3.4 0.4 - - - -
192B ALA* 3.4 22.5 - - - +
240B THR* 3.5 14.6 - - - +
241B ALA* 3.6 23.7 + - + +
242B GLU* 5.3 0.2 - - - -
243B ILE* 3.6 44.2 + - + +
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Residues in contact with SER 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLU* 5.0 2.9 + - - -
184A ARG* 5.3 2.1 + - - -
184B ARG 3.2 16.5 + - - -
185B ALA* 3.4 6.9 + - - -
186B LEU 3.3 0.6 - - - -
187B THR* 1.3 77.6 - - - +
189B SER* 1.3 58.1 + - - +
240B THR* 4.0 18.2 - - - -
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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