Contacts of the helix formed by residues 170 - 192 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B GLU* 4.2 7.0 - - - -
94B HIS* 2.7 49.7 + + + -
97B LYS* 3.2 23.1 - - + +
98B LEU* 3.3 26.1 + - + +
147B LEU* 3.8 34.4 - - + +
150B LEU* 6.4 0.2 - - + -
165B PHE* 3.6 33.2 - + - -
166B VAL* 3.0 20.2 + - + +
168B THR 3.6 0.2 - - - -
169B GLU* 1.3 93.8 - - + +
171B LEU* 1.3 58.4 + - - +
172B GLY 3.4 1.8 - - - -
173B ALA* 3.4 5.3 + - - +
174B GLN* 2.9 32.0 + - - +
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Residues in contact with LEU 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ASN* 4.3 9.3 - - - +
147B LEU* 3.8 28.3 - - + -
148B LEU* 3.8 26.0 - - + -
151B HIS* 4.2 7.9 - - + -
166B VAL* 3.1 23.3 + - + +
167B GLU* 3.6 22.3 + - + +
170B TYR* 1.3 74.9 - - - +
172B GLY* 1.3 61.7 + - - +
174B GLN* 3.3 4.6 + - - +
175B VAL* 3.1 27.0 + - - +
160E VAL* 3.3 33.9 - - + -
161E GLN* 3.7 18.3 - - + +
164E ASP* 5.7 0.4 - - - +
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Residues in contact with GLY 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B GLU 3.8 8.2 + - - -
168B THR 5.5 1.3 + - - -
170B TYR 3.4 0.4 - - - +
171B LEU* 1.3 74.5 - - - +
173B ALA* 1.3 65.3 + - - +
175B VAL* 3.2 5.4 + - - +
176B GLU* 3.1 27.8 + - - +
161E GLN* 3.6 23.2 - - - +
164E ASP* 5.6 0.6 + - - -
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Residues in contact with ALA 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B HIS* 5.9 8.3 - - + +
168B THR 5.8 0.8 + - - -
169B GLU 4.2 14.3 - - - +
170B TYR* 3.4 7.7 + - - +
171B LEU 3.4 0.4 - - - -
172B GLY* 1.3 75.4 - - - +
174B GLN* 1.3 57.8 + - - +
176B GLU* 3.2 10.7 + - - +
177B ALA* 2.9 29.0 + - - +
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Residues in contact with GLN 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B HIS* 5.7 1.6 - - - -
140B GLU* 2.7 56.9 + - - +
143B THR* 3.8 18.4 - - - +
144B ASN* 3.4 34.8 - - + +
147B LEU* 4.0 10.6 - - + +
170B TYR* 2.9 17.9 + - - +
171B LEU* 3.6 5.8 - - - +
172B GLY 3.2 0.4 - - - -
173B ALA* 1.3 76.0 - - - +
175B VAL* 1.3 65.2 + - - +
177B ALA* 3.3 5.8 + - - +
178B ILE* 3.0 26.6 + - + +
213B CA 4.1 8.7 - - - -
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Residues in contact with VAL 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ASN* 5.1 11.9 - - - +
171B LEU 3.1 16.0 + - - +
172B GLY 3.6 8.3 - - - +
174B GLN* 1.3 77.7 - - - +
176B GLU* 1.3 62.5 + - + +
178B ILE* 3.8 7.7 - - + +
179B LYS* 3.1 21.1 + - - +
101E TYR* 5.2 2.7 - - + -
104E LYS* 3.8 38.5 - - + +
105E ARG* 3.7 30.5 - - + +
161E GLN* 3.8 22.0 - - + +
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Residues in contact with GLU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B GLY 3.1 20.0 + - - +
173B ALA* 3.2 9.6 + - - +
175B VAL* 1.3 77.7 - - + +
177B ALA* 1.3 56.8 + - - +
179B LYS* 3.2 7.1 + - - +
180B ARG* 2.9 30.2 + - - +
104E LYS* 2.7 44.5 + - - +
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Residues in contact with ALA 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLU* 4.5 20.4 - - - +
173B ALA 2.9 16.2 + - - +
174B GLN* 3.7 9.4 - - - +
176B GLU* 1.3 75.5 - - - +
178B ILE* 1.3 57.6 + - - +
180B ARG* 3.3 9.7 + - - +
181B ILE* 3.0 37.9 + - + +
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Residues in contact with ILE 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LEU* 3.8 15.8 - - + +
140B GLU* 3.9 35.9 - - + +
141B LYS* 4.1 8.1 - - + +
144B ASN* 4.0 14.6 - - + +
174B GLN* 3.0 22.0 + - - +
175B VAL* 3.8 6.5 - - + +
177B ALA* 1.3 74.8 - - - +
179B LYS* 1.3 61.6 + - - +
181B ILE* 4.9 0.7 - - - -
182B SER* 2.8 33.8 + - - -
37E ALA* 3.6 34.3 - - + +
39E GLN* 3.5 24.9 - - + +
104E LYS 5.7 0.4 - - - +
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Residues in contact with LYS 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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175B VAL 3.1 14.8 + - - +
176B GLU* 3.8 8.5 - - - +
178B ILE* 1.3 76.9 - - - +
180B ARG* 1.3 64.8 + - - +
182B SER* 3.3 1.4 + - - -
183B GLU* 2.9 51.2 + - - +
37E ALA* 4.2 7.8 - - - +
100E GLU 5.2 0.6 + - - -
103E ASN* 3.8 21.0 - - - +
104E LYS* 3.9 30.4 - - + +
71I ASP* 2.9 49.2 + - - -
73I ASP* 3.9 17.7 - - + +
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Residues in contact with ARG 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B PHE* 3.7 29.6 - - - -
87B SER* 5.5 0.6 + - - -
90B GLU* 4.9 12.3 + - - -
176B GLU 2.9 17.4 + - - +
177B ALA* 3.5 9.9 - - - +
179B LYS* 1.3 75.6 - - - +
181B ILE* 1.3 65.8 + - + +
183B GLU* 3.2 16.5 + - - +
184B TYR* 2.8 57.7 + - + +
204B LEU* 5.1 1.4 - - - +
207B GLU* 4.1 6.5 + - - -
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Residues in contact with ILE 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B TYR* 3.7 11.9 - - - +
83B PHE* 4.5 22.0 - - + -
133B MET* 3.5 36.6 - - + +
136B ALA* 4.1 8.7 - - + +
137B LEU* 3.8 17.5 - - + +
140B GLU* 3.5 34.5 - - + +
177B ALA* 3.0 16.7 + - + +
178B ILE 4.2 2.0 - - - +
180B ARG* 1.3 76.2 - - + +
182B SER* 1.3 65.7 + - - +
184B TYR* 3.0 9.3 + - + +
185B VAL* 2.9 21.4 + - + +
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Residues in contact with SER 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LEU* 3.4 16.3 - - - +
178B ILE 2.8 23.9 + - - -
179B LYS 3.5 4.5 - - - -
181B ILE* 1.3 75.5 - - - +
183B GLU* 1.3 59.0 + - - +
185B VAL* 3.3 1.5 + - - +
186B ALA* 3.0 24.8 + - - +
36E LEU* 3.4 19.8 - - - +
37E ALA* 3.2 22.5 + - - -
73I ASP* 3.5 28.3 - - - -
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Residues in contact with GLU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B LYS* 2.9 50.5 + - - +
180B ARG* 3.5 15.6 - - - +
182B SER* 1.3 73.9 - - - +
184B TYR* 1.3 66.1 + - + +
186B ALA* 3.4 1.6 + - - +
187B GLN* 3.0 40.1 + - - +
71I ASP* 4.4 3.3 - - - +
72I ARG 5.1 0.7 - - - +
73I ASP* 3.7 25.6 - - + +
76I ALA* 3.9 11.9 - - + +
78I ARG* 4.8 19.7 - - - +
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Residues in contact with TYR 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B PHE* 3.7 25.8 - + - -
133B MET* 3.5 38.4 - - + -
180B ARG* 2.8 48.2 + - + +
181B ILE* 3.0 11.9 + - - +
183B GLU* 1.3 79.3 - - + +
185B VAL* 1.3 62.6 + - - +
187B GLN* 3.3 14.3 + - - +
188B LEU* 2.9 27.9 + - - +
200B PHE* 3.7 22.4 - + + -
203B MET* 4.9 0.7 - - + -
204B LEU* 3.5 17.8 - - + +
207B GLU* 2.7 34.5 + - - -
78I ARG* 6.1 0.4 - - - -
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Residues in contact with VAL 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LEU* 3.9 12.6 - - + -
133B MET* 3.8 35.4 - - + +
134B GLU* 4.0 11.0 - - + +
137B LEU* 4.5 9.6 - - + -
181B ILE* 2.9 19.6 + - + +
182B SER* 3.5 7.0 - - - +
184B TYR* 1.3 77.2 - - - +
186B ALA* 1.3 62.7 + - - +
188B LEU* 3.8 2.0 - - - +
189B ARG* 3.0 57.4 + - - +
36E LEU* 3.8 13.0 - - + -
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Residues in contact with ALA 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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182B SER 3.0 9.6 + - - +
183B GLU 3.7 3.4 - - - +
184B TYR 3.3 0.2 - - - -
185B VAL* 1.3 77.8 - - - +
187B GLN* 1.3 57.4 + - - +
189B ARG* 3.4 8.1 + - - +
190B ARG* 3.0 29.4 + - - +
36E LEU* 4.0 6.0 - - + +
73I ASP 3.4 25.1 - - - +
74I ASN* 3.7 22.2 - - - +
75I VAL 4.8 1.8 - - - +
76I ALA* 3.9 8.1 - - + -
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Residues in contact with GLN 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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183B GLU* 3.0 37.0 + - - +
184B TYR* 3.8 15.9 - - - +
186B ALA* 1.3 74.6 - - - +
188B LEU* 1.3 60.4 + - - +
190B ARG* 3.1 6.9 + - - +
191B VAL* 2.9 35.2 + - - +
200B PHE* 3.7 17.2 - - + -
203B MET* 3.8 6.1 - - - +
76I ALA* 3.9 21.8 - - + +
78I ARG* 3.0 34.5 + - - +
198I TRP* 2.8 34.8 + - + +
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Residues in contact with LEU 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU* 5.2 0.7 - - + -
129B ALA* 3.8 44.4 - - + +
130B LEU* 4.1 17.3 - - + +
133B MET* 4.0 20.0 - - + -
184B TYR 2.9 20.2 + - - +
185B VAL* 3.8 4.5 - - - +
187B GLN* 1.3 75.3 - - - +
189B ARG* 1.3 62.3 + - - +
191B VAL* 3.5 4.4 - - - +
192B GLY* 3.2 23.2 + - - -
197B VAL* 4.0 21.5 - - + +
200B PHE* 3.5 43.5 - - + -
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Residues in contact with ARG 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LYS* 5.6 0.2 - - - +
130B LEU* 3.9 20.7 - - + +
134B GLU* 2.8 31.7 + - - +
185B VAL* 3.0 34.9 + - - +
186B ALA* 3.6 7.4 - - - +
188B LEU* 1.3 77.4 - - - +
190B ARG* 1.3 61.7 + - - +
191B VAL 3.6 0.2 + - - -
192B GLY* 3.7 7.7 + - - -
30E THR* 4.2 29.2 + - - +
31E VAL 5.7 1.6 + - - -
32E PRO* 6.3 0.6 - - - +
36E LEU* 3.5 27.1 - - - +
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Residues in contact with ARG 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ALA 3.0 17.9 + - - +
187B GLN* 3.1 7.4 + - - +
189B ARG* 1.3 79.7 - - - +
191B VAL* 1.3 61.5 + - + +
192B GLY* 4.5 0.5 - - - -
74I ASN 5.0 1.6 + - - -
75I VAL* 3.2 28.5 + - - +
76I ALA 5.3 0.6 + - - -
77I LEU* 3.7 23.1 - - - +
128I ASP* 3.3 35.8 + - - -
194I GLY* 3.3 47.7 - - - +
197I VAL* 4.0 15.0 - - - +
198I TRP* 4.1 18.4 - - + +
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Residues in contact with VAL 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B GLN 2.9 23.6 + - - +
188B LEU* 3.5 12.1 - - - +
190B ARG* 1.3 76.7 - - - +
192B GLY* 1.3 67.9 + - - +
193B LYS 4.8 0.3 - - - +
196B GLY* 3.4 37.9 + - - +
197B VAL* 3.7 5.2 - - + +
200B PHE* 4.3 4.7 - - + -
195I HIS* 3.7 26.1 + - + +
198I TRP* 3.5 50.0 - - + -
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Residues in contact with GLY 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B LEU 3.2 13.6 + - - -
189B ARG* 4.3 6.1 - - - -
190B ARG 3.3 3.4 - - - -
191B VAL* 1.3 82.0 - - - +
193B LYS* 1.3 67.7 + - - +
196B GLY* 3.6 0.3 - - - -
197B VAL* 3.1 24.4 + - - +
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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