Contacts of the helix formed by residues 166 - 188 (chain A) in PDB entry 4CQM
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 GLN 166 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A THR* 4.0 11.1 - - - +
109A ASP* 3.3 37.8 + - - +
158A VAL* 3.7 6.8 - - - +
163A ASN* 2.9 46.4 + - + +
164A VAL 4.2 5.6 - - - +
165A GLY* 1.3 78.3 - - - +
167A THR* 1.3 59.8 + - - +
168A ASN* 3.3 8.1 - - - -
169A TYR* 3.4 40.3 - - + -
170A ALA* 2.9 28.6 + - - +
201A PHE* 6.1 0.2 - - - -
182D THR* 3.7 0.9 + - - -
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Residues in contact with THR 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 3.8 28.9 + - + +
115A MET* 3.8 14.7 - - - +
120A TRP* 3.8 0.8 - - + -
165A GLY 3.7 1.8 - - - -
166A GLN* 1.3 75.8 - - - +
168A ASN* 1.3 63.0 + - - +
170A ALA* 4.3 0.5 - - - +
171A ALA* 3.2 24.9 + - - +
132D PHE* 3.6 32.5 - - + -
179D LEU* 3.8 24.2 - - + +
182D THR* 3.3 22.4 - - - +
183D ALA 5.0 0.3 + - - -
186D GLU* 4.0 3.1 + - - -
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Residues in contact with ASN 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A GLN 2.9 29.4 + - - +
109A ASP* 4.7 0.9 - - - +
115A MET* 3.5 26.0 - - - +
119A ASP* 3.0 21.2 + - - +
120A TRP* 3.6 28.0 - - + +
123A VAL* 3.4 21.1 - - + +
124A ILE* 3.7 5.8 - - + +
165A GLY 4.5 1.0 - - - +
166A GLN* 3.8 8.0 - - - -
167A THR* 1.3 73.6 - - - +
169A TYR* 1.3 82.0 + - - +
172A SER* 3.2 24.3 + - - -
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Residues in contact with TYR 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ILE 3.6 9.4 - - - -
107A THR* 3.6 24.9 - - + -
109A ASP* 4.7 2.2 - - - +
123A VAL* 3.9 4.3 - - + -
127A ASN* 3.6 18.4 - - - -
155A SER 4.9 0.9 + - - -
156A SER* 3.9 22.0 + - - -
158A VAL* 3.8 14.8 - - + -
166A GLN* 3.4 40.8 + - + +
167A THR 3.4 0.4 - - - -
168A ASN* 1.3 83.6 + - - +
170A ALA* 1.3 58.3 + - - +
172A SER* 2.6 19.7 + - - -
173A LYS* 3.0 54.9 + - + +
206A MET* 4.2 15.9 - - + -
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Residues in contact with ALA 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A VAL* 3.6 33.7 - - + +
159A GLY* 3.8 4.2 - - - -
162A GLY* 3.9 0.4 - - - -
166A GLN 2.9 18.9 + - - +
167A THR 4.3 0.9 - - - +
169A TYR* 1.3 75.6 - - - +
171A ALA* 1.3 61.0 + - - +
173A LYS* 4.5 0.4 - - - +
174A ALA* 2.9 33.1 + - - +
178D GLY* 3.9 11.7 - - - +
182D THR* 3.3 19.1 - - - +
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Residues in contact with ALA 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A TRP* 3.6 28.0 - - + -
124A ILE* 4.5 2.5 - - + -
167A THR 3.2 19.3 + - - +
168A ASN 4.0 1.3 - - - +
170A ALA* 1.3 78.0 - - - +
172A SER* 1.3 57.6 + - - +
175A GLY* 3.2 12.0 + - - -
128D LEU* 4.2 7.1 - - + +
175D GLY* 3.2 45.4 - - - +
178D GLY* 4.5 0.2 - - - -
179D LEU* 4.0 7.4 - - + +
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Residues in contact with SER 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A VAL* 3.8 4.0 - - - +
124A ILE* 3.8 17.0 - - - +
127A ASN* 3.6 30.9 + - - +
128A LEU* 3.7 13.8 - - - +
168A ASN 3.2 15.4 + - - -
169A TYR* 2.6 25.6 + - - -
171A ALA* 1.3 76.1 - - - +
173A LYS* 1.3 61.0 + - - +
175A GLY* 3.2 2.3 + - - -
176A VAL* 2.9 33.2 + - - +
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Residues in contact with LYS 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ALA 5.3 1.6 + - - -
105A GLY* 5.0 8.5 - - - -
127A ASN* 3.8 24.1 + - + +
131A THR* 5.9 0.4 + - - -
154A ILE* 3.4 20.2 + - - +
155A SER* 2.9 43.9 + - - +
156A SER* 3.7 13.0 - - - -
159A GLY* 3.7 18.6 - - - +
169A TYR* 3.0 53.1 + - + +
172A SER* 1.3 79.8 + - - +
174A ALA* 1.3 64.6 + - - +
176A VAL* 3.2 15.1 + - + +
177A ILE* 3.3 7.3 + - - +
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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
----------------------------------------------------------
159A GLY* 3.3 24.1 - - - +
170A ALA 2.9 18.4 + - - +
173A LYS* 1.3 77.3 - - - +
175A GLY* 1.3 63.5 + - - +
177A ILE* 3.2 15.9 + - - +
178A GLY 3.3 3.3 + - - -
174D ALA* 3.2 39.7 - - + +
175D GLY* 4.2 1.8 - - - -
178D GLY* 4.1 10.8 - - - +
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Residues in contact with GLY 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU* 3.5 13.0 - - - -
171A ALA 3.2 9.2 + - - -
172A SER 3.2 8.1 + - - -
174A ALA* 1.3 78.4 - - - +
176A VAL* 1.3 58.4 + - - +
178A GLY 3.4 0.9 + - - -
179A LEU* 2.8 30.0 + - - +
171D ALA* 3.2 31.9 - - - +
175D GLY 4.0 0.8 - - - +
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Residues in contact with VAL 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ASN 3.5 24.2 - - - +
128A LEU* 3.6 6.9 - - + +
131A THR* 3.9 13.0 - - + +
153A ASN* 3.7 27.8 - - + -
154A ILE 4.8 3.4 - - - +
155A SER* 4.2 19.3 - - - +
172A SER 2.9 21.2 + - - +
173A LYS* 3.4 18.6 - - + +
174A ALA 3.2 0.2 - - - -
175A GLY* 1.3 76.3 - - - +
177A ILE* 1.3 54.1 + - - +
179A LEU* 3.2 8.2 + - - +
180A THR* 2.8 38.0 + - - +
196A SER* 4.5 1.3 - - - +
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Residues in contact with ILE 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A SER* 3.5 21.3 - - - +
159A GLY 3.6 24.9 - - - +
160A LYS* 5.2 1.6 - - + -
173A LYS 3.3 12.1 - - - +
174A ALA* 3.2 6.4 + - - +
176A VAL* 1.3 76.6 - - - +
178A GLY* 1.3 57.6 + - - +
180A THR* 3.2 2.9 + - - -
181A GLN* 3.0 50.1 + - + +
196A SER* 3.9 9.9 - - - +
198A LEU* 3.8 25.1 - - + -
252A SER* 3.5 20.6 - - - +
174D ALA* 5.8 0.2 - - + -
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Residues in contact with GLY 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 3.3 8.1 + - - -
175A GLY 3.8 2.5 - - - -
177A ILE* 1.3 78.8 - - - +
179A LEU* 1.3 60.0 + - - +
181A GLN* 3.5 16.1 - - - +
182A THR* 3.1 26.0 + - - -
158D VAL 5.3 1.6 - - - -
159D GLY 5.3 1.6 - - - -
162D GLY* 4.4 0.3 - - - -
170D ALA* 3.4 16.7 - - - +
171D ALA 4.4 0.7 - - - -
174D ALA* 4.2 15.6 - - - +
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Residues in contact with LEU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU* 3.9 14.6 - - + +
131A THR* 4.6 4.0 - - + -
132A PHE* 3.5 44.0 - - + +
135A THR* 4.3 23.1 - - + +
153A ASN* 4.8 3.1 - - - +
175A GLY 2.8 15.1 + - - +
176A VAL* 3.2 9.2 - - - +
178A GLY* 1.3 77.4 - - - +
180A THR* 1.3 64.6 + - - +
182A THR* 3.3 5.5 + - - -
183A ALA* 3.1 19.7 + - + +
112D LEU* 5.5 0.2 - - + -
120D TRP* 3.6 17.9 - - + -
167D THR* 4.0 30.9 - - + +
171D ALA* 4.2 2.2 - - + +
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Residues in contact with THR 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ILE 4.9 0.4 - - - +
153A ASN* 2.7 31.2 + - - +
176A VAL 2.8 18.1 + - - -
177A ILE 3.8 1.6 - - - -
179A LEU* 1.3 74.4 - - - +
181A GLN* 1.3 59.8 + - - +
183A ALA* 3.3 6.7 + - - +
184A ALA* 2.9 28.3 + - - +
194A CYS* 3.5 35.4 - - + +
195A ASN* 3.5 19.3 - - - +
196A SER* 3.1 16.8 + - - +
250A GLY* 5.4 1.6 - - - -
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Residues in contact with GLN 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ILE* 3.0 32.5 + - + +
178A GLY* 3.5 18.7 - - - +
179A LEU 3.3 0.2 - - - -
180A THR* 1.3 78.3 - - - +
182A THR* 1.3 61.6 + - - +
184A ALA* 3.3 3.4 + - - -
185A ARG* 3.2 18.5 + - - +
250A GLY* 4.7 12.9 + - - +
252A SER* 5.3 2.9 + - - +
234B GLN* 5.5 6.5 - - - +
235B LEU* 3.4 32.3 - - + +
159D GLY 5.0 0.5 - - - +
160D LYS* 2.8 35.9 + - - +
161D VAL* 3.4 23.4 - - - +
162D GLY 3.6 0.9 + - - -
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Residues in contact with THR 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A GLY 3.1 13.1 + - - -
179A LEU 3.3 8.6 + - - -
180A THR 3.3 0.2 - - - -
181A GLN* 1.3 74.9 - - - +
183A ALA* 1.3 66.1 + - - +
185A ARG* 3.3 6.0 + - - +
186A GLU* 3.1 33.2 + - - +
162D GLY* 3.6 0.8 - - - -
163D ASN 3.1 36.4 + - - +
167D THR* 3.2 35.2 - - - +
170D ALA* 3.3 18.0 - - - +
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Residues in contact with ALA 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A THR* 4.3 10.1 - - + -
179A LEU* 3.1 14.5 + - + +
180A THR* 3.3 11.4 + - - +
182A THR* 1.3 76.9 - - - +
184A ALA* 1.3 55.0 + - - +
186A GLU* 3.2 3.0 + - - -
187A LEU* 2.7 40.6 + - + +
194A CYS* 3.8 18.4 - - + -
112D LEU* 3.9 28.5 - - + -
167D THR* 5.1 1.1 + - + -
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Residues in contact with ALA 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A THR 2.9 16.8 + - - +
181A GLN 3.5 5.8 - - - +
182A THR 3.2 0.2 - - - -
183A ALA* 1.3 78.0 - - - +
185A ARG* 1.3 60.1 + - - +
188A GLY* 3.2 22.0 + - - -
192A ILE 4.8 1.5 - - - +
194A CYS* 3.6 11.4 - - - +
249A THR* 3.2 27.8 + - + +
250A GLY* 3.5 21.3 - - - +
199B PRO* 3.9 8.7 - - - +
235B LEU* 4.4 3.8 - - + -
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Residues in contact with ARG 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A GLN 3.2 10.0 + - - +
182A THR* 3.8 8.7 - - - +
183A ALA 3.3 0.4 - - - -
184A ALA* 1.3 80.3 - - - +
186A GLU* 1.3 61.1 + - - +
188A GLY* 4.4 2.5 + - - -
189A ARG* 3.6 22.3 + - - +
197B ASN* 5.2 8.4 + - - +
199B PRO* 4.2 27.7 - - + +
235B LEU* 4.4 14.1 + - + +
236B ILE* 3.4 31.2 - - + +
162D GLY 5.4 2.7 - - - -
163D ASN* 4.7 11.8 + - - +
164D VAL* 3.2 44.4 - - + +
221D MET* 5.9 4.4 - - - +
260D PHE* 6.2 0.6 - - - -
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Residues in contact with GLU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A THR* 3.1 28.3 + - - +
183A ALA* 3.9 2.9 - - - +
185A ARG* 1.3 78.1 - - - +
187A LEU* 1.3 64.7 + - + +
188A GLY 3.3 4.5 - - - -
189A ARG* 3.2 35.2 + - - +
190A HIS* 4.0 6.1 + - - -
111D PHE* 4.1 12.7 - - + +
112D LEU* 3.2 35.4 + - - +
164D VAL* 3.3 22.6 - - + -
165D GLY* 2.5 34.5 + - - -
167D THR* 4.1 2.2 + - - -
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Residues in contact with LEU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ALA* 3.6 34.1 - - + -
143A VAL* 4.5 5.2 - - + -
151A ILE* 4.2 6.3 - - + -
183A ALA* 2.7 25.1 + - + +
186A GLU* 1.3 75.5 - - + +
188A GLY* 1.3 64.2 + - - +
189A ARG 3.1 2.9 - - - -
190A HIS* 3.1 25.1 + - + +
192A ILE* 3.1 40.5 + - + +
194A CYS* 3.8 18.4 - - - -
112D LEU* 3.7 20.9 - - + -
113D LEU* 4.2 17.9 - - + -
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Residues in contact with GLY 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ALA 3.2 16.1 + - - -
185A ARG 4.4 1.1 - - - -
186A GLU 3.3 2.0 - - - +
187A LEU* 1.3 79.1 - - - +
189A ARG* 1.3 57.6 + - - +
190A HIS 3.2 1.2 + - - -
191A GLY* 3.4 10.8 + - - -
192A ILE 4.1 7.2 - - - -
199B PRO* 3.2 28.3 - - - +
200B LEU* 4.3 16.3 - - - +
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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