Contacts of the helix formed by residues 155 - 181 (chain A) in PDB entry 3DGR
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 155 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 4.0 4.7 - - - -
59A PHE* 5.5 0.9 - - - -
60A TYR 5.0 0.2 - - - -
62A LEU* 4.8 16.6 - - - -
65A ILE* 3.8 15.2 - - - +
132A PHE* 3.7 21.4 - - - -
152A LEU 2.8 21.5 + - - -
153A VAL 2.9 0.8 + - - -
154A GLN* 1.3 71.5 - - - +
156A TRP* 1.3 66.7 + - - +
157A TYR 2.9 3.7 + - - -
158A PRO* 3.3 12.7 - - - +
159A ILE* 3.0 37.1 + - - +
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Residues in contact with TRP 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 4.3 2.8 - - - -
153A VAL 2.7 25.4 + - - +
154A GLN* 3.8 4.9 - - - -
155A SER* 1.3 72.5 + - - +
157A TYR* 1.3 80.7 + + + +
159A ILE* 3.5 2.7 + - - +
160A THR* 2.5 53.1 + - + -
390A LEU* 3.5 22.2 - - + -
391A THR* 3.2 24.5 - - - -
392A ARG* 3.5 23.8 - - + -
397A CYS* 3.6 35.7 - - + -
196B ARG 3.2 23.2 + - - -
197B GLY 3.3 21.7 - - - -
198B VAL 2.9 22.6 + - - -
388B GLN* 3.7 16.2 - - + -
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Residues in contact with TYR 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A GLN 3.1 6.1 + - - +
155A SER 2.9 3.6 + - - -
156A TRP* 1.3 110.1 - + + +
158A PRO* 1.3 69.4 - - + +
160A THR* 3.2 1.4 + - - -
161A VAL* 2.9 50.9 + - + +
198A VAL* 4.4 0.2 - - - +
203A THR* 3.4 22.4 + - + +
206A ILE* 3.8 6.7 - - + -
207A GLY* 3.6 34.6 - - - -
387A LEU* 2.7 35.6 + - - +
390A LEU* 4.7 4.0 - - + -
199B SER* 3.4 40.8 - - - +
388B GLN* 4.8 3.6 - - - -
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Residues in contact with PRO 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TYR* 3.4 34.5 - - + +
61A GLY* 3.8 14.8 - - - +
64A TYR* 6.5 0.7 - - + -
65A ILE* 5.6 2.2 - - + -
154A GLN 3.5 10.1 - - - +
155A SER* 3.3 15.3 - - - +
157A TYR* 1.3 97.9 - - + +
159A ILE* 1.3 64.0 + - - +
161A VAL* 4.6 0.2 - - + -
162A ALA* 3.1 25.5 + - - +
206A ILE* 3.9 21.8 - - + -
210A ALA* 3.6 10.6 - - + +
199B SER 5.2 0.7 - - - +
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Residues in contact with ILE 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 3.7 29.2 - - + -
39A CYS* 4.2 13.5 - - - -
57A THR* 4.4 5.2 - - - +
58A VAL 3.5 18.0 - - - +
59A PHE* 3.8 21.5 - - + -
60A TYR 3.5 22.9 - - - +
131A LEU* 4.5 2.5 - - + -
155A SER* 3.0 32.8 + - - +
156A TRP 3.6 4.3 - - - +
158A PRO* 1.3 77.7 - - - +
160A THR* 1.3 54.9 + - - +
162A ALA* 3.8 0.2 - - - +
163A THR* 2.8 37.9 + - - +
395A LEU* 4.0 18.6 - - + -
397A CYS* 5.0 1.1 - - - -
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Residues in contact with THR 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A TRP* 2.5 41.5 + - - -
157A TYR 3.2 2.7 + - - -
159A ILE* 1.3 71.2 - - - +
161A VAL* 1.3 61.3 + - - +
163A THR* 3.8 0.5 - - - -
164A ASN* 2.9 28.9 + - - +
390A LEU* 4.1 19.3 - - + -
391A THR 4.3 9.3 + - - +
394A LEU* 3.8 29.6 - - + -
395A LEU* 3.7 24.4 + - + +
397A CYS* 4.1 6.9 - - - -
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Residues in contact with VAL 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A TYR* 2.9 56.1 + - + +
160A THR* 1.3 76.8 - - - +
162A ALA* 1.3 58.0 + - - +
164A ASN* 3.8 1.1 - - - +
165A SER* 2.9 34.7 + - - -
207A GLY* 3.5 23.8 - - - +
210A ALA* 3.7 11.9 - - + -
211A HIS* 3.9 9.9 - - + +
386A LEU* 3.9 8.8 - - + +
387A LEU* 3.7 13.0 - - + -
390A LEU* 3.5 18.8 - - + -
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Residues in contact with ALA 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A VAL* 3.9 24.8 - - + +
60A TYR* 4.4 9.6 - - + -
158A PRO 3.1 17.5 + - - +
159A ILE 3.8 2.7 - - - +
161A VAL* 1.3 79.2 - - - +
163A THR* 1.3 57.9 + - - +
166A ARG* 2.9 28.4 + - - +
210A ALA* 3.8 25.0 - - + +
213A VAL* 4.6 2.9 - - + -
214A ASN* 3.0 12.3 + - - +
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Residues in contact with THR 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A TYR* 4.2 18.2 - - + -
56A GLU 3.4 25.1 - - - +
57A THR* 3.5 9.5 - - - -
58A VAL* 2.9 28.1 + - + +
159A ILE 2.8 22.1 + - - -
160A THR 3.8 3.4 - - - -
162A ALA* 1.3 77.2 - - - +
164A ASN* 1.3 58.4 + - - +
166A ARG* 3.2 4.0 + - + +
167A GLU* 2.9 32.3 + - + +
395A LEU* 4.0 17.4 - - + +
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Residues in contact with ASN 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A TYR* 2.4 41.8 + - + -
160A THR 2.9 17.9 + - - +
161A VAL* 4.1 2.5 - - - +
163A THR* 1.3 76.4 - - - +
165A SER* 1.3 62.2 + - - +
167A GLU* 3.4 2.1 + - - +
168A GLN* 3.1 46.7 + - - +
358A ILE* 3.7 16.4 - - - +
385A GLY 4.1 12.1 + - - -
386A LEU* 4.8 5.7 + - - +
390A LEU* 4.0 26.8 - - + +
394A LEU* 4.9 1.6 - - + -
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Residues in contact with SER 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A VAL* 2.9 19.6 + - - -
164A ASN* 1.3 75.3 - - - +
166A ARG* 1.3 63.1 + - - +
168A GLN* 3.3 13.1 + - - +
169A LYS 3.1 18.0 + - - -
211A HIS* 2.9 35.6 + - - -
214A ASN* 3.2 18.2 + - - +
215A PHE* 3.4 17.9 - - - -
386A LEU* 4.3 7.4 - - - +
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Residues in contact with ARG 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLU* 2.7 33.5 + - - +
58A VAL* 3.5 23.8 - - + +
124A VAL* 3.6 20.6 - - - +
162A ALA 2.9 18.3 + - - +
163A THR* 3.6 4.0 - - + +
165A SER* 1.3 72.5 - - - +
167A GLU* 1.3 65.6 + - - +
169A LYS* 3.2 9.4 + - + +
170A LYS* 3.0 33.2 + - - +
214A ASN* 3.3 20.5 - - - +
480A ALA 2.7 25.4 + - - +
481A GLN 3.0 21.4 + - - -
482A LEU* 3.8 24.6 - - + +
483A ASN* 4.4 7.5 - - - +
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Residues in contact with GLU 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A TYR* 3.8 33.7 + - + +
55A GLU 5.5 1.2 + - - -
56A GLU* 4.4 13.3 + - - +
163A THR* 2.9 21.2 + - + +
164A ASN 3.7 2.5 - - - +
166A ARG* 1.3 78.6 + - - +
168A GLN* 1.3 61.3 + - - +
170A LYS* 3.0 52.1 + - - +
171A ILE* 3.3 17.7 + - - +
358A ILE* 3.6 21.1 - - + -
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Residues in contact with GLN 168 (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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164A ASN* 3.1 39.1 + - - +
165A SER* 3.7 5.8 - - - +
166A ARG 3.3 0.4 - - - -
167A GLU* 1.3 75.2 - - - +
169A LYS* 1.3 58.1 + - - +
171A ILE* 3.3 8.2 + - - +
172A LEU* 2.9 33.2 + - - +
190A LEU* 3.7 23.9 - - + +
356A VAL* 4.7 2.8 - - - +
357A ASP* 3.9 8.8 - - - +
358A ILE* 3.7 38.1 + - + -
361A LEU* 3.5 23.4 - - + +
382A SER* 4.9 2.4 + - - -
385A GLY 5.3 0.4 + - - -
386A LEU* 3.7 24.1 - - - +
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Residues in contact with LYS 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A SER 3.1 9.2 + - - +
166A ARG* 3.3 12.6 - - + +
168A GLN* 1.3 75.1 - - - +
170A LYS* 1.3 52.8 + - - +
172A LEU* 3.7 3.6 - - - +
173A ALA* 2.8 35.7 + - - +
186A LEU* 3.7 28.5 - - + -
187A GLU* 3.2 23.0 + - - -
213A VAL 5.3 1.0 + - - -
214A ASN* 2.8 43.7 + - + +
215A PHE* 3.4 27.2 - - + -
480A ALA 5.8 0.8 + - - -
481A GLN* 5.6 4.6 - - - +
482A LEU* 3.9 27.4 - - + +
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Residues in contact with LYS 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLU* 2.7 34.1 + - - +
166A ARG* 3.0 31.9 + - - +
167A GLU* 3.0 41.3 + - - +
168A GLN 3.3 0.2 - - - -
169A LYS* 1.3 74.8 - - - +
171A ILE* 1.3 59.8 + - + +
173A ALA* 3.4 2.5 + - - +
174A LYS* 3.0 30.8 + - - +
482A LEU* 3.6 22.9 - - + -
483A ASN* 6.2 1.8 - - - +
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Residues in contact with ILE 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A GLU 3.3 14.5 + - - +
168A GLN* 3.3 9.3 + - - +
170A LYS* 1.3 77.7 - - + +
172A LEU* 1.3 64.8 + - - +
174A LYS* 3.2 7.1 + - + +
175A TYR* 3.2 31.6 + - + +
358A ILE* 3.7 30.3 - - + +
361A LEU* 4.2 10.5 - - + -
362A GLN* 3.5 45.3 - - + +
365A VAL* 3.9 21.3 - - + -
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Residues in contact with LEU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A GLN 2.9 20.5 + - - +
169A LYS 3.7 2.0 - - - +
171A ILE* 1.3 76.0 - - - +
173A ALA* 1.3 56.5 + - - +
175A TYR* 3.8 3.2 - - - +
176A LEU* 2.9 33.6 + - + +
186A LEU* 3.6 17.3 - - + -
189A LYS* 3.9 28.5 - - + +
190A LEU* 4.1 12.1 - - + -
215A PHE* 4.0 21.5 - - + -
361A LEU* 3.7 31.9 - - + -
365A VAL* 4.3 7.4 - - + -
375A ILE* 4.7 9.7 - - + +
380A PHE* 3.9 19.3 - - + -
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Residues in contact with ALA 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A LYS 2.8 22.8 + - - +
170A LYS* 3.6 5.2 - - - +
171A ILE 3.4 0.2 - - - -
172A LEU* 1.3 71.4 - - - +
174A LYS* 1.3 63.4 + - - +
177A LEU* 3.0 28.2 + - - +
183A LEU* 3.4 16.0 - - + +
186A LEU* 3.6 18.6 - - + +
482A LEU* 3.9 17.9 - - + -
484A ILE* 5.0 12.8 - - + -
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Residues in contact with LYS 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A LYS 3.0 17.3 + - - +
171A ILE* 3.2 6.7 + - + +
173A ALA* 1.3 78.2 - - - +
175A TYR* 1.3 80.8 + - + +
177A LEU* 3.5 6.5 - - - +
178A GLU* 2.8 68.6 + - - +
362A GLN* 6.0 0.2 - - - +
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Residues in contact with TYR 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ILE* 3.2 25.2 + - + +
172A LEU 4.2 1.6 - - - +
174A LYS* 1.3 102.1 + - + +
176A LEU* 1.3 60.5 + - - +
178A GLU* 4.3 9.6 - - - -
179A THR* 2.8 36.8 + - + +
362A GLN* 3.0 34.2 + - - -
365A VAL* 3.6 32.8 - - + -
366A GLU* 2.7 40.7 + - + -
369A LYS* 4.0 22.9 - - + -
375A ILE* 3.8 15.7 - - + -
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Residues in contact with LEU 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LEU* 2.9 16.9 + - + +
173A ALA 3.9 2.7 - - - +
175A TYR* 1.3 75.8 - - - +
177A LEU* 1.3 53.4 + - - +
179A THR* 3.9 2.0 - - - -
180A SER* 2.8 43.0 + - - +
182A ASN* 3.6 11.9 - - - +
183A LEU* 4.2 8.7 - - + -
184A ASP 4.0 20.9 - - - +
186A LEU* 4.2 29.4 - - + -
189A LYS* 4.0 17.3 - - + -
375A ILE* 3.7 14.9 - - + +
376A GLU* 3.6 41.3 - - + +
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Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ALA 3.0 18.5 + - - +
174A LYS* 3.5 6.5 - - - +
176A LEU* 1.3 76.2 - - - +
178A GLU* 1.3 61.8 + - + +
181A GLY* 2.8 34.6 + - - +
182A ASN* 3.7 23.4 + - - +
183A LEU* 3.8 21.5 - - + -
339A LYS* 4.9 2.1 - - - +
484A ILE* 4.3 25.8 - - + -
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Residues in contact with GLU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LYS* 2.8 55.5 + - + +
175A TYR* 3.9 12.5 - - - +
177A LEU* 1.3 77.7 - - + +
179A THR* 1.3 64.4 + - + +
339A LYS* 4.2 11.3 - - - +
341A TYR* 4.0 13.0 + - - +
369A LYS* 4.0 27.7 + - + +
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Residues in contact with THR 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TYR* 2.8 26.6 + - - +
176A LEU* 3.7 2.9 + - - -
178A GLU* 1.3 80.5 - - + +
180A SER* 1.3 58.8 + - - +
337A ASN* 2.9 21.7 + - - -
339A LYS* 3.7 5.5 - - - +
341A TYR* 3.6 38.7 - - + +
369A LYS* 4.0 21.1 - - + -
373A TRP 4.3 2.2 - - - +
374A SER* 3.6 12.8 + - - -
375A ILE* 3.1 29.4 + - + +
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Residues in contact with SER 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A LEU* 2.8 25.9 + - - +
179A THR* 1.3 75.2 - - - +
181A GLY* 1.3 59.4 - - - +
182A ASN* 3.2 31.5 + - - +
337A ASN* 4.1 6.9 + - - +
338A SER* 4.6 6.8 + - - -
339A LYS* 3.8 10.3 - - - +
374A SER* 4.0 1.6 - - - -
376A GLU* 3.4 38.0 - - - +
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Residues in contact with GLY 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A LEU* 2.8 34.8 + - - +
180A SER* 1.3 72.7 + - - +
182A ASN* 1.3 61.9 + - - +
339A LYS* 3.9 19.8 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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