Contacts of the helix formed by residues 155 - 181 (chain C) in PDB entry 2GVG
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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C PHE* 4.0 7.8 - - - -
59C PHE* 5.5 0.9 - - - -
60C TYR 5.1 0.4 - - - -
61C GLY 4.9 0.9 - - - -
62C LEU* 4.8 15.7 - - - -
65C ILE* 3.7 20.6 - - - +
132C PHE* 3.8 19.5 - - - -
152C LEU 2.7 23.4 + - - -
153C VAL 2.8 2.8 + - - -
154C GLN* 1.3 74.6 - - - +
156C TRP* 1.3 65.1 + - - +
157C TYR 3.1 0.4 - - - -
158C PRO* 3.0 17.7 - - - +
159C ILE* 3.0 27.2 - - - +
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Residues in contact with TRP 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ARG 3.2 18.2 + - - -
197A GLY* 2.9 23.9 + - - -
198A VAL 2.9 28.9 + - - -
199A SER* 4.1 3.6 - - - -
388A GLN* 3.7 11.2 - - - -
37C PHE* 4.4 3.1 - - - -
153C VAL 2.8 24.0 + - - +
154C GLN* 2.8 7.8 - - - +
155C SER* 1.3 79.1 + - - +
157C TYR* 1.3 76.7 + + + +
159C ILE* 3.4 3.6 + - - +
160C THR* 2.8 51.0 + - - -
390C LEU* 3.6 12.3 - - + -
391C THR* 3.3 40.4 - - - -
392C ARG* 3.7 17.9 - - + -
397C CYS* 3.4 35.7 - - + -
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Residues in contact with TYR 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A SER* 3.3 41.5 - - - +
388A GLN* 5.1 3.4 - - - -
154C GLN 3.1 7.4 + - - +
155C SER 3.1 0.2 - - - -
156C TRP* 1.3 105.4 - + + +
158C PRO* 1.3 67.1 - - + +
160C THR* 3.2 1.7 + - - -
161C VAL* 2.9 44.2 + - + +
198C VAL* 3.9 0.3 - - - +
203C THR* 3.3 28.2 + - + +
206C ILE* 3.8 15.0 - - + -
207C GLY* 3.5 29.0 - - - -
387C LEU* 2.7 43.4 + - - +
390C LEU* 4.8 4.7 - - + -
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Residues in contact with PRO 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A SER 5.5 0.4 - - - +
60C TYR* 2.9 32.5 - - + +
61C GLY* 3.8 16.4 - - - +
64C TYR* 6.1 1.6 - - + -
65C ILE* 5.9 1.6 - - + -
154C GLN 3.3 4.9 - - - +
155C SER* 3.0 26.2 - - - +
157C TYR* 1.3 89.8 - - + +
159C ILE* 1.3 58.7 + - - -
161C VAL* 4.8 0.2 - - + -
162C ALA* 3.0 28.1 + - - +
206C ILE* 3.5 27.8 - - + -
210C ALA* 3.7 12.4 - - + +
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Residues in contact with ILE 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C PHE* 3.5 33.9 - - + -
39C CYS* 4.1 21.5 - - - -
57C THR* 4.3 5.6 - - - +
58C VAL 3.4 19.0 - - - +
59C PHE* 3.7 23.8 - - + -
60C TYR 3.5 21.5 + - - +
131C LEU* 4.6 1.6 - - + -
155C SER* 3.0 22.2 + - - +
156C TRP* 3.6 4.5 - - - +
158C PRO* 1.3 78.6 - - - +
160C THR* 1.3 52.9 + - - +
163C THR* 2.5 39.3 + - - +
395C LEU* 4.1 9.4 - - + -
397C CYS* 5.0 0.7 - - - -
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Residues in contact with THR 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C TRP* 2.8 40.1 + - - -
157C TYR 3.7 2.9 - - - -
159C ILE* 1.3 71.3 - - - +
161C VAL* 1.3 59.6 + - - +
163C THR* 3.7 0.5 - - - -
164C ASN* 2.8 30.1 + - - +
390C LEU* 3.9 21.3 - - + -
391C THR 4.4 5.0 + - - +
394C LEU* 3.7 34.8 - - + -
395C LEU* 3.7 23.3 - - + +
397C CYS* 4.1 5.4 - - - -
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Residues in contact with VAL 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C TYR* 2.9 57.1 + - + +
160C THR* 1.3 75.5 - - - +
162C ALA* 1.3 56.3 + - - +
164C ASN* 3.8 1.5 - - - +
165C SER* 2.8 37.2 + - - -
207C GLY* 3.6 12.6 - - - +
210C ALA* 3.7 9.4 - - + -
211C HIS* 4.1 9.2 - - + +
386C LEU* 3.8 12.0 - - + +
387C LEU* 3.5 26.2 - - + -
390C LEU* 3.8 16.8 - - + -
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Residues in contact with ALA 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C VAL* 4.0 27.2 - - + +
60C TYR* 4.6 7.9 - - + -
158C PRO 3.0 16.5 + - - +
159C ILE 4.0 1.6 - - - +
161C VAL* 1.3 80.5 - - - +
163C THR* 1.3 56.4 + - - +
165C SER* 4.3 0.2 - - - -
166C ARG* 2.9 26.5 + - - +
210C ALA* 3.7 26.4 - - + +
213C VAL* 4.7 3.1 - - + -
214C ASN* 3.0 12.8 + - - +
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Residues in contact with THR 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C TYR* 4.1 19.5 - - + -
56C GLU 3.3 25.8 - - - +
57C THR* 3.5 9.7 - - + -
58C VAL* 2.9 28.1 + - + +
159C ILE 2.5 24.5 + - - -
160C THR 3.7 3.1 - - - -
161C VAL 3.2 0.2 - - - -
162C ALA* 1.3 74.1 - - - +
164C ASN* 1.3 60.8 + - - +
166C ARG* 3.1 2.9 + - - +
167C GLU* 2.9 31.2 + - + +
395C LEU* 3.9 13.9 - - + +
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Residues in contact with ASN 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C TYR* 2.5 39.2 + - + +
160C THR 2.8 21.4 + - - +
161C VAL* 3.8 3.6 - - - +
163C THR* 1.3 73.2 - - - +
165C SER* 1.3 62.7 + - - +
167C GLU* 3.2 3.3 + - - +
168C GLN* 3.0 50.4 + - - +
358C ILE* 3.8 16.7 - - - +
385C GLY 4.0 16.8 + - - -
386C LEU* 4.5 6.7 + - - +
390C LEU* 4.0 19.9 - - + +
394C LEU* 5.0 1.6 - - + -
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Residues in contact with SER 165 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C VAL 2.8 19.8 + - - -
164C ASN* 1.3 79.3 - - - +
166C ARG* 1.3 59.8 + - - +
168C GLN* 3.5 12.9 + - - +
169C LYS 3.2 15.6 + - - -
190C LEU* 4.9 0.4 - - - -
211C HIS* 2.8 40.5 + - - -
214C ASN* 3.3 17.7 + - - -
215C PHE* 3.3 15.0 - - - -
386C LEU* 4.3 6.5 - - - -
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Residues in contact with ARG 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C GLU* 2.9 29.3 + - - +
58C VAL* 3.4 23.5 - - + +
124C VAL* 3.6 27.7 - - - +
162C ALA 2.9 17.8 + - - +
163C THR* 3.1 5.4 + - + +
165C SER* 1.3 77.1 - - - +
167C GLU* 1.3 67.0 + - - +
169C LYS* 3.2 7.0 + - + +
170C LYS* 3.2 34.6 + - - +
214C ASN* 3.4 20.0 - - + +
480C ALA* 2.9 22.4 + - - -
481C GLN 3.4 18.2 + - - -
482C LEU* 3.6 25.2 - - + +
483C ASN* 5.4 2.4 - - - +
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Residues in contact with GLU 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C TYR* 3.9 35.1 + - + -
55C GLU 6.0 0.7 - - - -
56C GLU* 4.5 8.8 - - - +
163C THR* 2.9 19.4 + - + +
164C ASN 3.2 8.0 + - - +
166C ARG* 1.3 80.3 + - - +
168C GLN* 1.3 65.3 + - - +
170C LYS* 2.7 61.8 + - - +
171C ILE* 3.2 11.6 + - - +
358C ILE* 4.3 13.0 - - + -
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Residues in contact with GLN 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C ASN* 3.0 43.3 + - - +
165C SER* 3.7 5.7 - - - +
166C ARG 3.3 0.2 - - - -
167C GLU* 1.3 76.5 - - - +
169C LYS* 1.3 57.4 + - - +
171C ILE* 3.3 6.8 + - - +
172C LEU* 3.0 33.0 + - - +
190C LEU* 3.7 19.2 - - + +
215C PHE* 4.7 0.2 - - - -
356C VAL* 4.9 1.6 - - - +
357C ASP* 3.9 4.7 - - - +
358C ILE* 3.2 41.0 + - + +
361C LEU* 3.3 26.5 - - + +
382C SER* 4.9 3.0 + - - -
385C GLY 5.3 0.6 + - - -
386C LEU* 3.7 20.8 - - - +
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Residues in contact with LYS 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C SER 3.2 8.4 + - - +
166C ARG* 3.2 11.6 + - + +
167C GLU 3.1 0.6 - - - -
168C GLN* 1.3 76.0 - - - +
170C LYS* 1.3 54.0 + - - +
172C LEU* 3.2 4.5 + - - +
173C ALA* 2.7 36.4 + - - +
186C LEU* 4.0 24.4 - - + +
187C GLU* 4.1 15.7 + - - +
213C VAL 5.4 0.2 + - - -
214C ASN* 2.8 43.5 + - + +
215C PHE* 3.4 26.9 - - + -
481C GLN* 5.9 3.6 - - - +
482C LEU* 3.5 30.4 - - + +
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Residues in contact with LYS 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C GLU* 3.0 24.1 + - - +
166C ARG* 3.2 28.7 + - - +
167C GLU* 2.7 46.5 + - - +
169C LYS* 1.3 79.6 - - - +
171C ILE* 1.3 57.0 + - + +
173C ALA* 3.6 5.9 - - - +
174C LYS* 2.9 31.0 + - - +
482C LEU* 3.7 20.2 - - + -
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Residues in contact with ILE 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C GLU 3.2 8.7 + - - +
168C GLN* 3.5 7.9 - - - +
169C LYS 3.2 0.2 - - - -
170C LYS* 1.3 76.6 - - + +
172C LEU* 1.3 66.8 + - - +
174C LYS* 3.3 5.3 + - - -
175C TYR* 3.2 27.5 + - + +
358C ILE* 3.6 34.1 - - + +
361C LEU* 4.2 10.5 - - + -
362C GLN* 3.0 52.0 - - + +
365C VAL* 3.8 17.3 - - + -
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Residues in contact with LEU 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C GLN 3.0 19.9 + - - +
169C LYS 3.7 3.4 - - - +
171C ILE* 1.3 78.1 - - - +
173C ALA* 1.3 58.3 + - - +
175C TYR* 4.2 2.3 - - - +
176C LEU* 3.0 33.8 + - - +
186C LEU* 3.5 15.3 - - + -
189C LYS* 3.4 31.4 - - + +
190C LEU* 4.0 22.7 - - + -
215C PHE* 4.0 11.2 - - + -
361C LEU* 3.6 29.8 - - + -
365C VAL* 4.2 6.3 - - + -
375C ILE* 4.8 8.6 - - + +
380C PHE* 4.0 20.6 - - + -
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Residues in contact with ALA 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C LYS 2.7 21.9 + - - +
170C LYS* 3.6 7.4 - - - +
172C LEU* 1.3 74.3 - - - +
174C LYS* 1.3 62.7 + - - +
176C LEU* 4.0 2.1 - - - +
177C LEU* 3.1 27.9 + - - +
183C LEU* 4.2 16.3 - - + +
186C LEU* 3.6 25.7 - - + +
482C LEU* 4.8 7.0 - - + -
484C ILE* 5.3 9.0 - - + -
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Residues in contact with LYS 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C LYS 2.9 18.7 + - - +
171C ILE* 3.7 5.8 - - - +
173C ALA* 1.3 76.7 - - - +
175C TYR* 1.3 88.4 + - + +
177C LEU* 3.9 5.0 - - - +
178C GLU* 3.1 52.9 + - + +
362C GLN* 5.4 0.6 + - - -
369C LYS* 5.8 1.8 - - - +
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Residues in contact with TYR 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C ILE* 3.2 18.8 + - + +
172C LEU 4.5 1.1 - - - +
174C LYS* 1.3 109.5 + - + +
176C LEU* 1.3 54.3 + - - +
177C LEU 3.2 1.3 - - - -
178C GLU* 4.0 7.3 - - - +
179C THR* 2.7 42.8 + - + +
362C GLN* 2.8 34.8 + - - -
365C VAL* 3.4 29.8 - - + -
366C GLU* 2.6 43.2 + - - -
369C LYS* 4.0 26.3 + - + -
375C ILE* 3.5 15.0 - - + +
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Residues in contact with LEU 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C LEU 3.0 19.6 + - - +
173C ALA* 4.1 2.9 - - - +
175C TYR* 1.3 78.7 - - - +
177C LEU* 1.3 61.3 + - - +
179C THR* 3.7 2.9 - - - +
180C SER* 2.6 39.3 + - - +
182C ASN* 3.3 14.4 - - - +
183C LEU* 4.2 12.3 - - - +
184C ASP 3.7 23.1 - - - +
186C LEU* 4.4 13.0 - - + -
189C LYS* 3.9 18.6 - - + -
375C ILE* 3.6 13.4 - - + +
376C GLU* 3.4 36.3 - - + +
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Residues in contact with LEU 177 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C ALA 3.1 18.8 + - - +
174C LYS* 3.9 6.7 - - - +
175C TYR 3.2 0.2 - - - -
176C LEU* 1.3 79.6 - - - +
178C GLU* 1.3 59.7 + - + +
181C GLY* 3.0 46.6 + - - +
182C ASN* 3.8 1.3 - - - +
183C LEU* 3.4 27.8 - - + -
339C LYS* 4.2 4.0 + - - -
484C ILE* 4.4 21.3 - - + -
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Residues in contact with GLU 178 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C LYS* 3.1 43.1 + - + +
175C TYR* 3.5 8.5 + - - +
176C LEU 3.4 0.2 - - - -
177C LEU* 1.3 83.9 - - + +
179C THR* 1.3 60.8 + - + +
180C SER 3.5 0.4 - - - -
339C LYS* 2.9 25.5 - - - +
341C TYR* 3.8 12.7 + - - +
369C LYS* 4.3 18.8 + - + +
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Residues in contact with THR 179 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C TYR* 2.7 25.2 + - + +
176C LEU* 3.7 5.4 + - - +
177C LEU 3.4 0.2 - - - -
178C GLU* 1.3 80.8 - - + +
180C SER* 1.3 59.6 + - - +
339C LYS* 3.5 14.4 - - - +
341C TYR* 3.6 42.7 - - + +
369C LYS* 4.6 12.6 - - + -
373C TRP 4.1 8.1 - - - +
374C SER* 3.1 25.5 + - - -
375C ILE* 3.2 23.2 + - + +
----------------------------------------------------------
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Residues in contact with SER 180 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C LEU* 2.6 29.2 + - - +
178C GLU 3.5 0.4 - - - -
179C THR* 1.3 83.5 - - - +
181C GLY* 1.3 58.6 + - - +
182C ASN* 2.8 38.9 + - - -
339C LYS* 4.0 13.6 - - - +
374C SER* 3.8 3.4 - - - -
376C GLU* 2.8 30.2 + - - -
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Residues in contact with GLY 181 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C LEU* 3.0 32.9 + - - +
180C SER* 1.3 77.1 - - - +
182C ASN* 1.3 60.0 + - - +
339C LYS* 4.1 14.1 - - - +
----------------------------------------------------------
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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