Contacts of the helix formed by residues 220 - 253 (chain A) in PDB entry 3NA1
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 ARG 220 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A TRP* 3.4 37.9 - - - -
32A THR* 6.3 0.6 - - - +
207A PRO* 2.9 43.0 + - - +
208A MET* 4.0 16.8 - - + -
211A LEU* 4.2 17.0 - - + +
216A PHE* 2.6 21.7 + - - +
219A PHE* 1.3 98.3 + - + +
221A THR* 1.3 58.5 + - - +
222A LYS 3.3 2.9 - - - -
223A THR* 3.1 12.3 + - - -
224A TRP* 2.8 27.7 + - - +
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Residues in contact with THR 221 (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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216A PHE 3.5 1.8 + - - -
217A ARG* 2.4 39.1 + - + +
218A LEU 4.0 6.1 + - - -
219A PHE 3.7 1.6 - - - -
220A ARG* 1.3 75.7 - - - +
222A LYS* 1.3 64.3 + - - +
224A TRP* 3.4 6.7 + - + +
225A LYS* 3.0 25.7 + - + +
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Residues in contact with LYS 222 (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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220A ARG 3.3 0.6 - - - -
221A THR* 1.3 80.2 - - - +
223A THR* 1.3 57.5 + - - +
225A LYS* 3.3 10.7 + - + +
226A ASP* 2.9 54.2 + - - +
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Residues in contact with THR 223 (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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204A THR* 3.0 36.4 - - + +
207A PRO* 3.9 29.8 - - + +
208A MET* 4.0 8.5 - - + -
220A ARG* 3.1 19.7 + - - -
222A LYS* 1.3 75.5 - - - +
224A TRP* 1.3 61.0 + - - +
226A ASP* 3.3 8.8 + - - +
227A HIS* 2.9 28.1 + - - +
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Residues in contact with TRP 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PRO* 3.5 21.1 - - + -
89A ALA* 3.9 11.4 - - + -
90A TYR* 3.5 30.3 - - + -
93A TYR* 5.3 4.7 - + + -
94A TYR* 4.3 16.5 + + - -
208A MET* 3.7 31.4 - - + -
216A PHE* 3.9 28.7 - + + +
217A ARG* 5.1 14.2 - - + +
220A ARG 2.8 16.4 + - - +
221A THR* 3.7 7.6 - - + +
223A THR* 1.3 76.3 - - - +
225A LYS* 1.3 62.0 + - + +
227A HIS* 3.2 10.8 + + - +
228A VAL* 2.9 55.1 + - + +
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Residues in contact with LYS 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A THR* 3.0 20.1 + - + +
222A LYS* 3.6 10.8 - - + +
223A THR 3.3 0.2 - - - -
224A TRP* 1.3 81.6 - - + +
226A ASP* 1.3 69.8 + - - +
228A VAL* 3.4 7.6 + - - +
229A ALA* 3.1 22.7 + - + +
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Residues in contact with ASP 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A GLN* 4.0 17.5 + - - +
204A THR* 3.9 18.1 - - + +
222A LYS* 2.9 47.8 + - - +
223A THR* 3.6 7.5 - - - +
225A LYS* 1.3 81.8 - - - +
227A HIS* 1.3 57.4 + - - +
229A ALA* 3.3 7.5 + - - +
230A ALA* 3.0 26.9 + - - +
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Residues in contact with HIS 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PRO* 3.8 17.8 + - + +
87A TRP* 3.4 14.0 - + - -
90A TYR* 4.9 1.6 - - + -
201A MET* 3.3 10.1 + - + -
204A THR* 2.9 25.6 + - - +
205A SER* 3.1 30.3 + - - -
208A MET* 3.6 20.9 - - + -
223A THR 2.9 18.2 + - - +
224A TRP* 3.4 13.0 - + - +
226A ASP* 1.3 74.7 - - - +
228A VAL* 1.3 64.0 + - - +
230A ALA* 3.2 5.4 + - - +
231A TRP* 3.1 56.9 + + - -
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Residues in contact with VAL 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TYR* 3.8 18.6 - - + -
94A TYR* 3.7 34.3 - - + +
224A TRP* 2.9 58.2 + - + +
225A LYS* 3.6 7.0 - - - +
227A HIS* 1.3 76.3 - - - +
229A ALA* 1.3 62.1 + - - +
231A TRP 3.4 0.5 + - - -
232A ASP* 3.0 36.8 + - - +
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Residues in contact with ALA 229 (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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225A LYS* 3.1 14.9 + - + +
226A ASP* 3.6 10.5 - - - +
227A HIS 3.2 0.2 - - - -
228A VAL* 1.3 77.3 - - - +
230A ALA* 1.3 62.0 + - - +
232A ASP* 3.4 10.1 + - - +
233A VAL* 3.2 27.9 + - + +
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Residues in contact with ALA 230 (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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197A ALA* 3.5 27.4 - - - +
200A GLN* 3.9 12.8 - - + -
201A MET* 3.6 20.0 - - - +
226A ASP 3.0 13.8 + - - +
227A HIS* 3.2 9.1 + - - +
229A ALA* 1.3 72.9 - - - +
231A TRP* 1.3 64.7 + - - +
233A VAL* 3.2 7.5 + - - +
234A ILE* 3.1 25.3 + - - +
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Residues in contact with TRP 231 (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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87A TRP* 3.8 26.4 - + + +
90A TYR* 3.3 38.8 - + + -
91A HIS* 3.8 23.6 - + - -
101A LEU* 5.8 1.8 - - + -
201A MET* 3.4 36.6 - - + +
227A HIS* 3.1 52.5 + + - -
228A VAL 3.8 1.3 - - - +
230A ALA* 1.3 75.8 - - - +
232A ASP* 1.3 56.2 + - - +
234A ILE* 3.1 27.1 + - + +
235A PHE* 2.8 56.2 + + - -
282A THR* 5.5 2.2 - - + -
283A GLU* 6.0 2.7 - - + -
286A ALA* 5.4 1.1 - - + -
602A HCD 4.3 21.8 - - + -
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Residues in contact with ASP 232 (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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90A TYR* 2.6 31.2 + - - -
94A TYR* 5.3 6.2 - - - -
96A ARG* 3.9 16.7 + - - +
228A VAL* 3.0 32.8 + - - +
229A ALA* 3.6 9.2 - - - +
230A ALA 3.2 0.2 - - - -
231A TRP* 1.3 75.1 - - - +
233A VAL* 1.3 56.8 + - + +
235A PHE* 4.1 2.1 - - - +
236A SER* 2.9 33.3 + - - -
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Residues in contact with VAL 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ARG* 3.8 39.3 - - - +
194A PHE* 4.2 3.8 - - - -
197A ALA* 3.6 23.8 - - + -
229A ALA* 3.2 15.8 + - + +
230A ALA* 3.5 7.4 - - - +
232A ASP* 1.3 73.0 - - + +
234A ILE* 1.3 68.4 + - - +
236A SER* 3.3 5.6 + - - -
237A LYS* 3.1 47.6 + - + +
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Residues in contact with ILE 234 (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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194A PHE* 3.3 23.6 - - + -
197A ALA* 4.0 7.0 - - + +
198A ILE* 3.9 38.1 - - + -
201A MET* 3.9 27.4 - - + -
230A ALA 3.1 14.9 + - - +
231A TRP* 3.1 26.4 + - + +
233A VAL* 1.3 75.9 - - - +
235A PHE* 1.3 57.9 + - - +
238A ALA* 3.0 28.4 + - - +
282A THR* 3.7 22.0 - - + -
286A ALA* 4.3 15.5 - - + -
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Residues in contact with PHE 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TYR* 3.9 7.6 - + - -
91A HIS* 3.5 32.8 - + - -
96A ARG* 3.6 48.5 - - + +
97A PRO* 3.8 24.2 - - + -
231A TRP* 2.8 46.5 + + - +
232A ASP 4.1 2.7 - - - +
234A ILE* 1.3 71.3 - - - +
236A SER* 1.3 66.0 + - - +
239A ASP* 2.9 45.6 + - - +
279A ALA* 5.6 3.6 - - - -
282A THR* 4.2 26.7 - - + -
283A GLU* 6.1 2.9 - - + -
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Residues in contact with SER 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ARG* 5.1 4.9 - - - +
193A ARG* 5.3 3.3 + - - -
232A ASP 2.9 23.5 + - - -
233A VAL* 3.4 8.8 + - - -
235A PHE* 1.3 73.9 - - - +
237A LYS* 1.3 68.1 + - - +
239A ASP* 3.5 5.8 - - - +
240A ILE* 3.2 38.6 + - - +
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Residues in contact with LYS 237 (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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190A GLU* 2.7 61.7 + - - +
193A ARG* 3.5 23.3 - - - +
194A PHE* 3.7 24.9 - - + -
233A VAL* 3.1 22.2 + - + +
236A SER* 1.3 81.7 + - - +
238A ALA* 1.3 65.0 + - - +
240A ILE* 3.3 16.1 + - + +
241A TYR* 3.0 40.1 + - + +
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Residues in contact with ALA 238 (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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194A PHE* 4.2 5.0 - - + -
234A ILE 3.0 20.2 + - - +
235A PHE 4.1 0.9 - - - +
237A LYS* 1.3 76.2 - - - +
239A ASP* 1.3 61.8 + - - +
241A TYR* 3.5 11.6 + - - +
242A THR* 3.1 29.1 + - - -
278A LYS* 5.7 0.7 - - - -
281A VAL* 5.1 1.2 - - + +
282A THR* 3.3 38.8 - - + +
285A LEU* 4.1 13.0 - - + -
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Residues in contact with ASP 239 (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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96A ARG* 5.9 0.7 + - - -
235A PHE* 2.9 42.6 + - - +
236A SER* 3.5 6.9 - - - +
238A ALA* 1.3 76.6 - - - +
240A ILE* 1.3 59.6 + - + +
242A THR* 3.4 3.8 + - - -
243A GLN* 2.9 37.6 + - - +
278A LYS* 3.3 44.4 + - - +
282A THR* 4.4 3.3 + - - -
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Residues in contact with ILE 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A SER* 3.2 24.3 + - - +
237A LYS* 3.3 18.8 + - + +
239A ASP* 1.3 74.4 - - + +
241A TYR* 1.3 65.4 + - + +
243A GLN* 4.5 4.5 - - - -
244A ASN* 2.8 59.3 + - - +
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Residues in contact with TYR 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A PHE* 3.7 32.3 - + - -
172A THR* 5.2 2.2 - - + -
176A PHE* 3.5 35.4 - + + -
180A GLN* 4.2 18.9 + - - -
188A ASN* 4.8 5.7 + - - -
190A GLU 5.1 0.7 + - - -
191A ALA* 3.8 20.3 + - - +
194A PHE* 4.9 8.8 - + - +
237A LYS* 3.0 35.1 + - + +
238A ALA* 3.8 8.7 - - - +
240A ILE* 1.3 80.8 - - + +
242A THR* 1.3 63.1 + - - +
244A ASN* 3.9 6.2 - - - +
245A PHE* 3.1 24.8 + - - +
285A LEU* 4.3 8.5 - - + -
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Residues in contact with THR 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A PHE* 4.4 1.8 - - - -
238A ALA 3.1 16.8 + - - -
239A ASP 3.8 3.1 - - - -
241A TYR* 1.3 77.2 - - - +
243A GLN* 1.3 59.1 + - - +
245A PHE* 3.4 2.9 + - - +
246A TYR* 3.0 27.5 + - - +
263A LEU* 4.2 27.1 - - + +
267A LEU* 5.8 0.4 - - + -
274A PHE* 3.9 26.2 - - + -
277A ILE* 5.2 0.2 - - + -
278A LYS* 4.1 24.7 + - + +
281A VAL* 3.5 25.4 - - + +
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Residues in contact with GLN 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ASP* 2.9 22.2 + - - +
240A ILE* 3.9 4.7 - - - +
242A THR* 1.3 74.8 - - - +
244A ASN* 1.3 68.7 + - - +
246A TYR* 3.3 6.8 + - + +
247A TRP* 3.2 48.8 + - + +
274A PHE* 4.9 10.1 - - + -
278A LYS* 5.3 7.8 + - + +
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Residues in contact with ASN 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ILE* 2.8 45.2 + - - +
241A TYR* 3.9 7.4 - - - +
243A GLN* 1.3 75.0 + - - +
245A PHE* 1.3 57.0 + - - +
247A TRP* 3.4 4.3 + - - +
248A GLU* 2.9 49.6 + - - +
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Residues in contact with PHE 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A PHE* 3.4 39.5 - + + -
178A GLU* 3.8 19.5 - - - -
241A TYR 3.1 17.8 + - - +
242A THR 3.6 4.3 - - - +
244A ASN* 1.3 73.9 - - - +
246A TYR* 1.3 66.0 + - - +
248A GLU* 3.5 9.1 + - + +
249A LEU* 3.0 37.1 + - + +
260A ARG* 4.7 3.4 - - + -
263A LEU* 3.5 25.6 - - + -
264A TYR* 3.8 43.1 - + + -
267A LEU* 3.8 11.9 - - + -
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Residues in contact with TYR 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A THR 3.0 18.5 + - - +
243A GLN* 3.5 8.1 - - + +
244A ASN 3.3 0.2 - - - -
245A PHE* 1.3 78.8 - - - +
247A TRP* 1.3 92.7 - + - +
249A LEU* 3.4 14.4 - - + +
250A ARG* 3.0 51.8 + - - +
267A LEU* 4.1 23.3 - - + -
274A PHE* 3.4 42.2 - + + -
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Residues in contact with TRP 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A GLN* 3.2 43.2 + - + +
244A ASN* 4.1 3.8 - - - +
246A TYR* 1.3 96.5 - + - +
248A GLU* 1.3 63.9 + - - +
249A LEU 3.1 1.8 - - - -
250A ARG* 3.1 47.0 + - + +
251A GLN* 3.0 38.3 + - + +
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Residues in contact with GLU 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A GLU* 4.0 19.4 - - - +
244A ASN* 2.9 38.6 + - - +
245A PHE* 3.9 6.9 - - + +
247A TRP* 1.3 75.2 - - - +
249A LEU* 1.3 62.1 + - - +
251A GLN* 3.2 20.3 + - - +
252A LYS* 3.1 53.3 + - + +
----------------------------------------------------------
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Residues in contact with LEU 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A PHE* 3.0 27.9 + - + +
246A TYR* 3.4 8.1 - - + +
247A TRP 3.1 0.2 - - - -
248A GLU* 1.3 78.4 - - - +
250A ARG* 1.3 60.1 + - + +
252A LYS* 5.2 1.1 - - - -
253A GLY* 3.2 39.4 + - - +
254A SER* 4.2 13.8 + - - +
264A TYR* 3.4 41.7 - - + +
267A LEU* 4.2 33.4 - - + -
268A GLY* 5.5 1.8 - - - +
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Residues in contact with ARG 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A TYR* 3.0 44.6 + - - +
247A TRP* 3.1 54.8 + - + +
249A LEU* 1.3 80.3 - - + +
251A GLN* 1.3 62.2 + - - +
252A LYS 3.3 0.8 + - - -
253A GLY* 3.9 6.3 + - - +
----------------------------------------------------------
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Residues in contact with GLN 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A TRP* 3.0 34.5 + - + +
248A GLU* 3.2 20.9 + - - +
250A ARG* 1.3 79.3 - - + +
252A LYS* 1.3 63.0 + - + +
----------------------------------------------------------
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Residues in contact with LYS 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A GLU* 5.5 3.6 + - - -
248A GLU* 3.1 39.5 + - + +
249A LEU* 5.0 1.6 - - - -
251A GLN* 1.3 82.2 - - + +
253A GLY* 1.3 64.8 + - - +
256A HIS* 5.3 8.1 + - - +
260A ARG* 6.2 0.8 - - - +
----------------------------------------------------------
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Residues in contact with GLY 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A LEU* 3.2 27.9 + - - +
250A ARG* 3.9 5.3 + - - -
251A GLN 3.7 1.8 - - - -
252A LYS* 1.3 82.9 - - - +
254A SER* 1.3 58.5 + - - -
255A VAL* 3.5 6.1 + - - -
256A HIS* 4.3 11.3 + - - -
----------------------------------------------------------
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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).
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