Contacts of the helix formed by residues 213 - 233 (chain A) in PDB entry 1UW9
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 213 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A SER* 3.5 13.8 + - - +
209A GLN* 3.4 27.5 + - - +
210A PRO* 3.5 21.9 + - - +
212A MET* 1.3 76.0 - - - +
214A TRP* 1.3 67.8 + - + +
215A ARG 3.3 2.1 + - - +
216A ASP* 3.3 25.4 + - - +
217A ARG* 3.3 18.2 + - - +
109B GLU* 5.5 0.2 - - - +
110B GLU* 2.8 43.6 + - - -
149O VAL 5.4 4.8 + - - -
152O PRO 5.6 0.7 - - - +
285O ARG* 3.6 47.6 - - - +
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Residues in contact with TRP 214 (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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207A ASN 3.5 17.9 - - - +
208A SER* 3.0 28.1 + - - -
212A MET 3.9 0.2 + - - -
213A ARG* 1.3 73.3 - - + +
215A ARG* 1.3 93.8 + - + +
217A ARG* 3.0 20.4 + - - +
218A PHE* 2.9 48.5 + + + -
249A GLU* 3.9 5.3 + - - -
252A LYS* 3.8 28.5 - - + +
253A ARG* 3.5 55.6 - - + +
256A SMC 3.6 39.9 - - + -
285O ARG* 6.4 0.8 - - - +
286O ASP* 5.2 11.8 + - - -
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Residues in contact with ARG 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A ARG* 3.4 1.8 - - + +
214A TRP* 1.3 115.3 - - + +
216A ASP* 1.3 64.5 + - - +
218A PHE* 3.4 2.3 + - - +
219A LEU* 3.1 51.6 + - + +
256A SMC 3.7 29.7 - - - +
161O LYS* 5.0 2.7 - - - +
258O LYS* 4.6 2.6 - - - +
285O ARG* 3.7 21.8 - - - +
286O ASP* 3.1 26.1 + - - +
287O ASN* 3.4 20.6 + - - +
288O GLY* 3.5 20.5 - - - +
63T VAL* 3.7 27.7 + - - +
65T CYS* 4.9 2.4 + - - +
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Residues in contact with ASP 216 (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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182A ALA* 3.6 19.5 - - + -
213A ARG* 3.3 24.6 + - - +
214A TRP 3.3 0.2 - - - -
215A ARG* 1.3 77.6 - - - +
217A ARG* 1.3 64.3 + - - +
219A LEU* 3.3 3.2 + - - +
220A PHE* 3.1 29.7 + - + -
152O PRO 4.9 3.3 - - - +
153O HIS* 3.4 13.4 + - - -
157O VAL* 3.4 31.8 - - + +
161O LYS* 3.0 32.8 + - - +
285O ARG* 6.0 1.6 - - - -
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Residues in contact with ARG 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ALA* 3.6 10.4 - - - +
185A TYR* 3.6 15.0 - - + -
202A ASP* 2.8 40.0 + - - +
206A VAL* 3.3 21.9 + - - +
207A ASN* 2.8 33.7 + - - +
209A GLN* 5.4 0.4 + - - -
212A MET* 3.6 38.3 + - - +
213A ARG 3.3 3.6 + - - +
214A TRP* 3.0 19.1 + - - +
216A ASP* 1.3 80.4 - - - +
218A PHE* 1.3 75.3 + - - +
220A PHE* 3.3 0.7 + - - +
221A VAL* 2.8 48.7 + - + +
240A LEU* 4.7 2.2 - - + +
241A ASN 4.1 4.6 + - - -
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Residues in contact with PHE 218 (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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214A TRP* 2.9 54.1 + + + -
215A ARG 3.7 7.4 - - - +
216A ASP 3.4 0.2 - - - -
217A ARG* 1.3 96.1 - - - +
219A LEU* 1.3 55.4 + - - +
221A VAL* 3.9 1.0 - - - +
222A THR* 2.7 37.8 + - - -
240A LEU* 3.6 48.5 - - + +
241A ASN 3.4 21.1 - - - -
242A ALA* 5.1 0.2 - - - -
253A ARG* 3.3 29.4 - - + -
256A SMC 3.8 14.6 - - + -
257A ALA* 4.3 7.6 - - + -
260A LEU* 4.1 11.4 - - + -
265A ILE* 5.4 1.3 - - + -
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Residues in contact with LEU 219 (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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215A ARG* 3.1 47.9 + - - +
216A ASP* 3.6 9.4 - - - +
217A ARG 3.2 0.2 - - - -
218A PHE* 1.3 76.2 - - - +
220A PHE* 1.3 68.1 + - + +
222A THR* 3.2 8.0 + - - -
223A GLU* 3.1 18.4 + - - +
256A SMC 4.5 2.5 - - + -
260A LEU* 4.2 26.2 - - + -
161O LYS* 4.6 14.6 - - - +
63T VAL 4.8 2.9 - - - +
65T CYS 3.4 25.8 - - - +
66T LEU 3.9 16.8 - - - +
67T TYR* 4.0 20.3 - - + +
71T ARG* 5.1 3.3 + - - +
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Residues in contact with PHE 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ALA* 3.6 19.3 - - + +
183A LYS* 3.5 31.6 - - + -
186A GLY* 4.2 3.1 - - - -
216A ASP* 3.1 25.9 + - + +
217A ARG 4.1 1.1 - - - +
219A LEU* 1.3 74.1 - - + +
221A VAL* 1.3 65.5 + - - +
223A GLU* 3.3 7.7 + - - +
224A ALA* 3.1 18.2 + - - +
157O VAL* 5.2 3.8 - - + -
160O ASP* 3.5 45.1 - - + -
161O LYS* 3.7 24.0 - - + -
71T ARG* 4.2 26.0 - - + -
72T TYR* 3.4 36.4 - + - +
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Residues in contact with VAL 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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185A TYR* 4.2 15.9 - - + -
186A GLY* 4.4 7.0 - - - +
189A VAL* 4.2 12.8 - - + -
217A ARG* 2.8 37.6 + - + +
218A PHE 4.0 0.2 - - - +
220A PHE* 1.3 76.3 - - + +
222A THR* 1.3 58.1 + - - +
224A ALA* 3.0 8.2 + - - +
225A ILE* 2.8 34.2 + - + +
238A HIS* 3.5 39.9 - - + +
240A LEU* 3.8 15.5 - - + -
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Residues in contact with THR 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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218A PHE 2.7 25.7 + - - -
219A LEU* 3.2 7.8 + - - -
221A VAL* 1.3 76.3 - - - +
223A GLU* 1.3 62.4 + - - +
225A ILE* 3.2 9.4 + - - +
226A TYR* 3.1 51.6 + - + -
240A LEU* 4.8 2.6 - - - +
260A LEU* 3.4 18.8 - - + +
262A VAL* 3.5 17.5 - - + +
60T PHE* 4.1 12.6 - - + -
67T TYR* 4.0 11.2 - - + -
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Residues in contact with GLU 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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219A LEU 3.1 10.1 + - - +
220A PHE* 3.5 11.5 - - - +
222A THR* 1.3 74.9 - - - +
224A ALA* 1.3 56.5 + - - +
226A TYR* 3.4 1.6 + - - +
227A LYS* 2.9 34.7 + - + +
67T TYR* 3.3 24.6 + - + +
68T TYR 3.2 18.2 - - - +
69T ASP* 4.3 6.4 - - - +
70T ASN* 3.6 4.7 + - - +
71T ARG* 2.9 43.6 + - - +
72T TYR* 2.9 45.6 + - + +
1141T EDO 6.3 0.7 - - - -
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Residues in contact with ALA 224 (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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186A GLY 3.2 28.0 - - - +
189A VAL* 3.8 9.2 - - + -
190A TYR* 3.6 24.5 - - + +
193A LEU* 4.5 2.7 - - - -
220A PHE 3.1 10.7 + - - +
221A VAL 3.0 9.5 + - - +
223A GLU* 1.3 74.7 - - - +
225A ILE* 1.3 65.9 + - - +
227A LYS* 3.9 3.3 - - - +
228A ALA* 3.0 26.0 + - - +
72T TYR* 4.4 4.9 - - + -
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Residues in contact with ILE 225 (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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189A VAL* 4.9 0.2 - - + -
193A LEU* 3.9 13.9 - - + -
221A VAL* 2.8 27.9 + - + +
222A THR* 3.7 6.7 - - - +
224A ALA* 1.3 72.7 - - - +
226A TYR* 1.3 76.5 + - + +
228A ALA* 3.9 1.6 - - - +
229A GLN* 2.9 29.9 + - - +
236A LYS* 3.4 31.7 - - + +
237A GLY* 4.3 1.1 - - - -
238A HIS* 3.8 41.7 - - + +
240A LEU* 5.3 1.3 - - + -
262A VAL* 4.0 28.0 - - + -
263A PRO* 4.7 4.0 - - + -
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Residues in contact with TYR 226 (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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222A THR* 3.1 37.2 + - + +
223A GLU 4.1 2.5 - - - +
225A ILE* 1.3 91.7 - - + +
227A LYS* 1.3 64.5 + - - +
229A GLN* 3.8 17.2 - - - +
230A ALA* 3.1 18.2 + - - +
260A LEU 2.7 23.4 + - - -
261A GLY 3.1 12.8 + - - -
262A VAL* 3.6 7.9 + - + -
263A PRO* 5.8 0.9 - - + -
54I ASN* 5.8 1.8 - - - -
68I TYR* 5.4 2.9 - + - -
56T SER* 3.4 34.5 - - - +
59T ARG* 3.0 42.1 + - - -
60T PHE* 3.9 9.2 - + - -
67T TYR* 3.8 3.6 - - - +
1141T EDO 3.3 13.3 - - - -
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Residues in contact with LYS 227 (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 TYR* 3.4 45.0 + - + -
223A GLU* 2.9 23.5 + - + +
224A ALA* 3.9 3.8 - - - +
226A TYR* 1.3 77.0 - - - +
228A ALA* 1.3 57.8 + - - +
230A ALA* 3.3 3.3 + - - +
231A GLU* 2.9 33.2 + - + +
45T ALA* 5.7 1.4 - - - +
49T LYS* 4.1 32.7 + - - +
70T ASN* 4.6 6.5 + - - +
72T TYR* 3.4 38.7 + - + +
73T TRP* 4.3 5.9 - - - +
74T THR* 4.5 2.7 + - - -
1141T EDO 3.6 20.8 + - - +
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Residues in contact with ALA 228 (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 TYR* 3.9 12.5 - - + +
193A LEU* 3.5 34.3 - - + -
194A ARG* 3.7 14.6 - - - +
224A ALA 3.0 16.6 + - - +
225A ILE 3.9 2.0 - - - +
227A LYS* 1.3 76.6 - - - +
229A GLN* 1.3 56.7 + - - +
231A GLU* 3.7 4.9 - - - +
232A THR* 2.9 37.4 + - - +
236A LYS* 4.0 2.9 - - + -
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Residues in contact with GLN 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 ILE* 2.9 21.2 + - - +
226A TYR* 3.8 16.3 - - - +
228A ALA* 1.3 76.7 - - - +
230A ALA* 1.3 57.3 + - - +
232A THR* 3.7 0.2 + - - -
233A GLY* 2.8 30.1 + - - -
234A GLU 3.3 21.7 + - - +
235A VAL* 3.4 13.9 - - - +
236A LYS* 3.0 37.1 + - + +
52I VAL* 3.5 25.8 - - + +
54I ASN* 4.9 4.0 + - - +
68I TYR* 3.6 22.7 + - - -
59T ARG* 6.0 0.2 - - - -
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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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226A TYR 3.1 18.9 + - - +
227A LYS 3.8 2.5 - - - +
229A GLN* 1.3 78.2 - - - +
231A GLU* 1.3 63.7 + - - +
233A GLY* 3.9 1.0 + - - -
10I LYS* 3.2 23.7 + - - -
49T LYS* 4.2 14.6 - - - +
1141T EDO 3.7 21.5 - - - +
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Residues in contact with GLU 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A TYR* 2.6 28.8 + - - -
194A ARG* 3.0 45.1 + - - +
227A LYS* 2.9 22.3 + - + +
228A ALA* 3.7 5.8 - - - +
229A GLN 3.2 0.2 - - - -
230A ALA* 1.3 80.0 - - - +
232A THR* 1.3 61.7 + - + +
4I TRP* 5.2 0.3 - - - -
5I THR 4.3 1.4 - - - +
6I PRO* 3.3 37.0 - - + +
9I ASN* 4.3 6.5 + - + +
10I LYS* 3.9 23.0 + - - +
49T LYS* 6.3 1.8 - - - +
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Residues in contact with THR 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ARG* 3.5 36.1 - - + +
228A ALA 2.9 20.6 + - - +
231A GLU* 1.3 81.2 - - + +
233A GLY* 1.3 59.9 + - - +
234A GLU* 3.2 19.8 + - - +
236A LYS* 3.3 22.9 - - - +
9I ASN 4.6 3.6 - - - +
10I LYS* 3.6 3.8 - - - +
11I MET* 2.8 42.3 + - + +
17I TYR* 4.8 5.6 - - - +
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Residues in contact with GLY 233 (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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229A GLN 2.8 13.5 + - - -
230A ALA* 3.9 3.1 + - - -
231A GLU 3.6 1.8 - - - -
232A THR* 1.3 76.8 - - - +
234A GLU* 1.3 60.3 - - - +
235A VAL 4.4 0.2 + - - -
10I LYS* 4.0 6.5 - - - +
11I MET 4.6 2.1 - - - +
12I PHE* 5.9 0.3 - - - -
13I GLU* 6.0 0.3 - - - +
51I TYR* 3.9 35.0 - - - +
52I VAL* 4.8 13.5 + - - +
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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
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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