Contacts of the helix formed by residues 195 - 219 (chain A) in PDB entry 5HK1
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 ASP 195 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A THR* 3.2 15.7 + - + +
193A THR* 3.4 17.5 - - - +
194A GLN* 1.3 73.2 - - - +
196A PHE* 1.3 61.0 + - - +
197A LEU 3.6 2.1 + - - -
198A THR* 2.7 26.9 + - + -
199A LEU 3.0 17.2 + - - -
116B HIS* 2.8 33.3 + - + +
119B ARG* 2.3 46.2 + - + +
159B ALA* 4.0 0.3 - - - +
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Residues in contact with PHE 196 (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 THR 5.5 1.8 - - - -
190A VAL* 5.2 13.9 - - + -
194A GLN* 3.3 35.0 + - + -
195A ASP* 1.3 74.0 - - - +
197A LEU* 1.3 57.1 + - - +
199A LEU* 3.2 18.6 + - + +
200A PHE* 2.9 28.4 + - - +
121B TRP* 5.8 9.0 - + - -
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Residues in contact with LEU 197 (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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195A ASP* 3.2 2.4 + - - +
196A PHE* 1.3 79.2 - - - +
198A THR* 1.3 56.3 + - - +
200A PHE* 3.2 14.5 + - + +
201A TYR* 3.0 63.8 + - + +
119B ARG* 3.5 41.7 - - - +
157B GLY* 4.6 5.2 - - - +
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Residues in contact with THR 198 (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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82A VAL* 3.7 9.3 - - + +
83A PHE* 3.2 38.8 + - + +
84A VAL* 5.5 0.2 - - - -
85A ASN* 5.7 1.8 - - - +
186A LEU* 5.9 0.7 - - + -
189A THR* 4.4 13.7 - - + +
195A ASP* 2.7 36.0 + - - -
197A LEU* 1.3 75.3 - - - +
199A LEU* 1.3 65.9 + - - +
201A TYR* 3.3 9.9 + - - +
202A THR* 3.0 30.6 + - - +
116B HIS* 6.0 0.4 - - - +
119B ARG* 2.9 12.1 + - - +
138B GLU* 5.1 1.7 + - - -
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Residues in contact with LEU 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A LEU* 3.6 43.1 - - + -
189A THR* 4.1 12.3 - - + +
190A VAL* 5.0 12.6 - - + -
195A ASP 3.0 12.1 + - - +
196A PHE* 3.2 23.8 + - + +
198A THR* 1.3 78.6 - - - +
200A PHE* 1.3 64.7 + - + +
202A THR* 3.5 1.7 + - - -
203A LEU* 3.2 47.1 + - + +
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Residues in contact with PHE 200 (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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196A PHE 2.9 13.4 + - - +
197A LEU* 3.5 16.2 - - + +
198A THR 3.2 0.2 - - - -
199A LEU* 1.3 78.8 - - + +
201A TYR* 1.3 82.9 + + - +
203A LEU* 3.3 6.8 + - + +
204A ARG* 2.9 65.0 + - + +
305A SO4 5.3 1.3 - - - -
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Residues in contact with TYR 201 (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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80A GLN* 3.3 25.6 - - - +
82A VAL* 4.1 15.5 - - + -
197A LEU* 3.0 50.4 + - + +
198A THR* 3.3 10.7 + - - +
200A PHE* 1.3 95.3 - + - +
202A THR* 1.3 61.1 + - - +
204A ARG* 3.5 33.2 + - - +
205A SER* 3.0 29.9 + - - -
305A SO4 4.2 19.0 + - - -
119B ARG* 4.5 0.7 - - - -
138B GLU* 3.9 20.4 - - - -
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Residues in contact with THR 202 (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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82A VAL* 3.7 18.4 - - - +
83A PHE 4.7 1.4 + - - -
84A VAL* 5.7 4.4 - - + +
93A MET* 5.8 4.4 - - - -
182A LEU* 4.7 14.8 - - + -
185A ALA* 6.2 1.8 - - + -
186A LEU* 3.8 33.5 - - + +
198A THR* 3.0 21.3 + - - +
199A LEU 3.6 5.2 - - - -
201A TYR* 1.3 76.1 - - - +
203A LEU* 1.3 64.0 + - - +
205A SER* 3.2 8.1 + - - -
206A TYR* 3.1 21.0 + - - +
301A 61W 4.9 14.3 - - + -
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Residues in contact with LEU 203 (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 LEU* 4.4 18.6 - - + -
186A LEU* 4.0 21.5 - - + -
199A LEU* 3.2 38.2 + - + +
200A PHE* 3.3 6.0 + - + +
202A THR* 1.3 80.7 - - + +
204A ARG* 1.3 57.4 + - - +
206A TYR* 3.4 7.4 + - + +
207A ALA* 3.0 28.3 + - - +
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Residues in contact with ARG 204 (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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80A GLN* 2.9 27.9 + - - -
200A PHE* 2.9 46.8 + - + +
201A TYR* 3.5 28.2 + - - +
203A LEU* 1.3 74.9 - - - +
205A SER* 1.3 61.0 + - - +
207A ALA* 3.1 8.4 + - + +
208A ARG* 2.8 67.1 + - + +
302A SO4 4.2 14.5 + - - +
305A SO4 3.2 35.6 + - - -
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Residues in contact with SER 205 (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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74A LEU* 4.4 4.9 - - - +
78A GLU 5.3 4.1 + - - -
80A GLN* 5.0 14.6 + - - +
82A VAL* 4.8 11.5 - - - +
93A MET* 5.6 2.2 - - - -
95A LEU* 3.3 29.4 + - - +
201A TYR 3.0 18.8 + - - -
202A THR* 3.2 7.3 + - - -
204A ARG* 1.3 77.2 + - - +
206A TYR* 1.3 63.0 + - - +
208A ARG* 3.3 15.8 + - - +
209A GLY* 3.0 17.5 + - - -
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Residues in contact with TYR 206 (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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95A LEU* 3.8 6.6 - - - +
98A ALA* 3.7 13.2 - - + -
99A SER 3.0 28.0 + - - -
100A LEU* 3.7 6.5 - - + +
178A ILE* 3.8 4.4 - - + +
179A PRO* 3.6 31.9 - - + +
182A LEU* 3.4 33.9 - - + -
202A THR 3.1 11.9 + - - +
203A LEU* 3.7 11.7 - - + +
204A ARG 3.3 0.2 - - - -
205A SER* 1.3 76.6 - - - +
207A ALA* 1.3 57.1 + - - +
209A GLY* 3.2 1.4 + - - -
210A LEU* 2.9 52.7 + - + +
301A 61W 3.4 28.5 - - + -
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Residues in contact with ALA 207 (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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203A LEU 3.0 14.7 + - - +
204A ARG* 3.4 13.0 - - + +
206A TYR* 1.3 76.9 - - - +
208A ARG* 1.3 56.6 + - + +
210A LEU* 3.3 10.4 + - - +
211A ARG* 2.8 31.9 + - - +
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Residues in contact with ARG 208 (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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74A LEU* 3.6 14.8 - - + +
77A GLU 4.3 4.6 + - - -
78A GLU* 3.3 62.4 + - - +
80A GLN* 4.4 8.5 + - - +
204A ARG* 2.8 62.9 + - + +
205A SER* 3.6 12.4 + - - +
207A ALA* 1.3 76.1 - - + +
209A GLY* 1.3 58.4 + - - +
211A ARG* 3.4 14.0 + - - +
212A LEU* 3.1 23.0 + - - +
302A SO4 3.2 46.0 + - - +
305A SO4 4.5 4.8 + - - -
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Residues in contact with GLY 209 (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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74A LEU* 3.9 15.5 - - - +
97A HIS* 5.7 0.4 - - - -
98A ALA* 3.1 30.3 - - - +
205A SER 3.0 14.7 + - - -
206A TYR 3.2 3.6 + - - -
208A ARG* 1.3 76.4 - - - +
210A LEU* 1.3 62.1 + - - +
212A LEU* 3.4 3.8 + - - +
213A GLU* 3.2 22.9 + - - +
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Residues in contact with LEU 210 (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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98A ALA 3.7 13.7 - - - +
99A SER* 3.7 23.8 - - - -
100A LEU* 4.1 18.2 - - + +
206A TYR* 2.9 48.1 + - + +
207A ALA* 3.7 8.3 - - - +
209A GLY* 1.3 73.2 - - - +
211A ARG* 1.3 66.1 + - - +
213A GLU* 3.5 4.2 + - + +
214A LEU* 3.1 25.4 + - - +
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Residues in contact with ARG 211 (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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78A GLU* 2.7 33.6 + - - -
207A ALA* 2.8 19.6 + - - +
208A ARG* 3.5 14.4 - - - +
210A LEU* 1.3 78.5 - - - +
212A LEU* 1.3 64.2 + - - +
214A LEU* 3.3 7.4 + - - +
215A THR* 3.2 37.6 + - + +
302A SO4 2.4 42.4 + - - -
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Residues in contact with LEU 212 (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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71A GLY* 3.6 21.3 - - - +
72A HIS* 3.7 7.6 - - - +
73A VAL 3.5 43.5 - - - +
74A LEU* 3.8 16.8 - - + +
75A PRO* 5.1 6.7 - - + -
97A HIS* 6.1 0.9 - - - -
208A ARG 3.1 17.6 + - - +
209A GLY* 3.7 4.9 - - - +
210A LEU 3.3 0.2 - - - -
211A ARG* 1.3 78.5 - - - +
213A GLU* 1.3 67.3 + - - +
215A THR* 2.9 25.1 + - - +
216A THR* 3.0 18.4 + - - +
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Residues in contact with GLU 213 (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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36A VAL* 4.2 2.8 - - + +
71A GLY 4.5 0.7 - - - -
72A HIS* 2.2 47.7 + - + +
97A HIS* 3.1 35.7 + - + -
98A ALA 4.4 5.7 + - - +
99A SER* 4.2 16.6 - - - -
209A GLY 3.2 16.0 + - - +
210A LEU* 4.0 5.2 - - + +
211A ARG 3.4 0.2 - - - -
212A LEU* 1.3 84.4 - - - +
214A LEU* 1.3 60.1 + - - +
216A THR* 4.2 3.1 - - - -
217A TYR* 3.2 24.4 + - - +
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Residues in contact with LEU 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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210A LEU 3.1 18.4 + - - +
211A ARG* 3.6 7.9 - - - +
212A LEU 3.1 0.4 - - - -
213A GLU* 1.3 76.4 - - - +
215A THR* 1.3 65.9 + - + +
217A TYR* 3.5 5.5 + - + +
218A LEU* 3.2 52.7 + - + +
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Residues in contact with THR 215 (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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211A ARG* 3.2 24.3 + - + +
212A LEU* 2.9 17.3 + - - +
214A LEU* 1.3 74.8 - - + +
216A THR* 1.3 65.7 + - - +
218A LEU* 2.9 7.8 + - - +
219A PHE* 2.4 41.3 + - - +
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Residues in contact with THR 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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70A PRO 4.7 2.5 - - - +
71A GLY* 2.6 40.2 + - - +
72A HIS* 4.0 21.5 - - + +
212A LEU* 3.0 18.6 + - - +
213A GLU* 4.2 4.5 - - - -
215A THR* 1.3 80.9 + - - +
217A TYR* 1.3 62.6 + - - +
218A LEU 3.3 0.7 + - - -
219A PHE* 3.5 40.8 + - + +
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Residues in contact with TYR 217 (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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29A TRP* 3.2 42.5 + + - -
213A GLU 3.2 17.8 + - - +
214A LEU* 3.7 7.6 - - + +
215A THR 3.2 0.6 - - - -
216A THR* 1.3 79.5 - - - +
218A LEU* 1.3 73.4 + - + +
219A PHE* 5.3 1.3 - - - -
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Residues in contact with LEU 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 LEU* 3.2 40.8 + - + +
215A THR* 2.9 7.2 + - - +
217A TYR* 1.3 102.2 - - + +
219A PHE* 1.3 73.0 + - - +
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Residues in contact with PHE 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 THR* 2.4 22.3 + - - +
216A THR* 3.5 33.2 + - + -
217A TYR 5.7 1.3 - - - -
218A LEU* 1.3 83.7 - - - +
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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
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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