Contacts of the helix formed by residues 200 - 225 (chain A) in PDB entry 3KSY
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 THR 200 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A GLU* 3.9 15.8 - - + +
199A GLN* 1.3 78.1 - - - +
201A TYR* 1.3 63.6 + - - +
202A TYR* 4.3 4.6 - - - +
203A ASP* 3.0 30.1 + - - +
204A LEU* 3.4 20.5 + - - +
363A LYS* 5.2 0.2 - - - -
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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
----------------------------------------------------------
199A GLN 3.8 1.2 + - - -
200A THR* 1.3 73.7 - - - +
202A TYR* 1.3 59.2 + - - +
204A LEU* 3.1 27.8 - - + +
205A VAL* 3.4 12.2 - - + +
276A HIS* 3.0 48.2 - + + -
277A PRO* 4.0 7.2 + - + -
279A VAL* 3.8 18.6 - - + +
359A GLN 4.7 0.4 - - - -
360A LEU* 3.5 45.9 - - + +
363A LYS* 3.1 40.1 - - + +
364A SER* 4.1 6.7 - - - -
365A GLU* 5.8 0.9 - - + -
369A ASP* 3.3 18.5 + - - -
373A LEU* 4.7 2.6 - - - +
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Residues in contact with TYR 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A THR* 3.3 4.1 + - - +
201A TYR* 1.3 80.9 - - - +
203A ASP* 1.3 68.9 + - - +
205A VAL* 3.3 10.8 + - + +
206A LYS* 3.3 33.1 + - + +
267A VAL* 4.6 16.0 - - + +
275A PRO 4.7 11.4 - - - +
276A HIS* 4.7 5.3 - - + +
277A PRO* 3.8 33.7 - - + -
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Residues in contact with ASP 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ARG* 4.0 15.8 + - - -
196A SER* 5.0 7.4 + - - -
198A GLU 5.3 4.0 - - - +
199A GLN* 6.0 0.4 - - - -
200A THR* 3.0 26.8 + - - +
202A TYR* 1.3 82.2 - - - +
204A LEU* 1.3 55.7 + - - +
206A LYS* 3.1 7.0 + - - +
207A ALA* 2.7 36.0 + - - +
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Residues in contact with LEU 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A GLN* 5.1 4.0 - - + +
200A THR 3.4 15.0 + - - +
201A TYR* 3.1 24.0 - - - +
203A ASP* 1.3 78.4 - - - +
205A VAL* 1.3 80.7 + - + +
207A ALA* 3.6 7.6 - - - +
208A PHE* 2.8 31.6 + - + +
356A LEU* 4.4 17.9 - - + +
359A GLN* 4.3 35.2 - - + +
360A LEU* 3.4 32.3 - - + -
363A LYS* 5.0 4.7 - - + -
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Residues in contact with VAL 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A TYR* 3.4 31.9 - - + +
202A TYR* 3.3 11.8 + - + +
203A ASP 3.1 0.6 - - - -
204A LEU* 1.3 85.8 - - + +
206A LYS* 1.3 59.9 + - - +
208A PHE* 3.3 5.6 + - + +
209A MET* 2.9 53.4 + - + +
263A ILE* 4.5 14.1 - - + -
267A VAL* 4.4 15.3 - - + -
277A PRO* 5.6 6.7 - - + -
279A VAL* 4.6 14.1 - - + -
360A LEU* 4.9 2.9 - - + -
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Residues in contact with LYS 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ARG* 3.4 15.5 + - - +
155A TYR* 4.2 24.4 + - - -
202A TYR* 3.3 25.1 + - + +
203A ASP* 3.1 11.5 + - - +
205A VAL* 1.3 78.8 - - - +
207A ALA* 1.3 60.1 + - - +
209A MET* 3.8 13.7 + - + +
210A ALA* 3.3 16.8 + - - +
213A ARG* 4.6 19.6 + - - +
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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
----------------------------------------------------------
153A ARG* 3.3 28.3 + - - +
203A ASP* 2.7 25.1 + - - +
204A LEU* 3.6 9.6 - - - +
206A LYS* 1.3 72.4 - - - +
208A PHE* 1.3 65.4 + - - +
209A MET 3.2 0.2 - - - -
210A ALA* 3.0 5.5 + - - +
211A GLU* 2.9 29.5 + - + +
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Residues in contact with PHE 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LEU* 2.8 22.8 + - + +
205A VAL* 3.8 4.7 - - + +
207A ALA* 1.3 72.9 - - - +
209A MET* 1.3 67.7 + - + +
211A GLU* 3.0 11.2 + - + +
212A ILE* 2.8 40.6 + - + +
259A LEU* 3.7 23.3 - - + -
263A ILE* 5.1 8.3 - - + -
283A PHE* 5.4 10.1 - + - -
349A HIS* 4.7 8.5 - + - -
352A HIS* 4.2 16.2 - + - -
353A TYR* 3.4 50.0 - + - -
356A LEU* 3.6 31.6 - - + -
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Residues in contact with MET 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A VAL* 2.9 33.0 + - - +
206A LYS* 4.0 14.8 - - + +
208A PHE* 1.3 79.1 - - + +
210A ALA* 1.3 58.9 + - - +
212A ILE* 3.3 13.5 - - + +
213A ARG* 2.8 60.6 + - - +
260A LEU* 4.3 0.6 - - + +
263A ILE* 3.7 39.3 - - + +
264A GLU* 3.5 28.9 - - + -
267A VAL* 4.2 11.2 - - + -
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Residues in contact with ALA 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ARG* 3.9 28.0 - - + +
155A TYR* 4.1 11.9 - - - +
206A LYS 3.3 13.0 + - - +
207A ALA 3.0 9.9 + - - +
209A MET* 1.3 80.1 - - - +
211A GLU* 1.3 64.7 + - + +
213A ARG* 3.5 12.8 + - - +
214A GLN* 3.5 18.9 + - - +
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Residues in contact with GLU 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ARG* 5.2 9.5 + - - -
207A ALA* 2.9 24.0 + - + +
208A PHE* 3.0 13.9 + - + +
210A ALA* 1.3 76.3 - - - +
212A ILE* 1.3 60.7 + - - +
213A ARG 3.1 1.6 - - - -
214A GLN* 3.1 11.2 + - - +
215A TYR* 2.8 27.9 + - - +
349A HIS* 5.0 5.4 - - + +
352A HIS* 5.6 9.6 - - + +
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Residues in contact with ILE 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A PHE* 2.8 29.5 + - + +
209A MET* 3.3 19.1 - - + +
211A GLU* 1.3 72.0 - - - +
213A ARG* 1.3 60.6 + - - +
215A TYR* 3.9 6.5 - - + -
216A ILE* 2.9 46.3 + - + +
256A SER* 3.4 30.1 - - - +
259A LEU* 3.7 26.9 - - + -
260A LEU* 3.6 22.7 - - + -
263A ILE* 5.4 0.7 - - + -
349A HIS* 4.2 15.4 - - + -
353A TYR* 4.1 11.7 - - - +
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Residues in contact with ARG 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ARG* 3.6 29.5 + - - +
155A TYR* 5.3 2.2 + - - -
206A LYS* 4.6 17.1 + - - +
209A MET* 2.8 67.8 + - - +
210A ALA* 3.5 16.1 - - - +
211A GLU 3.1 0.8 - - - -
212A ILE* 1.3 77.8 - - - +
214A GLN* 1.3 61.8 + - - +
216A ILE* 3.6 9.0 + - - +
217A ARG* 3.2 16.8 + - - +
260A LEU* 4.3 14.4 - - + -
264A GLU* 2.9 28.6 + - - -
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Residues in contact with GLN 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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150A ARG* 3.2 21.6 + - - +
151A ASN* 2.9 48.2 + - - +
210A ALA 3.5 10.1 + - - +
211A GLU* 3.1 13.6 + - - +
213A ARG* 1.3 75.4 - - - +
215A TYR* 1.3 67.5 + - - +
217A ARG* 3.1 14.3 + - - +
218A GLU* 3.0 49.2 + - - +
551A GLU* 5.4 4.6 + - - -
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Residues in contact with TYR 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A GLU 2.8 15.3 + - - +
212A ILE* 3.5 5.6 - - + +
214A GLN* 1.3 76.9 - - - +
216A ILE* 1.3 63.6 + - - +
218A GLU* 2.9 30.4 + - - +
219A LEU* 2.9 40.6 + - + +
252A ILE* 3.2 15.9 - - - +
256A SER* 3.2 26.9 - - - -
295A TYR* 3.5 3.0 + - - -
345A ALA* 4.1 5.8 - - + -
346A PRO* 3.1 39.3 - - + +
349A HIS* 3.4 55.9 - + + +
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Residues in contact with ILE 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ILE* 2.9 31.7 + - + +
213A ARG* 3.9 6.5 - - - +
215A TYR* 1.3 72.4 - - + +
217A ARG* 1.3 61.9 + - - +
219A LEU* 3.3 9.3 + - - +
220A ASN* 3.0 38.5 + - - +
253A HIS* 4.0 16.2 - - + +
256A SER* 3.6 45.8 - - - +
257A VAL* 3.8 13.7 - - + +
260A LEU* 3.9 19.3 - - + -
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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
----------------------------------------------------------
147A ASN* 3.4 31.7 + - - +
150A ARG* 3.4 29.7 - - - +
151A ASN* 5.0 4.8 + - - +
213A ARG 3.2 12.9 + - - +
214A GLN* 3.1 22.5 + - - +
215A TYR 3.1 0.6 - - - -
216A ILE* 1.3 78.6 - - - +
218A GLU* 1.3 62.1 + - + +
220A ASN* 3.4 7.9 + - - +
221A LEU* 3.1 20.8 + - - +
551A GLU* 2.7 32.4 + - - +
554A LEU* 3.7 17.5 - - + +
555A ASP* 3.1 28.0 + - - -
558A MET* 6.3 0.6 - - - +
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Residues in contact with GLU 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A GLN* 3.0 38.6 + - - +
215A TYR* 2.9 17.6 + - + +
217A ARG* 1.3 73.8 - - + +
219A LEU* 1.3 67.0 + - + +
221A LEU* 3.1 16.1 + - + +
222A ILE* 3.0 32.8 + - + +
342A LEU* 6.4 3.4 - - + -
345A ALA* 3.8 24.5 - - + +
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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
----------------------------------------------------------
215A TYR* 2.9 64.0 + - + +
216A ILE* 3.4 14.6 - - - +
218A GLU* 1.3 77.2 - - + +
220A ASN* 1.3 56.6 + - - +
222A ILE* 2.9 11.0 + - + +
223A ILE* 2.8 36.7 + - + +
249A ILE* 4.2 24.0 - - + +
252A ILE* 4.4 1.8 - - + +
253A HIS* 3.7 40.6 - - + +
256A SER* 4.0 5.8 - - - +
345A ALA* 6.2 0.9 - - + -
346A PRO* 4.5 4.0 - - + -
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Residues in contact with ASN 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A ILE* 3.0 20.3 + - - +
217A ARG* 3.7 8.4 - - - +
218A GLU 3.3 0.2 - - - -
219A LEU* 1.3 75.1 - - - +
221A LEU* 1.3 58.0 + - - +
223A ILE* 4.4 6.6 - - - +
224A LYS* 2.8 43.2 + - + +
225A VAL 3.9 0.2 + - - -
253A HIS* 2.9 35.3 + - - -
554A LEU* 3.7 16.8 - - + +
558A MET* 3.5 29.1 - - + +
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Residues in contact with LEU 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ARG 3.1 12.5 + - - +
218A GLU* 3.1 17.7 + - + +
219A LEU 3.1 0.4 - - - -
220A ASN* 1.3 79.1 - - - +
222A ILE* 1.3 58.5 + - + +
225A VAL* 3.0 47.2 - - + +
226A PHE* 3.1 15.9 - - + -
342A LEU* 4.9 11.2 - - + -
550A LEU* 3.6 50.9 - - + +
551A GLU* 4.3 17.3 - - - +
554A LEU* 3.8 13.7 - - + +
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Residues in contact with ILE 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A GLU* 3.0 22.4 + - + +
219A LEU* 2.9 14.6 + - + +
221A LEU* 1.3 78.3 - - + +
223A ILE* 1.3 59.6 + - + +
226A PHE* 3.3 10.3 - - + +
227A ARG* 2.8 26.2 + - - +
246A PHE* 3.8 15.0 - - + -
249A ILE* 4.4 19.1 - - + -
339A LEU* 4.3 6.1 - - + -
342A LEU* 3.3 46.7 - - + +
343A LEU* 3.6 28.0 - - + -
345A ALA* 5.7 1.1 - - + -
346A PRO* 5.5 2.2 - - + -
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Residues in contact with ILE 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A LEU* 2.8 22.6 + - + +
220A ASN* 4.2 5.2 - - - +
222A ILE* 1.3 80.9 - - - +
224A LYS* 1.3 70.5 + - + +
225A VAL 3.4 0.2 - - - -
227A ARG* 3.2 17.0 + - - +
228A GLU* 3.0 27.0 + - - +
249A ILE* 4.3 21.5 - - + +
250A VAL* 4.2 28.5 - - + -
253A HIS* 3.8 37.0 - - + +
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Residues in contact with LYS 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ASN* 2.8 30.1 + - + +
223A ILE* 1.3 85.3 - - + +
225A VAL* 1.3 62.3 + - - +
228A GLU* 3.5 23.5 - - - +
253A HIS* 5.8 4.8 + - - -
554A LEU* 4.7 4.0 - - + -
557A THR* 4.0 24.6 + - + +
558A MET* 3.2 39.4 - - - +
561A GLU* 2.8 39.1 + - - +
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Residues in contact with VAL 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A LEU* 3.0 34.4 + - + +
223A ILE 3.4 0.2 - - - -
224A LYS* 1.3 86.0 - - - +
226A PHE* 1.3 60.6 + - + +
229A PRO* 3.2 22.5 - - - +
331A PHE* 3.7 15.5 - - + -
550A LEU* 3.6 30.1 - - + -
553A MET* 4.5 22.6 - - + +
554A LEU* 3.9 30.5 - - + +
557A THR* 5.1 0.9 - - - +
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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