Contacts of the helix formed by residues 250 - 273 (chain A) in PDB entry 2YEV
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 HIS 250 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A TRP* 3.0 13.8 + - - +
249A SER* 1.3 75.2 - - - +
251A PRO* 1.4 74.3 - - + +
252A THR 2.9 1.8 - - - -
253A VAL* 2.8 32.6 + - + +
254A TYR* 1.3 81.9 + + - -
293A GLY 3.4 12.6 - - - -
296A VAL* 3.6 12.5 - - + +
297A TRP* 4.2 13.9 - - - -
299A HIS* 3.2 29.4 + + - -
300A HIS* 4.1 13.7 + - - +
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Residues in contact with PRO 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LEU* 3.6 15.6 - - + +
208A SER* 3.3 28.3 - - - +
246A TRP 3.7 2.5 - - - +
247A PHE 3.1 25.4 - - - +
248A TYR 3.0 10.5 - - - +
250A HIS* 1.4 94.3 - - + +
252A THR* 1.3 57.3 + - - +
254A TYR* 3.0 6.5 + - + -
255A VAL* 2.9 31.3 + - - +
293A GLY 3.3 22.4 - - - +
294A THR* 4.4 7.4 - - + -
297A TRP* 5.2 2.5 - - + -
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Residues in contact with THR 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 6.0 0.2 - - + -
79A PHE* 5.4 3.9 - - + -
83A ILE* 3.4 11.6 - - - +
139A TRP* 4.9 9.9 - - + -
248A TYR* 2.8 49.4 + - + -
249A SER* 3.3 26.7 - - - +
250A HIS 2.8 1.6 + - - -
251A PRO* 1.3 76.6 - - - +
253A VAL* 1.3 63.8 + - + +
255A VAL* 3.1 10.3 + - - +
256A MET* 2.8 49.3 + - + +
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Residues in contact with VAL 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 6.0 2.0 - - + -
139A TRP* 6.2 1.8 - - + -
249A SER 3.9 12.6 - - - +
250A HIS* 2.8 33.8 + - + +
252A THR* 1.3 77.4 - - + +
254A TYR* 1.3 80.2 + - + +
256A MET* 3.2 18.9 + - + +
257A LEU* 3.0 25.5 + - - +
300A HIS* 6.3 1.8 - - + +
390A LEU* 5.4 12.2 - - + +
394A SER* 5.4 0.2 + - - -
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Residues in contact with TYR 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LEU* 3.9 12.6 - - + -
250A HIS* 1.3 77.0 + + - -
251A PRO* 3.0 8.2 + - + +
253A VAL* 1.3 82.0 - - + +
255A VAL* 1.3 60.8 + - - +
256A MET 3.1 1.3 - - - -
257A LEU* 4.1 20.4 - - + +
258A LEU* 3.0 39.0 + - - +
289A ILE* 3.8 27.1 - - + -
293A GLY* 4.2 12.8 - - - -
296A VAL* 5.0 0.2 - - - +
299A HIS* 5.1 0.7 - - - -
318A THR* 5.9 1.7 - - - +
321A ILE* 3.4 39.8 - - + +
325A THR* 5.2 2.5 - - - -
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Residues in contact with VAL 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ILE* 3.9 18.0 - - + +
87A LEU* 4.1 16.1 - - + +
201A ALA* 3.8 22.8 - - + +
204A LEU* 3.7 23.3 - - + -
205A ASN* 3.7 36.1 - - + +
248A TYR* 5.2 0.4 - - + -
251A PRO* 2.9 20.1 + - + +
252A THR* 3.1 11.6 + - - +
254A TYR* 1.3 78.9 - - - +
256A MET* 1.3 54.3 + - - +
259A PRO* 3.2 24.9 - - - +
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Residues in contact with MET 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 3.6 45.8 - - + +
79A PHE* 5.9 2.0 - - + -
82A ILE* 3.4 28.5 - - + -
83A ILE* 3.9 16.6 - - + +
252A THR* 2.8 47.4 + - + +
253A VAL* 3.4 17.5 - - - +
254A TYR 3.1 0.4 - - - -
255A VAL* 1.3 76.5 - - - +
257A LEU* 1.3 51.4 + - - +
259A PRO* 4.4 1.1 - - - -
260A TYR* 2.7 39.0 - - - -
390A LEU* 3.8 18.8 - - + -
394A SER* 3.3 9.6 + - - +
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Residues in contact with LEU 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A VAL 3.0 15.8 + - - +
254A TYR* 3.2 25.7 + - + +
256A MET* 1.3 79.6 - - - +
258A LEU* 1.3 68.5 + - + +
259A PRO 3.4 0.7 - - - -
260A TYR* 2.9 16.2 + - + +
261A LEU* 3.0 34.7 + - + +
289A ILE* 5.2 4.3 - - + -
325A THR* 4.7 10.1 - - + +
353A PHE* 4.0 18.2 - - + -
357A PHE* 3.7 37.9 - - + -
389A VAL 5.3 1.3 - - - +
394A SER* 4.2 11.9 - - - +
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Residues in contact with LEU 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A SER* 3.3 19.3 - - - +
200A ALA* 4.0 9.4 - - + +
201A ALA* 4.1 10.8 - - + +
204A LEU* 4.6 4.3 - - + -
254A TYR* 3.0 22.9 + - + +
257A LEU* 1.3 76.3 - - + +
259A PRO* 1.3 71.0 - - + +
261A LEU* 3.1 13.1 + - + +
262A GLY 2.9 17.8 + - - -
286A GLN* 3.9 35.1 - - + +
289A ILE* 4.0 31.9 - - + -
290A VAL* 4.0 26.7 - - + -
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Residues in contact with PRO 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLY* 3.5 26.7 - - - +
87A LEU* 4.0 18.6 - - + -
194A TYR* 3.7 6.1 - - + -
197A SER* 3.5 14.4 - - - +
198A VAL* 4.9 0.9 - - + -
201A ALA* 3.7 16.2 - - + -
255A VAL 3.2 24.0 - - - +
256A MET 4.4 2.0 - - - -
257A LEU 3.6 2.7 - - - +
258A LEU* 1.3 93.3 - - + +
260A TYR* 1.3 61.6 + - + +
262A GLY* 3.2 2.6 + - - -
263A ILE* 2.9 31.7 + - - +
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Residues in contact with TYR 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ILE* 2.6 38.9 + - + +
85A ALA* 3.7 6.4 - - - +
86A GLY* 3.0 33.9 + - - -
256A MET* 2.7 31.0 - - - -
257A LEU* 2.9 7.1 + - - +
259A PRO* 1.3 76.7 - - + +
261A LEU* 1.3 61.9 + - - +
263A ILE* 3.2 13.5 + - + +
264A LEU* 2.8 34.9 + - - +
353A PHE* 4.5 6.3 - - + -
394A SER* 3.7 27.1 - - - +
397A GLY* 3.5 13.7 - - - -
398A ALA* 3.4 39.8 - - + +
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Residues in contact with LEU 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A LEU* 3.0 42.5 + - + +
258A LEU* 3.1 14.1 + - + +
260A TYR* 1.3 74.8 - - - +
262A GLY* 1.3 62.3 + - - +
264A LEU* 3.3 8.7 + - + +
265A ALA* 3.0 23.0 + - - +
286A GLN* 6.0 0.2 - - + -
289A ILE* 4.6 15.3 - - + -
325A THR* 5.0 4.9 - - + -
328A LYS* 3.9 32.5 + - + +
329A LEU* 4.2 18.2 - - + -
332A ILE* 3.9 8.5 - - + +
353A PHE* 3.9 29.6 - - + -
357A PHE* 5.5 2.2 - - + -
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Residues in contact with GLY 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ILE* 3.7 5.0 - - - +
194A TYR* 4.2 10.5 - - - -
197A SER* 3.6 20.4 - - - -
258A LEU 2.9 10.3 + - - -
259A PRO 3.5 4.7 - - - -
260A TYR 3.1 0.2 - - - -
261A LEU* 1.3 77.3 - - - +
263A ILE* 1.3 61.4 + - - +
265A ALA* 3.2 4.9 + - - +
266A GLU* 3.0 28.6 + - - +
328A LYS* 4.2 6.8 - - - +
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Residues in contact with ILE 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLY* 4.3 2.9 - - - -
90A PHE* 4.0 25.8 - - + -
194A TYR* 3.6 20.9 - - + -
259A PRO 2.9 19.5 + - - +
260A TYR* 3.2 30.5 + - + +
262A GLY* 1.3 72.4 - - - +
264A LEU* 1.3 66.7 + - + +
266A GLU* 3.1 8.4 + - - +
267A VAL* 2.9 32.8 + - + +
397A GLY 4.0 7.6 - - - +
400A ALA* 4.4 4.0 - - + -
401A GLY* 3.8 26.5 - - - +
404A TYR* 5.5 0.7 - - + -
405A TRP* 3.9 13.0 - - + -
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Residues in contact with LEU 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A TYR 2.8 23.2 + - - +
261A LEU* 3.6 15.9 - - + +
262A GLY 3.3 0.2 - - - -
263A ILE* 1.3 73.8 - - + +
265A ALA* 1.3 58.3 + - - +
267A VAL* 3.4 1.6 + - - +
268A ALA* 2.9 30.5 + - - +
329A LEU* 5.0 0.2 - - + -
332A ILE* 4.0 13.9 - - + -
350A VAL* 3.7 40.7 - - + +
353A PHE* 3.3 56.8 - - + -
354A ILE* 4.6 9.4 - - + -
397A GLY* 4.3 12.3 - - - -
400A ALA* 4.6 4.5 - - + -
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Residues in contact with ALA 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ILE* 3.5 25.4 - - + -
261A LEU 3.0 13.2 + - - +
262A GLY 3.5 3.1 - - - +
263A ILE 3.1 0.2 - - - -
264A LEU* 1.3 77.8 - - - +
266A GLU* 1.3 62.1 + - - +
268A ALA* 3.3 4.6 + - - +
269A SER* 3.0 18.9 + - - -
276A LEU* 3.5 23.1 - - + +
282A MET* 4.2 9.0 - - - -
328A LYS* 4.5 1.3 - - - -
332A ILE* 4.2 19.2 - - + +
335A THR* 5.9 0.2 - - - -
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Residues in contact with GLU 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A MET* 3.9 16.5 - - + +
192A PRO* 3.2 8.9 - - - +
193A ILE* 3.0 18.5 + - + -
194A TYR* 2.9 38.2 + - + +
262A GLY 3.0 19.7 + - - +
263A ILE* 3.1 8.5 + - - +
265A ALA* 1.3 75.8 - - - +
267A VAL* 1.3 63.4 + - - +
269A SER* 3.5 6.3 + - - -
270A THR* 3.1 27.9 + - - -
276A LEU* 5.2 2.9 - - - +
404A TYR* 4.1 19.8 + - + +
405A TRP* 5.1 2.9 - - + -
503A THR* 4.1 16.3 + - - +
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Residues in contact with VAL 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ILE* 2.9 27.8 + - + +
266A GLU* 1.3 72.5 - - - +
268A ALA* 1.3 66.2 + - - +
270A THR 3.4 0.2 + - - -
271A PHE* 3.0 45.3 + - + +
346A PRO* 3.8 16.4 - - + +
347A LEU* 4.0 4.9 - - + +
350A VAL* 3.4 30.1 - - + -
400A ALA* 4.5 3.4 - - + +
404A TYR* 3.8 38.8 - - + -
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Residues in contact with ALA 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LEU 2.9 17.7 + - - +
265A ALA* 3.3 5.4 + - - +
267A VAL* 1.3 78.8 - - - +
269A SER* 1.3 61.5 + - - +
271A PHE 3.9 0.3 - - - -
272A ALA* 3.0 30.7 + - - +
332A ILE* 4.3 12.3 - - + +
335A THR* 3.9 17.0 - - + -
336A LEU* 3.7 28.0 - - + +
347A LEU* 5.0 3.4 - - - -
350A VAL* 5.0 2.7 - - + +
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Residues in contact with SER 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ALA 3.0 15.4 + - - -
266A GLU* 3.8 7.6 - - - -
267A VAL 3.3 0.2 - - - -
268A ALA* 1.3 77.1 - - - +
270A THR* 1.3 61.8 + - - +
273A ARG* 3.1 19.9 + - - -
274A LYS 2.7 31.6 + - - +
275A PRO* 4.2 1.6 - - - +
276A LEU* 4.1 22.6 + - - +
335A THR* 3.6 8.0 - - - +
502A TYR* 3.9 14.3 - - - -
529A ARG* 4.3 4.3 - - - +
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Residues in contact with THR 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A GLU* 3.1 12.7 + - - -
267A VAL 3.9 3.1 - - - -
269A SER* 1.3 78.2 - - - +
271A PHE* 1.3 65.8 + - + +
273A ARG* 2.9 30.4 + - - +
342A GLN* 5.1 0.2 - - - +
404A TYR* 2.9 31.6 + - + -
499A TRP* 3.6 37.8 - - + +
501A GLY* 3.9 21.1 - - - -
502A TYR* 4.3 12.1 + - - -
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Residues in contact with PHE 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A VAL* 3.0 36.9 + - + +
268A ALA 3.9 0.9 - - - +
270A THR* 1.3 79.5 - - + +
272A ALA* 1.3 56.8 + - - +
273A ARG 3.5 0.2 - - - -
336A LEU* 5.8 0.2 - - - -
340A LYS 3.4 1.9 - - - +
341A LEU* 3.2 4.9 - - - -
342A GLN* 2.8 62.4 + - + +
344A LYS* 3.5 26.2 - - + -
346A PRO* 3.8 24.9 - - + -
347A LEU* 4.1 16.3 - - + +
404A TYR* 3.5 26.0 - + - -
499A TRP* 3.4 46.0 - + + -
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Residues in contact with ALA 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ALA 3.0 19.7 + - - +
271A PHE* 1.3 77.5 - - - +
273A ARG* 1.3 72.0 + - - +
274A LYS* 3.1 4.0 + - - +
335A THR 3.8 20.4 - - - +
336A LEU* 4.1 4.9 - - + -
339A GLY* 3.3 9.2 - - - -
340A LYS 2.9 22.5 + - - -
341A LEU* 3.5 26.5 - - + -
74B PRO* 3.8 0.5 - - - +
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Residues in contact with ARG 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A SER 3.1 5.6 + - - -
270A THR 2.9 23.1 + - - -
272A ALA* 1.3 81.7 - - - +
274A LYS* 1.3 57.1 + - - +
340A LYS* 3.7 19.5 - - + +
342A GLN* 4.1 23.8 - - - +
499A TRP 3.5 11.9 + - - -
500A GLY* 2.8 35.9 + - - -
502A TYR* 3.1 45.5 + - - +
73B GLU* 4.7 5.4 - - + +
74B PRO* 3.3 28.1 - - + +
76B GLN* 3.3 10.4 + - - +
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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