Contacts of the helix formed by residues 325 - 346 (chain D) in PDB entry 1CX2
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 325 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245D ARG* 3.4 10.8 + - - -
247D PHE* 3.0 35.6 + - - +
248D LYS* 2.7 33.2 + - - +
249D ASP 4.1 5.5 - - - +
250D GLY* 2.8 37.3 + - - +
324D GLY* 1.3 70.2 - - - +
326D GLU* 1.3 66.8 + - - +
327D GLN 2.9 0.7 + - - -
328D LEU* 3.1 0.8 + - - +
329D PHE* 2.8 22.5 + - - +
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Residues in contact with GLU 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C TYR* 3.3 20.5 + - - -
136C TYR* 3.5 12.6 + - - +
238D LEU* 5.7 1.6 - - - +
242D HIS* 4.7 7.6 - - - -
245D ARG* 3.6 30.5 + - - +
247D PHE* 5.7 1.6 - - + -
324D GLY 3.3 0.8 - - - -
325D ASP* 1.3 80.6 + - - +
327D GLN* 1.3 62.1 + - - +
330D GLN* 3.0 43.5 + - - +
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Residues in contact with GLN 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C MET* 3.3 27.6 - - - +
49C SER* 4.8 0.3 + - - -
136C TYR* 2.8 48.5 + - + +
323D TRP* 3.2 48.3 + - + -
324D GLY* 2.9 14.4 + - - +
326D GLU* 1.3 74.6 - - - +
328D LEU* 1.3 56.2 - - - +
330D GLN* 3.2 2.3 + - - +
331D THR* 2.7 46.1 + - - +
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Residues in contact with LEU 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D ASP* 3.5 31.2 - - - +
250D GLY* 3.6 13.7 - - - +
313D CYS* 3.8 4.0 - - - +
316D LEU* 3.3 32.1 - - + +
317D LYS* 3.5 30.1 - - + +
320D HIS 5.3 0.7 - - - +
323D TRP* 3.5 33.7 - - + +
324D GLY 3.1 16.2 + - - +
325D ASP 3.1 1.1 + - - +
327D GLN* 1.3 73.9 - - - +
329D PHE* 1.3 67.3 + - - +
331D THR* 3.9 2.2 - - - -
332D SER* 2.9 29.8 + - - -
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Residues in contact with PHE 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D TYR* 3.8 32.5 - + + -
241D GLN* 2.8 44.2 - - + -
245D ARG* 3.2 46.4 - - + +
250D GLY* 3.5 23.3 - - - +
252D LEU* 4.5 6.7 - - + -
309D HIS* 3.8 9.7 - - - -
325D ASP 2.8 15.9 + - - +
326D GLU 3.8 2.5 - - - +
328D LEU* 1.3 78.8 - - - +
330D GLN* 1.3 81.7 + - + +
332D SER* 3.3 2.1 + - - -
333D LYS* 3.2 31.0 + - + +
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Residues in contact with GLN 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C TYR* 3.9 9.8 + - + -
136C TYR* 4.4 6.7 - - + +
138C SER* 3.4 20.0 + - - -
139C TRP* 3.2 29.5 + - - +
140C GLU* 3.4 25.3 + - - +
238D LEU* 6.1 1.0 - - - +
241D GLN* 4.1 7.5 - - - +
326D GLU* 3.0 39.7 + - - +
327D GLN 3.8 2.7 - - - +
329D PHE* 1.3 101.2 - - + +
331D THR* 1.3 61.5 + - - +
333D LYS* 4.1 5.9 + - - +
334D LEU* 3.6 23.9 + - - +
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Residues in contact with THR 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C TYR* 5.4 1.7 - - - -
316D LEU* 3.8 16.4 - - + -
323D TRP* 3.5 14.1 - - + -
327D GLN* 2.7 31.9 + - - +
328D LEU 4.0 0.4 - - - -
330D GLN* 1.3 75.5 - - - +
332D SER* 1.3 67.5 + - - +
334D LEU* 3.1 12.8 + - - +
335D ILE* 3.1 19.5 + - + +
549D THR 4.0 4.3 - - - +
550D PHE* 3.2 13.7 - - - +
551D GLY* 3.1 37.9 - - - +
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Residues in contact with SER 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D TYR* 4.1 2.0 - - - -
309D HIS* 3.2 28.5 - - - -
312D VAL* 3.9 10.4 - - - +
313D CYS* 3.3 30.1 + - - -
316D LEU* 3.7 11.9 - - - +
328D LEU 2.9 19.7 + - - -
329D PHE 3.3 0.4 + - - -
331D THR* 1.3 72.5 - - - +
333D LYS* 1.3 66.1 + - - +
335D ILE* 2.8 15.8 + - - +
336D LEU* 2.9 15.1 + - - +
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Residues in contact with LYS 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C TRP* 3.9 38.4 - - + +
229D ASP* 3.2 29.5 + - - +
230D LEU 4.6 1.0 + - - -
231D ASN* 4.7 3.4 - - - +
234D TYR* 3.2 60.5 + - + +
235D GLY 5.4 1.8 + - - -
241D GLN* 5.9 2.2 - - - +
329D PHE* 3.2 22.2 + - + +
330D GLN* 4.3 8.3 - - - +
331D THR 3.5 0.2 - - - -
332D SER* 1.3 77.6 - - - +
334D LEU* 1.3 56.9 + - - +
336D LEU* 3.9 1.6 - - - +
337D ILE* 2.8 43.0 + - + +
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Residues in contact with LEU 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C LYS* 4.6 1.1 - - + -
138C SER 4.3 19.7 - - - +
139C TRP* 4.4 30.3 - - + +
330D GLN 3.6 15.9 - - - +
331D THR* 3.1 10.8 + - - +
332D SER 2.9 0.6 + - - -
333D LYS* 1.3 76.9 - - - +
335D ILE* 1.3 60.9 + - - +
337D ILE* 3.4 6.4 + - + +
338D GLY* 2.9 24.4 + - - -
539D ILE* 3.9 26.5 - - + +
544D TYR* 5.2 6.5 - - + -
549D THR* 3.3 37.2 - - + +
550D PHE* 3.7 18.2 - - + -
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Residues in contact with ILE 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312D VAL* 3.9 27.1 - - + -
316D LEU* 4.0 11.2 - - + -
331D THR 3.1 8.6 + - - +
332D SER 2.8 13.0 + - - +
334D LEU* 1.3 70.3 - - - +
336D LEU* 1.3 50.0 + - - +
338D GLY* 2.7 22.7 + - - -
339D GLU* 2.8 20.7 + - - +
550D PHE* 3.2 42.0 - - + +
555D GLY* 3.3 19.3 - - - -
558D ILE* 3.6 24.2 - - + -
559D ILE* 3.4 20.2 - - + +
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Residues in contact with LEU 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D LEU* 4.7 7.6 - - + -
233D ILE* 4.1 23.3 - - + -
234D TYR* 3.3 23.1 - - + +
305D TRP* 4.3 17.6 - - + +
308D GLU* 3.9 7.6 - - + -
309D HIS* 4.0 24.9 - - + +
312D VAL* 3.6 24.9 - - + -
332D SER 2.9 20.1 + - - +
333D LYS 3.9 4.3 - - - +
335D ILE* 1.3 70.2 - - - +
337D ILE* 1.3 52.7 + - - +
339D GLU* 2.9 25.9 + - - +
340D THR* 2.7 38.2 + - - -
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Residues in contact with ILE 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C TRP* 4.1 26.0 - - + -
228D VAL* 3.7 24.9 - - + +
229D ASP 4.2 10.3 - - - +
230D LEU* 3.5 26.4 - - + +
333D LYS* 2.8 41.9 + - + +
334D LEU* 3.6 9.2 - - + +
336D LEU* 1.3 74.9 - - - +
338D GLY* 1.3 57.9 + - - +
340D THR* 3.2 4.0 + - - -
341D ILE* 2.9 37.4 + - + +
537D ASN* 4.4 11.7 - - - +
539D ILE* 4.3 13.2 - - + -
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Residues in contact with GLY 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334D LEU 2.9 7.4 + - - -
335D ILE 2.7 15.5 + - - -
337D ILE* 1.3 71.9 - - - +
339D GLU* 1.3 61.0 + - - +
341D ILE* 3.3 2.9 + - - -
342D LYS 3.3 13.0 + - - -
361D PHE* 3.6 5.1 - - - -
539D ILE* 3.5 20.2 - - - -
559D ILE* 3.3 32.9 - - - +
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Residues in contact with GLU 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305D TRP* 4.8 8.0 - - + -
308D GLU* 2.9 29.3 - - - +
311D ARG* 5.2 0.2 + - - -
312D VAL* 4.3 1.2 - - - +
335D ILE* 2.8 17.3 + - - +
336D LEU* 2.9 39.0 + - - +
338D GLY* 1.3 71.3 - - - +
340D THR* 1.3 56.6 + - - +
342D LYS* 2.6 24.6 + - - +
343D ILE* 2.9 19.9 + - + +
558D ILE* 3.6 29.8 - - + +
559D ILE* 3.8 6.0 - - - +
562D ALA* 3.8 24.9 - - + +
567D LEU* 4.7 3.7 - - - +
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Residues in contact with THR 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D PHE* 5.5 1.8 - - + -
205D PHE* 3.8 32.3 - - + -
228D VAL* 4.2 11.7 - - + -
230D LEU* 3.6 19.7 - - + +
232D HIS* 5.9 0.9 - - - +
305D TRP* 3.4 29.4 - - + -
336D LEU 2.7 18.7 + - - -
337D ILE* 3.4 11.9 - - - -
339D GLU* 1.3 72.8 - - - +
341D ILE* 1.3 63.8 + - - +
343D ILE* 4.6 3.4 - - - +
344D VAL* 2.9 26.6 + - + +
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Residues in contact with ILE 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D VAL* 4.7 10.1 - - + -
337D ILE* 2.9 30.4 + - + +
338D GLY 3.9 0.7 - - - +
339D GLU 3.2 0.2 - - - -
340D THR* 1.3 76.2 - - - +
342D LYS* 1.3 64.1 + - - +
344D VAL* 3.9 4.3 - - - -
345D ILE* 3.3 22.7 + - + +
361D PHE* 3.3 35.3 - - + -
534D LEU* 3.4 48.9 - - + +
535D MET* 4.7 0.9 - - - -
537D ASN* 4.3 18.2 - - + +
539D ILE* 4.5 5.8 - - + -
540D CYS* 3.8 13.7 - - - -
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Residues in contact with LYS 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338D GLY 3.3 6.4 + - - +
339D GLU 2.6 16.4 + - - +
341D ILE* 1.3 69.1 - - - +
343D ILE* 1.3 58.0 + - - +
345D ILE 3.0 1.6 + - - -
346D GLU* 2.7 71.4 + - + +
360D LYS* 5.9 1.0 - - - +
361D PHE* 3.7 27.5 + - + -
559D ILE 3.5 24.9 - - - +
560D ASN* 3.4 41.0 + - - +
561D THR* 3.9 2.9 - - - +
562D ALA* 3.6 24.2 - - + +
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Residues in contact with ILE 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D PHE* 3.7 23.8 - - + -
305D TRP* 4.3 12.1 - - + -
339D GLU* 2.9 18.0 + - + +
340D THR* 4.0 3.4 - - - +
342D LYS* 1.3 75.3 - - - +
344D VAL* 1.3 59.5 + - - +
345D ILE 2.8 1.9 + - - -
346D GLU* 4.8 0.2 - - - -
347D ASP* 2.7 47.9 + - + +
348D TYR 3.1 5.8 + - - -
562D ALA* 4.3 4.0 - - + -
563D SER* 3.5 43.3 - - - +
564D ILE* 3.7 15.3 - - + +
567D LEU* 4.1 23.1 - - + -
580D PHE* 4.2 3.4 - - + -
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Residues in contact with VAL 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D PHE* 3.6 28.3 - - + -
205D PHE* 3.3 51.8 - - + -
340D THR* 2.9 20.5 + - + +
341D ILE* 4.3 2.9 - - - +
343D ILE* 1.3 74.0 - - - +
345D ILE* 1.3 56.5 + - - +
348D TYR* 3.7 17.0 - - + -
349D VAL* 2.8 24.4 + - + +
530D SER* 5.6 1.8 - - - +
534D LEU* 4.1 20.6 - - + -
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Residues in contact with ILE 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D MET* 4.6 9.0 - - + -
117D LEU* 5.4 1.1 - - + -
341D ILE* 3.3 22.6 + - + +
342D LYS 3.0 2.5 + - - +
343D ILE 2.8 1.8 + - - -
344D VAL* 1.3 75.2 - - - +
346D GLU* 1.3 63.5 + - - +
347D ASP 3.3 1.3 - - - -
349D VAL* 3.5 9.1 - - + +
350D GLN* 3.0 28.4 + - - +
359D LEU* 3.8 24.4 - - + +
360D LYS 4.2 4.9 - - - +
361D PHE* 4.2 27.4 - - + +
531D LEU* 3.8 19.1 - - + -
534D LEU* 3.3 35.4 - - + -
535D MET* 5.3 6.7 - - - -
701D S58 6.2 0.2 - - - -
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Residues in contact with GLU 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D ARG* 3.5 9.6 + - - -
342D LYS* 2.7 58.1 + - + +
343D ILE* 4.8 0.2 - - - -
345D ILE* 1.3 72.3 - - - +
347D ASP* 1.3 64.4 + - - +
350D GLN* 3.1 20.4 + - - +
358D LYS* 5.1 2.3 - - - +
359D LEU 2.6 26.9 - - - +
360D LYS* 3.5 8.4 - - - +
361D PHE* 3.2 26.2 + - + +
562D ALA 5.3 3.1 - - - +
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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