Contacts of the helix formed by residues 420 - 442 (chain C) in PDB entry 1XVP
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 LEU 420 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356C LYS* 5.6 1.8 - - - +
416C ALA 2.9 10.9 + - - +
417C LYS* 3.7 18.8 - - + +
418C LEU 3.3 0.8 - - - -
419C LEU* 1.3 76.1 - - - +
421C ARG* 1.3 77.3 + - - +
423C PRO* 3.2 15.5 - - + +
424C ALA* 4.7 1.7 + - - +
265D MET* 3.9 18.8 - - + -
285D GLN* 2.8 40.1 - - + +
286D GLU* 4.7 16.6 - - + +
289D ALA* 4.1 4.9 - - + -
309D TYR* 3.5 24.7 - - - +
313D LEU* 3.7 9.6 - - + -
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Residues in contact with ARG 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C GLU* 3.1 41.3 + - - -
353C LEU* 4.9 11.3 - - + +
356C LYS* 3.7 40.8 - - - +
357C MET* 5.6 9.0 - - + +
360C MET* 6.4 2.0 - - - -
362C MET* 6.3 2.7 - - - -
370C LEU* 5.0 6.3 - - + -
417C LYS 4.6 7.3 + - - +
418C LEU* 3.7 16.2 - - - +
419C LEU 2.8 0.2 + - - -
420C LEU* 1.3 94.9 + - - +
422C LEU* 1.3 65.2 + - + +
424C ALA* 3.2 23.0 + - - +
425C LEU* 3.1 21.4 + - + +
270D PRO* 6.0 1.2 - - - +
278D ARG* 5.7 0.4 - - - +
282D ASP* 4.8 1.0 + - - -
285D GLN* 3.9 20.2 + - - -
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Residues in contact with LEU 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C GLU* 4.6 3.1 - - - +
370C LEU* 5.1 12.1 - - + +
373C ILE* 4.0 16.4 - - + -
374C VAL* 3.9 27.1 - - + -
393C ARG* 4.8 10.8 - - - +
397C TYR* 5.5 0.2 - - - +
419C LEU* 2.9 40.7 + - + +
421C ARG* 1.3 76.2 - - + +
423C PRO* 1.4 70.7 - - + +
425C LEU* 3.1 11.7 + - + +
426C ARG* 3.0 21.5 + - - +
310D ALA 5.2 3.4 - - - +
313D LEU* 4.5 13.7 - - + +
314D GLY* 5.1 4.3 - - - +
317D ALA* 4.4 6.6 - - + +
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Residues in contact with PRO 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419C LEU 3.9 2.2 - - - +
420C LEU* 3.2 20.2 - - + +
422C LEU* 1.4 92.6 - - + +
424C ALA* 1.3 62.4 + - - +
426C ARG* 3.1 19.6 - - - +
427C SER* 3.2 10.6 + - - -
313D LEU* 3.9 23.8 - - + +
316D LEU* 4.1 19.1 - - + -
317D ALA* 4.0 15.5 - - - +
320D ARG* 3.7 25.2 - - - +
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Residues in contact with ALA 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C GLU* 4.5 13.9 - - + -
353C LEU* 4.8 3.6 - - + -
420C LEU 4.7 1.5 + - - +
421C ARG* 3.2 30.6 + - - +
423C PRO* 1.3 79.5 - - - +
425C LEU* 1.3 62.2 + - - +
427C SER* 3.4 2.1 + - - -
428C ILE* 2.9 30.2 + - + +
271D ASP* 3.9 27.1 - - + +
320D ARG* 3.9 1.5 - - - +
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Residues in contact with LEU 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C GLU* 3.3 48.3 - - + +
310C ILE* 3.6 32.3 - - + -
311C ALA* 4.3 11.9 - - + +
353C LEU* 3.9 18.1 - - + +
374C VAL* 4.2 15.5 - - + -
421C ARG* 3.1 12.9 + - + +
422C LEU* 3.1 15.0 + - + +
424C ALA* 1.3 76.6 - - - +
426C ARG* 1.3 53.0 + - - +
428C ILE* 4.4 2.5 - - - -
429C GLY* 2.7 33.1 + - - -
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Residues in contact with ARG 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C ALA 5.9 1.2 + - - -
307C GLU* 2.8 35.8 + - - +
377C ASN* 4.4 14.5 - - - +
422C LEU 3.0 10.8 + - - +
423C PRO 3.1 11.0 - - - +
425C LEU* 1.3 75.2 - - - +
427C SER* 1.3 63.6 + - - +
429C GLY* 3.2 2.4 + - - -
430C LEU* 3.0 42.4 + - + +
314D GLY 5.7 0.6 + - - -
317D ALA* 2.7 70.3 + - + +
318D GLU* 3.3 24.4 + - - -
320D ARG* 3.9 11.0 - - + -
321D SER* 3.4 21.9 + - - -
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Residues in contact with SER 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C ARG* 3.7 27.0 + - - -
423C PRO 3.2 1.4 + - - -
424C ALA 3.8 6.1 - - - -
426C ARG* 1.3 76.9 - - - +
428C ILE* 1.3 58.0 + - - +
430C LEU* 3.0 16.9 + - - +
431C LYS* 2.9 28.7 + - - +
271D ASP* 4.4 0.2 - - - -
272D ARG* 5.1 0.7 + - - -
320D ARG* 2.7 44.5 + - - +
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Residues in contact with ILE 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C ILE* 4.1 18.4 - - + -
345C ILE* 4.2 3.4 - - + -
348C ARG* 3.3 56.5 - - + +
349C VAL* 4.0 21.1 - - + -
352C GLU* 4.0 9.4 - - + -
353C LEU* 3.9 20.2 - - + -
424C ALA* 2.9 22.1 + - + +
425C LEU* 3.8 4.0 - - - +
427C SER* 1.3 76.4 - - - +
429C GLY* 1.3 63.8 + - - +
431C LYS* 3.4 6.9 + - - +
432C CYS* 3.1 29.0 + - - -
271D ASP* 5.7 0.2 - - - +
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Residues in contact with GLY 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C ASN* 2.9 29.4 - - - +
307C GLU* 4.3 7.2 - - - -
310C ILE* 3.3 10.5 - - - -
425C LEU 2.7 20.0 + - - -
426C ARG 3.7 1.6 - - - -
428C ILE* 1.3 73.9 - - - +
430C LEU* 1.3 62.0 + - - +
432C CYS 3.3 1.6 + - - -
433C LEU* 3.3 20.7 + - - +
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Residues in contact with LEU 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426C ARG* 3.0 43.3 + - + +
427C SER* 3.2 16.2 - - - +
429C GLY* 1.3 77.1 - - - +
431C LYS* 1.3 60.6 + - - +
433C LEU* 3.1 31.5 + - + +
434C GLU* 3.4 10.4 + - - +
320D ARG* 3.9 22.7 - - + +
321D SER* 4.0 15.9 - - - +
324D GLU* 4.2 36.9 - - + +
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Residues in contact with LYS 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A ASP* 4.7 12.5 + - - -
344C ALA* 5.2 10.8 - - - -
345C ILE* 3.7 24.7 - - + +
348C ARG* 4.1 19.7 - - - +
427C SER 2.9 14.9 + - - +
428C ILE 3.9 0.4 - - - +
430C LEU* 1.3 76.7 - - - +
432C CYS* 1.3 60.2 + - - +
433C LEU 3.2 1.2 + - - -
434C GLU* 3.5 30.7 + - - +
435C HIS* 2.9 53.9 + - + +
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Residues in contact with CYS 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C ASN* 4.4 3.8 - - - +
310C ILE* 4.0 17.5 - - + -
313C PHE* 5.6 0.4 - - - -
345C ILE* 3.6 25.6 - - - -
349C VAL* 5.0 2.7 - - - -
428C ILE* 3.1 29.9 + - - +
429C GLY 3.3 5.8 + - - +
430C LEU 3.2 0.2 - - - -
431C LYS* 1.3 74.3 - - - +
433C LEU* 1.3 61.3 + - - +
435C HIS* 4.1 9.8 - - - +
436C LEU* 3.2 29.9 + - - +
1001C F15 3.6 33.2 - - + +
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Residues in contact with LEU 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C TRP* 4.5 15.7 - - + -
306C ASN* 3.9 22.2 - - + +
429C GLY 3.3 15.9 + - - +
430C LEU* 3.1 23.3 + - + +
432C CYS* 1.3 76.8 - - - +
434C GLU* 1.3 68.9 + - - +
436C LEU* 3.1 8.7 + - + +
437C PHE* 2.8 54.7 + - + -
455C LEU* 4.7 7.6 - - + -
457C ALA* 6.2 2.5 - - + -
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Residues in contact with GLU 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A PHE* 3.7 13.6 - - + -
442A ILE* 3.8 32.3 - - + +
443A GLY* 5.2 4.7 - - - -
444A ASP* 4.9 8.9 - - - +
430C LEU 3.4 8.1 + - - +
431C LYS* 3.5 39.9 + - - +
433C LEU* 1.3 77.0 - - - +
435C HIS* 1.3 67.0 + - - +
437C PHE* 3.0 22.7 + - + +
438C PHE 3.0 10.6 + - - -
324D GLU* 4.0 17.9 - - - +
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Residues in contact with HIS 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341C GLY 4.0 13.2 + - - -
342C VAL* 3.4 26.7 - - + -
344C ALA* 5.8 2.9 - - + +
345C ILE* 3.9 24.6 + - + +
431C LYS* 2.9 53.0 + - + +
432C CYS* 4.2 7.5 - - - +
433C LEU 3.3 0.2 - - - -
434C GLU* 1.3 81.4 - - - +
436C LEU* 1.3 63.1 + - - +
438C PHE* 3.0 20.5 + - - +
439C PHE* 3.0 32.9 + + + -
1001C F15 4.6 6.7 - - + -
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Residues in contact with LEU 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C ILE* 5.2 2.9 - - + -
269C CYS* 4.8 7.9 - - - -
272C ALA* 5.3 2.2 - - + -
305C TRP* 3.9 28.9 - - + -
306C ASN* 3.9 11.0 - - - +
432C CYS 3.2 21.2 + - - +
433C LEU* 3.1 10.6 + - + +
435C HIS* 1.3 78.6 - - - +
437C PHE* 1.3 61.3 + - - +
439C PHE* 3.3 22.2 + - + +
440C LYS* 3.3 20.8 + - - +
447C ILE* 4.5 4.7 - - + +
451C LEU* 4.8 22.9 - - + -
455C LEU* 4.5 16.5 - - + +
1001C F15 4.0 26.2 - - + -
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Residues in contact with PHE 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438A PHE* 4.1 12.8 - - + -
442A ILE* 4.8 11.2 - - + -
433C LEU* 2.8 56.8 + - + -
434C GLU* 3.3 9.9 - - + +
436C LEU* 1.3 69.2 - - - +
438C PHE* 1.3 62.3 + - - +
440C LYS* 3.0 6.6 + - + -
441C LEU* 2.8 53.7 + - + +
455C LEU* 3.6 25.8 - - + -
456C GLU* 4.1 18.4 - - - -
457C ALA* 3.5 40.6 - - + -
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Residues in contact with PHE 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A ALA 5.3 0.9 - - - -
341A GLY* 3.2 38.4 - - - -
342A VAL* 4.0 2.9 - - + -
435A HIS* 3.8 22.9 - + - -
438A PHE* 3.6 25.7 - + + -
439A PHE* 3.7 23.8 - + - -
434C GLU 3.0 12.0 + - - +
435C HIS* 3.2 12.8 - - - +
437C PHE* 1.3 75.6 - - - +
439C PHE* 1.3 78.3 + + + +
442C ILE* 3.3 35.3 + - + +
443C GLY* 3.1 32.6 + - - -
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Residues in contact with PHE 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A GLY* 6.1 3.4 - - - -
265C VAL* 3.8 36.8 - - + -
268C ILE* 5.1 5.8 - - + -
269C CYS* 3.9 19.5 - - - -
340C ALA 5.4 2.2 - - - -
341C GLY 5.8 0.7 - - - -
342C VAL* 4.0 20.9 - - + -
435C HIS* 3.0 39.9 + + + -
436C LEU* 3.8 18.8 - - + +
437C PHE 3.2 0.4 - - - -
438C PHE* 1.3 92.1 - + - +
440C LYS* 1.3 58.3 + - - +
443C GLY* 2.9 21.5 - - - +
445C THR* 3.4 31.6 + - - +
447C ILE* 4.6 2.5 - - + -
1001C F15 4.7 10.5 - - + -
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Residues in contact with LYS 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C LEU 3.3 7.3 + - - +
437C PHE* 3.0 9.2 + - + +
439C PHE* 1.3 79.6 - - - +
441C LEU* 1.3 86.5 + - + +
442C ILE 3.4 1.1 + - - +
443C GLY 3.9 4.9 - - - +
445C THR 4.9 0.4 - - - -
447C ILE* 3.1 32.3 - - + +
452C MET* 3.3 37.3 + - + +
455C LEU* 4.1 31.9 + - + -
456C GLU* 4.5 14.1 + - - +
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Residues in contact with LEU 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A LYS* 4.8 2.0 + - - -
434A GLU* 3.8 16.8 - - - +
438A PHE* 5.5 4.3 - - + -
437C PHE* 2.8 41.0 + - + +
440C LYS* 1.3 104.4 - - + +
442C ILE* 1.3 64.3 + - + +
456C GLU 6.1 0.7 - - - +
459C HIS* 3.6 36.1 - - + +
460C GLN* 4.6 14.6 - - - +
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Residues in contact with ILE 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A LYS* 3.0 28.1 + - - -
434A GLU* 4.2 10.8 - - + +
435A HIS* 3.1 58.6 - - + +
438A PHE* 3.1 47.6 - - + -
438C PHE* 3.3 31.0 + - + +
440C LYS 3.4 0.4 - - - +
441C LEU* 1.3 85.2 - - + +
443C GLY* 1.3 70.5 + - - +
444C ASP* 3.7 0.2 - - - +
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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