Contacts of the helix formed by residues 397 - 420 (chain A) in PDB entry 2CSX
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 ASN 397 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A PHE* 5.9 1.3 - - - -
327A PRO* 5.4 1.7 - - - +
328A PHE* 5.4 4.0 + - - -
392A TYR* 2.9 31.3 + - + +
393A MET* 5.0 0.7 - - - -
395A LYS* 3.0 8.6 - - + +
396A VAL* 1.3 75.3 - - - +
398A PHE* 1.3 58.5 + - - +
399A TYR* 3.5 9.5 + - - +
400A LYS* 2.9 48.4 + - - +
401A ALA* 3.0 28.4 + - - +
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Residues in contact with PHE 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA* 3.4 39.7 - - + -
33A THR* 3.0 22.9 - - - -
34A ILE* 3.6 28.0 - - + -
255A LEU* 5.5 0.9 - - + -
323A LEU* 3.5 39.5 - - + +
328A PHE* 3.9 23.8 - + + +
393A MET* 3.9 21.1 - - + -
396A VAL* 2.9 34.9 + - + -
397A ASN* 1.3 72.7 - - - +
399A TYR* 1.3 55.3 + - - +
401A ALA* 3.5 5.1 - - - +
402A ILE* 2.8 42.2 + - + +
454A ILE* 6.4 0.4 - - + -
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Residues in contact with TYR 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LEU 3.8 6.0 + - - -
324A ARG* 3.1 38.7 + - - +
325A GLU 3.6 13.0 - - - -
326A VAL 3.3 18.6 + - - +
327A PRO* 3.6 39.7 - - + -
328A PHE 4.4 2.3 - - - +
397A ASN* 3.2 5.8 - - - +
398A PHE* 1.3 80.8 - - - +
400A LYS* 1.3 93.6 + - + +
402A ILE* 3.5 3.5 + - - +
403A GLU* 3.1 29.3 + - + +
13C C 5.2 5.4 + - - -
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Residues in contact with LYS 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A PRO* 5.6 4.0 - - - +
392A TYR* 3.3 51.2 - - + +
397A ASN* 2.9 32.0 + - - +
399A TYR* 1.3 101.3 - - + +
401A ALA* 1.3 61.6 + - - +
403A GLU* 3.1 35.8 - - - +
404A GLU* 3.1 8.0 + - - +
14C A 5.7 4.2 + - - -
15C G 5.9 0.4 + - - -
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Residues in contact with ALA 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A TYR* 3.9 10.9 - - + -
392A TYR* 3.9 15.0 - - + +
393A MET* 3.5 34.1 - - + +
397A ASN 3.0 19.6 + - - +
398A PHE 3.5 4.7 - - - +
399A TYR 3.1 0.2 - - - -
400A LYS* 1.3 73.5 - - - +
402A ILE* 1.3 64.6 + - - +
403A GLU 2.9 4.0 - - - -
404A GLU* 2.8 17.8 + - - +
405A ILE* 3.1 13.8 + - - +
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Residues in contact with ILE 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A TYR* 4.0 13.7 - - + -
323A LEU* 3.4 41.7 - - + +
324A ARG* 3.5 31.0 - - + -
393A MET* 5.5 3.1 - - + -
398A PHE* 2.8 21.2 + - + +
399A TYR 3.9 3.6 - - - +
401A ALA* 1.3 73.0 - - + +
403A GLU* 1.3 56.7 + - - +
405A ILE* 3.1 16.3 + - + +
406A LEU* 2.9 36.2 + - + +
451A LEU* 6.1 0.7 - - + -
454A ILE* 3.6 33.4 - - + -
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Residues in contact with GLU 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A TYR* 5.3 1.6 + - - -
399A TYR* 3.1 22.4 + - + +
400A LYS* 3.1 38.5 - - - +
401A ALA 2.9 0.4 - - - -
402A ILE* 1.3 79.3 - - - +
404A GLU* 1.3 64.4 + - - +
406A LEU* 3.3 11.5 + - + +
407A LYS* 2.8 60.4 + - + +
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Residues in contact with GLU 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A GLU 4.4 2.3 - - - +
385A SER* 4.4 13.4 + - - +
388A ASN* 3.6 34.3 + - + +
389A TYR* 4.0 17.9 - - + +
392A TYR* 3.8 24.6 + - + -
400A LYS 3.1 11.5 + - - +
401A ALA 2.8 7.8 + - - +
403A GLU* 1.3 81.3 - - - +
405A ILE* 1.3 68.4 + - - +
407A LYS* 3.7 25.7 - - - +
408A PHE* 2.9 26.2 + - - +
450A LEU* 5.8 1.6 - - + -
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Residues in contact with ILE 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A TYR* 6.0 0.2 - - + -
351A ILE* 4.9 6.1 - - + -
389A TYR* 3.3 22.9 - - + -
401A ALA 3.1 12.2 + - - +
402A ILE* 3.1 22.4 + - + +
404A GLU* 1.3 79.0 - - - +
406A LEU* 1.3 57.5 + - + +
408A PHE* 3.4 4.2 - - - +
409A THR* 2.8 40.2 + - + +
447A LEU* 3.8 16.4 - - + -
450A LEU* 3.2 44.4 - - + +
451A LEU* 3.5 28.0 - - + -
454A ILE* 5.8 1.3 - - + -
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Residues in contact with LEU 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A TYR* 3.6 26.0 - - + +
324A ARG* 4.5 9.0 - - + +
346A GLU* 4.0 24.9 - - + +
350A GLU* 4.3 16.7 - - - +
351A ILE* 4.3 20.0 - - + -
402A ILE* 2.9 32.0 + - + +
403A GLU* 3.6 12.1 - - + +
405A ILE* 1.3 79.6 - - + +
407A LYS* 1.3 55.8 + - + +
409A THR* 3.2 8.1 + - - +
410A SER* 3.0 33.8 + - - -
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Residues in contact with LYS 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A SER* 5.4 1.1 - - - +
403A GLU* 2.8 53.0 + - + +
404A GLU* 3.8 28.7 - - - +
406A LEU* 1.3 72.9 - - - +
408A PHE* 1.3 58.6 + - - +
410A SER* 4.0 7.0 - - - -
411A TYR* 3.5 18.2 + - - +
23C A 5.8 2.2 + - - -
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Residues in contact with PHE 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A TYR* 4.2 17.5 - + - -
381A ILE* 4.7 9.0 - - + -
382A ALA* 4.1 20.9 - - + -
385A SER* 3.4 26.7 + - - +
404A GLU 2.9 17.4 + - - +
405A ILE* 3.4 3.6 - - - +
407A LYS* 1.3 76.5 - - - +
409A THR* 1.3 67.3 + - - +
410A SER 3.1 1.6 - - - -
411A TYR* 3.4 10.5 + + - +
412A LEU* 3.1 46.0 + - + +
443A GLY* 3.4 26.5 - - - -
446A VAL* 4.0 21.8 - - + -
447A LEU* 4.0 11.9 - - + -
450A LEU* 4.2 14.4 - - + -
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Residues in contact with THR 409 (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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350A GLU* 3.9 26.8 + - - +
351A ILE* 4.5 10.9 - - + +
354A LEU* 3.6 6.4 - - - +
405A ILE* 2.8 25.3 + - + +
406A LEU* 3.2 11.6 + - - +
408A PHE* 1.3 72.2 - - - +
410A SER* 1.3 62.1 + - - +
412A LEU* 3.5 13.3 + - - +
413A ASN* 2.9 30.5 + - - -
447A LEU* 3.4 34.1 - - + -
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Residues in contact with SER 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A GLU* 3.6 15.5 + - - -
406A LEU 3.0 15.7 + - - -
407A LYS* 4.0 8.3 - - - -
409A THR* 1.3 79.5 + - - +
411A TYR* 1.3 67.6 + - - +
413A ASN* 2.8 21.7 + - - +
414A LYS* 2.8 15.8 + - - +
40C U 4.2 12.1 + - - -
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Residues in contact with TYR 411 (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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375A ASP* 5.4 0.2 + - - -
377A GLU* 4.6 2.1 + - - +
378A TYR* 3.3 47.3 - + - +
381A ILE* 4.1 40.8 - - + +
407A LYS 3.5 12.0 + - - +
408A PHE* 3.4 13.2 + + - +
410A SER* 1.3 78.1 - - - +
412A LEU* 1.3 69.6 + - + +
414A LYS* 3.2 8.5 + - + +
415A TYR* 2.7 60.9 + + + +
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Residues in contact with LEU 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A LEU* 3.4 30.5 - - + -
378A TYR* 4.2 6.1 - - + -
408A PHE* 3.1 45.3 + - + +
409A THR* 3.6 4.0 - - - +
410A SER 3.1 0.6 - - - -
411A TYR* 1.3 96.3 - - + +
413A ASN* 1.3 68.8 + - - +
415A TYR* 3.0 15.5 + - + +
416A VAL* 3.1 17.5 + - - +
439A ALA 5.1 0.7 - - - +
440A LEU* 4.0 17.2 - - + +
443A GLY* 3.9 29.6 - - - +
444A LEU* 4.6 1.8 - - + +
447A LEU* 4.8 4.5 - - + -
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Residues in contact with ASN 413 (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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349A ASN 4.9 0.3 - - - +
350A GLU* 3.1 38.6 + - - +
353A ASN* 4.6 1.4 + - - -
354A LEU* 3.8 13.9 + - - +
357A ARG* 2.8 35.9 + - - +
409A THR 2.9 21.6 + - - -
410A SER* 2.8 14.1 + - - +
412A LEU* 1.3 69.8 - - - +
414A LYS* 1.3 64.1 + - - +
416A VAL* 2.9 17.0 + - - +
417A ASP 3.3 7.4 + - - -
39C G 3.5 33.8 + - - +
40C U 3.9 2.9 + - - +
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Residues in contact with LYS 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A SER 2.8 14.2 + - - +
411A TYR* 3.6 11.2 - - + +
413A ASN* 1.3 74.4 - - - +
415A TYR* 1.3 51.2 + - - +
417A ASP* 3.0 3.7 + - + +
418A GLU* 2.8 60.5 + - + +
40C U 3.6 32.9 - - - +
41C C 2.8 36.8 + - - +
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Residues in contact with TYR 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ASP* 3.0 27.4 + - - +
378A TYR* 4.6 5.6 - + + -
411A TYR* 2.7 51.0 + + + +
412A LEU* 3.0 14.8 + - - +
414A LYS* 1.3 72.4 - - - +
416A VAL* 1.3 57.3 + - - +
418A GLU* 4.5 4.9 - - - -
419A LYS* 2.9 68.6 + - + +
435A LYS* 5.3 0.2 - - - +
436A VAL* 3.5 41.3 - - + +
439A ALA* 4.0 11.2 - - + +
440A LEU* 3.3 25.6 - - + -
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Residues in contact with VAL 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A LEU* 4.2 7.4 - - + -
357A ARG* 3.8 15.5 - - + +
358A VAL* 4.1 13.5 - - + -
361A MET* 4.2 17.0 - - - -
412A LEU 3.3 14.6 - - - +
413A ASN 2.9 7.8 + - - +
415A TYR* 1.3 76.1 - - - +
417A ASP* 1.3 58.4 + - - +
420A GLN 3.2 21.0 + - - -
421A PRO* 3.5 4.8 - - + +
422A TRP* 3.5 9.5 - - + -
440A LEU* 3.5 29.4 - - + -
34C C 3.7 27.6 - - + +
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Residues in contact with ASP 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A ARG* 5.2 2.7 - - - +
413A ASN 3.3 7.3 + - - +
414A LYS* 3.0 8.1 + - - +
416A VAL* 1.3 79.5 - - - +
418A GLU* 1.3 61.0 + - - +
419A LYS 3.4 0.2 - - - -
420A GLN* 3.5 18.2 + - - +
422A TRP* 4.2 8.7 - - - -
32C C 3.5 9.8 - - - +
34C C 4.5 2.4 + - - -
39C G 2.6 37.3 + - - +
40C U 3.4 36.6 + - - +
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Residues in contact with GLU 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A LYS* 2.8 40.3 + - + +
415A TYR* 4.0 4.7 - - - +
417A ASP* 1.3 79.8 - - - +
419A LYS* 1.3 76.3 + - + +
420A GLN* 3.6 4.1 - - - +
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Residues in contact with LYS 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ASP* 4.7 5.9 + - - -
377A GLU* 5.6 3.8 + - - -
415A TYR* 2.9 63.8 + - + +
418A GLU* 1.3 97.5 + - - +
420A GLN* 1.3 75.8 + - - +
421A PRO* 3.2 2.7 - - + -
424A LEU* 3.7 16.5 - - + +
432A GLU* 5.3 6.0 + - - +
436A VAL* 3.3 35.4 - - + -
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Residues in contact with GLN 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A VAL 3.2 6.9 + - - -
417A ASP 3.5 16.4 + - - +
418A GLU 4.6 3.4 - - - +
419A LYS* 1.3 81.0 - - - +
421A PRO* 1.3 68.8 - - - +
422A TRP* 3.0 28.9 - - + +
423A ALA* 2.8 37.9 + - + +
424A LEU* 3.1 4.5 + - - +
32C C 3.8 19.2 + - - -
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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