Contacts of the helix formed by residues 404 - 427 (chain A) in PDB entry 5Q1B
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 404 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316A ASP* 6.2 1.6 - - + -
319A ASP* 3.2 14.8 + - - +
402A ILE* 3.7 3.3 - - - +
403A LYS* 1.3 75.9 - - + +
405A ARG* 1.3 59.4 + - - +
406A GLU* 3.5 16.3 + - - +
407A ALA* 3.3 34.5 + - + +
408A VAL* 3.5 17.8 - - - +
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Residues in contact with ARG 405 (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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397A PRO* 2.8 48.0 + - + +
398A ASP* 3.4 15.2 - - - +
399A ARG 3.1 24.0 + - - +
400A GLN* 4.5 6.1 - - - +
401A TYR 4.6 1.0 - - - +
402A ILE* 3.8 30.9 + - + +
403A LYS 3.9 2.5 + - - +
404A ASP* 1.3 70.0 + - - +
406A GLU* 1.3 59.7 + - - +
408A VAL* 3.4 1.8 + - - -
409A GLU* 3.0 32.0 + - - +
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Residues in contact with GLU 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A ASP* 3.3 11.8 + - - +
405A ARG* 1.3 75.1 - - - +
407A ALA* 1.4 58.1 + - - +
409A GLU* 3.3 10.3 + - - +
410A LYS* 3.0 57.3 + - + +
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Residues in contact with ALA 407 (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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315A LEU* 3.7 22.0 - - + +
404A ASP* 3.3 31.7 + - + +
405A ARG 3.4 0.2 - - - -
406A GLU* 1.4 78.6 + - - +
408A VAL* 1.3 59.4 + - - +
410A LYS* 3.6 12.1 - - - +
411A LEU* 3.4 23.6 + - - +
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Residues in contact with VAL 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A LEU* 4.4 11.4 - - + -
319A ASP* 5.1 4.0 - - + +
323A LEU* 3.9 28.9 - - + -
395A LEU* 3.5 35.4 - - + +
397A PRO* 3.9 13.5 - - + -
402A ILE* 4.0 17.3 - - + -
404A ASP 3.5 15.9 - - - +
405A ARG 3.4 6.0 + - - +
406A GLU 3.3 0.6 - - - -
407A ALA* 1.3 71.7 - - - +
409A GLU* 1.3 60.9 + - - +
410A LYS 3.2 1.6 - - - -
411A LEU* 2.9 23.2 + - - +
412A GLN* 3.0 12.5 + - - +
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Residues in contact with GLU 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A PRO* 3.7 22.9 - - + +
405A ARG* 3.0 20.0 + - - +
406A GLU* 3.3 10.3 + - - +
408A VAL* 1.3 75.4 - - - +
410A LYS* 1.4 56.3 + - + +
412A GLN* 4.0 6.9 - - - +
413A GLU* 3.1 54.9 + - + +
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Residues in contact with LYS 410 (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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406A GLU* 3.0 46.9 + - + +
407A ALA* 3.6 11.4 - - - +
408A VAL 3.2 0.4 - - - -
409A GLU* 1.4 76.4 - - - +
411A LEU* 1.3 62.2 + - + +
413A GLU* 3.9 12.1 - - - +
414A PRO* 3.3 21.7 - - - +
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Residues in contact with LEU 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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310A PRO* 3.7 18.6 - - - +
311A GLY* 3.5 37.7 - - - +
312A PHE* 3.7 3.6 - - - +
314A THR* 5.2 2.7 - - - +
315A LEU* 3.7 28.3 - - + -
395A LEU* 4.0 21.7 - - + +
407A ALA 3.4 13.7 - - - +
408A VAL* 2.9 7.4 + - - +
410A LYS* 1.3 82.1 - - + +
412A GLN* 1.3 61.8 + - - +
414A PRO* 3.7 12.7 - - - +
415A LEU* 3.6 16.6 - - - +
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Residues in contact with GLN 412 (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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392A ILE* 3.1 42.9 + - + +
395A LEU* 3.3 30.6 + - + +
396A SER* 3.7 11.7 + - - +
397A PRO* 3.4 16.3 - - - +
398A ASP* 5.0 1.2 + - - -
408A VAL 3.0 9.9 + - - +
409A GLU* 3.3 10.9 + - - +
411A LEU* 1.3 77.5 - - - +
413A GLU* 1.4 63.9 + - - +
415A LEU* 3.1 10.3 + - - +
416A LEU* 3.0 42.0 + - + +
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Residues in contact with GLU 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A GLU* 3.1 45.0 + - + +
410A LYS* 3.9 11.0 + - - +
412A GLN* 1.4 73.1 - - + +
414A PRO* 1.4 69.0 - - + +
416A LEU* 3.0 16.8 + - + +
417A ASP* 2.9 33.2 + - - +
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Residues in contact with PRO 414 (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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253A GLN* 5.0 0.9 + - - +
256A LEU* 4.5 13.2 - - + -
310A PRO* 6.4 2.5 - - + -
410A LYS 3.3 21.1 - - - +
411A LEU* 3.7 12.3 - - - +
413A GLU* 1.4 89.5 - - + +
415A LEU* 1.3 58.5 + - + +
417A ASP* 3.3 13.1 + - + +
418A VAL* 3.1 33.6 + - + +
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Residues in contact with LEU 415 (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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256A LEU* 3.9 30.7 - - + -
260A ILE* 4.2 12.6 - - + -
309A LEU* 5.3 2.7 - - + -
310A PRO* 5.4 6.3 - - + -
388A LEU* 3.9 22.8 - - + +
391A ALA* 4.0 20.0 - - + -
392A ILE* 3.9 17.6 - - + +
395A LEU* 3.7 23.3 - - + -
411A LEU 3.6 18.8 - - - +
412A GLN* 3.1 9.2 + - - +
414A PRO* 1.3 74.1 - - + +
416A LEU* 1.3 65.0 + - - +
418A VAL* 3.3 5.3 + - - +
419A LEU* 3.1 24.4 + - - +
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Residues in contact with LEU 416 (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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392A ILE* 4.0 24.5 - - + -
412A GLN* 3.0 38.2 + - + +
413A GLU* 3.0 19.8 + - + +
415A LEU* 1.3 75.2 - - - +
417A ASP* 1.4 58.5 + - - +
419A LEU 3.4 0.7 + - - -
420A GLN* 3.0 32.4 + - - +
434A PHE* 3.6 17.6 - - + -
438A LEU* 3.9 32.1 - - + -
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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
----------------------------------------------------------
253A GLN* 4.0 15.0 + - - +
413A GLU* 2.9 27.6 + - - +
414A PRO* 3.3 13.7 - - + +
416A LEU* 1.4 75.4 - - - +
418A VAL* 1.4 62.3 + - - +
420A GLN* 3.6 13.5 + - - +
421A LYS* 3.2 28.6 + - - +
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Residues in contact with VAL 418 (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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249A LEU* 4.0 19.5 - - + -
253A GLN* 3.9 31.0 - - + +
256A LEU* 4.0 19.1 - - + -
257A LEU* 4.3 21.3 - - + -
388A LEU* 3.7 24.0 - - + -
414A PRO 3.1 17.0 + - - +
415A LEU 3.8 4.9 - - - +
417A ASP* 1.4 72.8 - - - +
419A LEU* 1.4 60.4 + - - +
421A LYS* 3.1 5.4 + - - +
422A LEU* 2.9 30.0 + - + +
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Residues in contact with LEU 419 (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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385A GLU* 4.1 30.5 - - + +
388A LEU* 3.9 19.7 - - + +
389A LEU* 3.6 29.6 - - + +
392A ILE* 3.8 15.3 - - + -
415A LEU 3.1 17.3 + - - +
416A LEU 3.8 4.3 - - - +
418A VAL* 1.4 74.7 - - - +
420A GLN* 1.3 63.6 + - - +
422A LEU* 3.2 5.9 + - + +
423A CYS* 3.1 28.3 + - - -
434A PHE* 3.8 21.8 - - + -
437A LEU* 3.9 24.5 - - + -
438A LEU* 4.7 2.5 - - + -
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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
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416A LEU 3.0 18.3 + - - +
417A ASP* 3.8 13.1 + - - +
418A VAL 3.3 0.2 - - - -
419A LEU* 1.3 74.3 - - - +
421A LYS* 1.4 63.1 + - + +
423A CYS* 3.5 3.5 + - - +
424A LYS* 3.3 50.5 + - + +
434A PHE* 3.5 43.4 - - + +
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Residues in contact with LYS 421 (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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247A MET* 4.0 23.9 - - - +
248A GLU 2.9 30.1 + - - +
249A LEU* 3.8 15.5 - - + -
250A THR* 3.8 12.1 - - - +
253A GLN* 2.8 38.0 + - - +
417A ASP* 3.2 14.5 + - - +
418A VAL 3.1 9.7 + - - +
420A GLN* 1.4 75.7 - - + +
422A LEU* 1.4 63.4 + - - +
424A LYS* 3.2 19.5 + - + +
425A ILE* 3.3 21.8 + - + +
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Residues in contact with LEU 422 (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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249A LEU* 4.3 13.2 - - + -
257A LEU* 4.0 23.1 - - + -
384A GLU* 3.8 26.9 - - + -
385A GLU* 4.4 13.0 - - + +
388A LEU* 3.5 31.0 - - + -
418A VAL* 2.9 17.3 + - + +
419A LEU* 3.2 6.7 + - - +
421A LYS* 1.4 74.3 - - - +
423A CYS* 1.3 57.2 + - - +
425A ILE* 3.3 6.4 + - + +
426A HIS* 2.9 60.4 + - + +
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Residues in contact with CYS 423 (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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385A GLU* 3.7 5.6 - - - -
419A LEU* 3.1 21.3 + - - -
420A GLN 3.7 7.9 - - - +
421A LYS 3.3 0.2 - - - -
422A LEU* 1.3 77.2 - - - +
424A LYS* 1.4 56.0 + - + +
425A ILE 3.1 0.2 - - - -
427A GLN* 3.0 43.4 + - - +
433A HIS* 3.4 30.7 - - + +
434A PHE* 3.9 25.4 - - + +
437A LEU* 3.6 21.5 - - - -
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Residues in contact with LYS 424 (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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247A MET* 3.8 42.5 - - + +
420A GLN* 3.3 44.5 + - + +
421A LYS* 3.2 14.6 + - + +
423A CYS* 1.4 75.1 - - + +
425A ILE* 1.3 59.5 + - + +
427A GLN 4.9 2.0 - - - -
428A PRO* 4.0 19.4 - - - +
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Residues in contact with ILE 425 (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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247A MET* 3.6 27.1 - - + +
248A GLU* 4.3 16.6 - - + -
249A LEU* 4.7 9.6 - - + +
421A LYS* 3.3 20.4 + - + +
422A LEU* 3.3 9.8 + - + +
423A CYS 3.1 0.4 - - - -
424A LYS* 1.3 81.9 - - + +
426A HIS* 1.3 82.7 + - + +
427A GLN 3.5 0.7 - - - -
428A PRO* 3.4 18.4 - - - +
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Residues in contact with HIS 426 (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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382A THR* 4.6 22.0 + - + +
384A GLU* 5.5 5.8 - - + -
385A GLU* 4.6 4.9 + - - -
422A LEU* 2.9 49.9 + - + +
425A ILE* 1.3 91.5 - - + +
427A GLN* 1.3 80.4 + - - +
428A PRO* 3.5 6.1 - - - +
429A GLU* 4.5 1.7 - - - +
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Residues in contact with GLN 427 (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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379A LEU 4.0 1.5 + - - +
380A LYS* 3.7 16.9 + - + +
382A THR* 5.1 3.0 - - - +
385A GLU* 3.2 28.7 + - - +
423A CYS* 3.0 19.3 + - - +
424A LYS* 4.9 0.9 - - - -
426A HIS* 1.3 95.0 + - - +
428A PRO* 1.4 60.4 - - - +
429A GLU* 3.2 14.8 - - - +
430A ASN* 2.9 25.8 - - + +
431A PRO* 4.9 0.5 - - - +
433A HIS* 3.2 51.6 + - + +
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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) + - + + + + + -
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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