Contacts of the helix formed by residues 412 - 436 (chain A) in PDB entry 4HNE
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 412 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A LYS* 3.1 27.1 + - - +
168A LYS* 4.6 10.6 - - - +
188A GLN* 5.0 0.6 - - - +
410A GLY 3.2 2.6 + - - +
411A PHE* 1.3 80.4 - - - +
413A ARG* 1.3 64.6 + - - +
414A GLY* 3.1 9.0 + - - -
415A GLN* 2.8 56.4 + - + +
416A PHE* 3.0 22.2 + - - +
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Residues in contact with ARG 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A TYR* 3.0 36.9 + - + -
406A LYS* 5.2 4.2 - - - +
411A PHE* 3.7 30.6 - - + -
412A ASP* 1.3 73.5 + - - +
414A GLY* 1.3 60.8 + - - +
416A PHE* 3.8 2.4 - - + +
417A HIS* 3.0 52.5 + - + +
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Residues in contact with GLY 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A ASP* 3.1 9.7 + - - -
413A ARG* 1.3 75.3 - - - +
415A GLN* 1.3 65.1 + - - +
417A HIS* 3.2 16.9 + - - +
418A LYS* 3.3 20.4 + - - +
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Residues in contact with GLN 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LYS* 5.9 0.6 - - - -
167A THR* 4.6 19.3 - - - +
185A VAL* 3.7 29.4 - - + +
186A LEU* 5.3 2.4 - - - +
188A GLN* 4.8 5.2 + - - -
353A LEU* 3.8 26.2 - - + +
410A GLY 4.6 4.2 - - - +
412A ASP* 2.8 43.2 + - - +
414A GLY* 1.3 69.7 - - - +
416A PHE* 1.3 57.2 + - - +
418A LYS* 3.1 15.2 + - - +
419A GLN* 2.9 33.2 + - - +
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Residues in contact with PHE 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A GLU* 3.6 19.5 - - + -
401A LEU* 4.0 2.5 - - + -
402A TYR* 3.4 52.0 - + + -
405A PHE* 3.8 24.2 - + - -
411A PHE* 3.6 30.1 - + + -
412A ASP 3.0 8.5 + - - +
413A ARG* 3.8 5.2 - - + +
414A GLY 3.2 0.6 - - - -
415A GLN* 1.3 76.5 - - - +
417A HIS* 1.3 71.5 + + - +
419A GLN* 3.2 23.3 + - + +
420A ILE* 2.9 57.8 + - + +
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Residues in contact with HIS 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A GLU* 4.8 14.1 + - - -
402A TYR* 6.6 0.2 - + - -
413A ARG* 3.0 40.5 + - + +
414A GLY* 3.2 10.9 + - - +
416A PHE* 1.3 86.2 - + - +
418A LYS* 1.3 60.7 + - + +
420A ILE* 3.4 5.4 + - - +
421A ALA* 2.9 30.2 + - - +
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Residues in contact with LYS 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A GLN* 6.0 2.4 - - - +
353A LEU* 3.2 34.7 + - + +
414A GLY 3.3 17.8 - - - +
415A GLN* 3.1 13.2 + - - +
417A HIS* 1.3 73.4 - - + +
419A GLN* 1.3 64.3 + - - +
421A ALA* 3.4 6.8 + - - +
422A VAL* 3.2 28.4 + - - +
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Residues in contact with GLN 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A VAL* 4.1 23.6 - - - +
188A GLN* 4.6 5.3 + - - +
351A PHE* 3.1 40.1 - - + +
352A PRO 3.5 13.0 - - - +
353A LEU* 4.0 9.6 - - + +
405A PHE* 4.0 17.4 - - + -
411A PHE* 5.5 1.8 - - - -
415A GLN* 2.9 14.5 + - - +
416A PHE* 3.3 41.2 - - + +
418A LYS* 1.3 76.1 - - - +
420A ILE* 1.3 65.8 + - + +
422A VAL* 3.5 3.3 + - - +
423A MET* 3.2 21.8 + - - +
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Residues in contact with ILE 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A GLU* 3.7 41.1 - - + +
401A LEU* 4.1 24.0 - - + -
416A PHE* 2.9 50.3 + - + +
417A HIS* 4.0 7.9 - - - +
418A LYS 3.3 0.2 - - - -
419A GLN* 1.3 77.4 - - + +
421A ALA* 1.3 61.0 + - - +
423A MET* 3.4 14.9 + - + +
424A ARG* 2.9 57.6 + - + +
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Residues in contact with ALA 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A HIS 2.9 18.7 + - - +
418A LYS* 3.8 7.6 - - - +
419A GLN 3.3 0.2 - - - -
420A ILE* 1.3 74.1 - - - +
422A VAL* 1.3 66.2 + - - +
424A ARG* 3.5 2.9 + - - +
425A GLY 3.2 9.9 + - - -
450A ILE* 3.8 20.3 - - + -
451A VAL 3.1 44.2 + - - +
452A GLU* 4.5 9.2 - - + -
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Residues in contact with VAL 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ARG* 4.6 4.5 - - + -
352A PRO* 4.1 25.6 - - + +
353A LEU 3.7 5.4 - - - +
354A LYS* 3.6 31.4 - - - -
355A HIS* 3.7 29.8 - - + +
418A LYS 3.2 14.8 + - - +
419A GLN 3.7 7.4 - - - +
421A ALA* 1.3 76.8 - - + +
423A MET* 1.3 58.8 + - - +
425A GLY* 3.0 5.5 + - - -
426A GLN* 3.0 34.4 + - + +
449A VAL 4.0 2.6 - - - +
450A ILE* 4.5 12.3 - - + -
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Residues in contact with MET 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A VAL* 5.1 2.2 - - - -
303A ILE* 3.7 32.3 - - - +
304A ILE* 5.7 0.4 - - - -
351A PHE* 4.8 11.9 - - + -
394A VAL* 5.3 3.8 - - + +
397A LEU* 3.6 38.6 - - + -
398A GLU* 4.8 5.2 - - + +
401A LEU* 3.7 27.1 - - + -
419A GLN 3.2 15.0 + - - +
420A ILE* 3.8 18.4 - - + +
422A VAL* 1.3 80.1 - - - +
424A ARG* 1.3 58.2 + - + +
426A GLN* 3.3 5.0 + - - +
427A ILE* 2.9 42.2 + - + +
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Residues in contact with ARG 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A VAL* 4.3 22.7 - - + +
395A LYS* 4.9 5.5 - - - +
398A GLU* 2.7 35.0 + - - -
420A ILE* 2.9 39.3 + - + +
421A ALA* 3.6 6.8 - - - +
423A MET* 1.3 77.4 - - + +
425A GLY* 1.3 57.6 + - - +
427A ILE* 3.3 10.0 + - - +
428A LEU* 3.0 27.7 + - - +
451A VAL* 3.6 36.3 + - + +
453A THR* 3.0 39.5 + - - +
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Residues in contact with GLY 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A ALA 3.2 4.2 + - - -
422A VAL 3.0 4.8 + - - -
424A ARG* 1.3 76.6 - - - +
426A GLN* 1.3 63.8 + - - +
428A LEU* 3.4 2.9 + - - +
429A ASN* 3.1 23.0 + - - +
449A VAL* 3.3 36.3 - - - +
451A VAL* 3.8 16.3 - - - +
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Residues in contact with GLN 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A TYR* 2.9 68.6 + - + +
303A ILE* 4.1 8.1 - - - +
305A ARG* 3.7 27.6 - - + +
355A HIS* 3.1 29.5 + - - -
422A VAL* 3.0 21.3 + - + +
423A MET* 3.6 9.6 - - - +
424A ARG 3.3 0.2 - - - -
425A GLY* 1.3 77.2 + - - +
427A ILE* 1.3 64.3 + - - +
429A ASN* 3.4 0.9 + - - +
430A LEU* 3.0 24.8 + - - +
448A PRO* 4.9 3.2 - - - +
449A VAL 4.8 4.2 + - - +
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Residues in contact with ILE 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ILE* 4.2 24.9 - - + -
388A ILE* 3.6 40.7 - - + +
394A VAL* 3.8 32.5 - - + -
397A LEU* 4.8 6.7 - - + -
423A MET* 2.9 38.9 + - + +
424A ARG* 3.3 10.1 + - - +
426A GLN* 1.3 75.0 - - - +
428A LEU* 1.3 55.2 + - - +
430A LEU* 3.3 7.8 + - - +
431A THR* 2.6 39.7 + - - +
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Residues in contact with LEU 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A ARG 3.0 14.5 + - - +
425A GLY* 3.5 6.5 - - - +
426A GLN 3.1 0.2 - - - -
427A ILE* 1.3 78.0 - - - +
429A ASN* 1.3 65.1 + - - +
431A THR* 3.4 9.9 + - - -
432A GLN* 3.3 21.9 + - + +
449A VAL* 4.5 11.0 - - + -
451A VAL* 3.8 26.9 - - + -
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Residues in contact with ASN 429 (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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302A TYR* 3.0 29.3 + - + +
425A GLY 3.1 7.2 + - - +
426A GLN* 3.7 6.3 - - - +
428A LEU* 1.3 77.9 - - - +
430A LEU* 1.3 63.5 + - - +
432A GLN* 3.2 6.0 + - - +
433A ALA* 3.0 22.9 + - - +
443A LEU* 3.9 2.5 - - - -
446A MET* 3.4 36.9 - - - +
447A PRO* 3.2 24.9 + - - +
448A PRO* 4.7 2.2 - - - +
449A VAL* 3.3 23.4 - - - +
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Residues in contact with LEU 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A VAL* 4.2 13.9 - - + -
302A TYR* 4.2 14.4 - - + -
303A ILE* 3.8 26.0 - - + -
376A PHE* 4.4 13.9 - - + -
384A ILE* 4.1 6.1 - - + -
388A ILE* 3.6 14.1 - - + -
426A GLN 3.0 17.5 + - - +
427A ILE* 3.4 6.1 - - - +
429A ASN* 1.3 76.4 - - - +
431A THR* 1.3 53.1 + - - +
433A ALA 3.4 0.2 + - - -
434A LEU* 2.8 62.9 + - + +
443A LEU* 3.7 29.3 - - + +
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Residues in contact with THR 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A LEU* 3.8 19.3 - - + -
388A ILE* 3.4 18.4 + - + +
389A SER* 4.0 13.5 - - - -
427A ILE* 2.6 26.6 + - - +
428A LEU* 3.5 13.2 + - - -
429A ASN 3.2 0.2 - - - -
430A LEU* 1.3 75.2 - - - +
432A GLN* 1.3 63.8 + - - +
434A LEU* 3.1 6.0 + - - +
435A LYS* 2.8 50.1 + - + +
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Residues in contact with GLN 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A LEU* 3.3 10.5 + - + +
429A ASN* 3.2 9.5 + - - +
431A THR* 1.3 77.7 - - - +
433A ALA* 1.3 58.9 + - - +
435A LYS* 2.9 16.5 + - - +
436A ASP* 2.7 65.2 + - - +
438A LYS* 6.4 0.7 - - + -
446A MET* 4.0 18.2 - - + -
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Residues in contact with ALA 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A PHE* 4.2 7.2 - - + -
429A ASN 3.0 15.9 + - - +
430A LEU 3.7 2.2 - - - +
432A GLN* 1.3 75.9 - - - +
434A LEU* 1.3 61.6 - - - +
437A ASN* 3.4 3.6 + - - -
438A LYS* 3.0 59.6 + - + +
443A LEU* 3.7 27.8 - - + -
446A MET* 4.2 2.8 - - - +
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Residues in contact with LEU 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A VAL* 5.0 2.2 - - + -
376A PHE* 3.5 45.8 - - + -
380A ILE* 4.5 7.9 - - + -
381A LYS* 3.3 47.0 + - + +
384A ILE* 3.8 20.2 - - + -
385A LEU* 4.0 19.0 - - + +
388A ILE* 4.3 4.7 - - + -
430A LEU* 2.8 52.0 + - + +
431A THR 3.4 4.7 - - - +
432A GLN 3.1 0.2 - - - -
433A ALA* 1.3 74.6 - - - +
435A LYS* 1.3 60.4 + - - +
437A ASN* 3.8 0.9 + - - -
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Residues in contact with LYS 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A LYS* 4.6 1.7 + - - +
385A LEU* 4.2 20.2 - - + -
389A SER* 5.1 6.9 - - - -
431A THR* 2.8 40.0 + - + +
432A GLN* 3.5 18.1 + - - +
434A LEU* 1.3 75.6 - - - +
436A ASP* 1.3 65.4 + - - +
437A ASN* 3.3 13.6 + - - +
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Residues in contact with ASP 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A GLN* 2.7 52.4 + - - +
433A ALA 4.7 0.2 - - - +
435A LYS* 1.3 75.9 - - - +
437A ASN* 1.3 75.3 + - - +
438A LYS* 3.0 17.7 + - + +
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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