Contacts of the helix formed by residues 408 - 431 (chain A) in PDB entry 1KU7
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 THR 408 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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399A GLU* 5.7 2.0 - - - -
407A VAL* 1.3 80.7 - - - +
409A ARG* 1.3 65.4 + - - +
410A GLU* 3.7 6.1 + - - +
411A ARG* 3.2 14.9 + - - +
412A ILE* 3.2 20.0 + - - +
3B T 2.9 53.9 + - + +
4B T 4.2 16.8 - - + +
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Residues in contact with ARG 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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398A LEU* 3.7 20.5 - - + +
399A GLU* 3.6 54.0 + - - +
402A GLY* 4.9 0.6 - - - -
408A THR* 1.3 76.3 - - - +
410A GLU* 1.3 61.3 + - + +
412A ILE* 3.3 3.5 + - - +
413A ARG* 2.9 27.9 + - - +
6B A 3.9 8.7 - - - +
7B C 4.4 1.6 - - - +
17C T 3.6 27.4 - - - +
18C G 2.6 52.9 + - - -
19C T 3.5 16.1 + - + -
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Residues in contact with GLU 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A THR* 3.2 7.9 + - - +
409A ARG* 1.3 82.3 - - + +
411A ARG* 1.3 58.9 + - - +
413A ARG* 2.6 49.8 + - - +
414A GLN* 2.8 51.7 + - - +
3B T 4.0 4.0 - - + +
4B T 3.3 31.4 - - + +
5B G 4.9 0.4 - - - +
19C T 3.7 6.2 - - + +
20C C 2.9 25.7 + - - +
21C A 3.6 8.7 + - - +
22C A 4.9 0.2 + - - -
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Residues in contact with ARG 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A VAL* 3.6 20.6 - - + -
408A THR* 3.2 12.7 + - - +
410A GLU* 1.3 79.0 - - - +
412A ILE* 1.3 64.3 + - - +
414A GLN* 2.9 49.7 + - - +
415A ILE* 2.9 46.0 + - + +
1B C 3.3 35.4 + - - +
2B C 2.7 68.6 + - - +
3B T 3.6 18.6 - - + +
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Residues in contact with ILE 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A VAL* 3.6 21.3 - - + -
387A ARG* 4.9 0.2 - - - -
398A LEU* 3.6 19.7 - - + +
401A VAL* 3.4 38.8 - - + +
402A GLY* 3.5 32.3 - - - +
405A PHE* 4.2 9.9 - - + -
407A VAL* 3.9 15.0 - - + -
408A THR 3.2 8.4 + - - +
409A ARG 3.6 6.3 - - - +
411A ARG* 1.3 76.6 - - - +
413A ARG* 1.3 54.4 + - - +
415A ILE* 3.1 11.3 + - + +
416A GLU* 2.7 33.4 + - - +
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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
----------------------------------------------------------
398A LEU* 3.8 22.4 - - + +
409A ARG 2.9 14.1 + - - +
410A GLU* 2.6 54.3 + - - +
412A ILE* 1.3 77.2 - - - +
414A GLN* 1.3 67.9 + - - +
416A GLU* 3.8 3.1 - - - +
417A ASN* 3.0 47.9 + - - +
19C T 3.8 53.4 + - - +
20C C 3.2 32.0 + - - +
21C A 5.6 1.0 + - - -
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Residues in contact with GLN 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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410A GLU* 2.8 43.1 + - - +
411A ARG* 2.9 43.3 + - - +
413A ARG* 1.3 80.8 - - - +
415A ILE* 1.3 57.4 - - - +
417A ASN* 3.2 8.5 + - - +
418A LYS* 2.9 29.4 + - - +
2B C 3.7 17.1 + - - +
3B T 3.0 25.3 + - - +
22C A 4.3 4.2 - - - +
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Residues in contact with ILE 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A ARG* 3.8 37.9 - - + +
380A GLU* 4.2 26.6 - - + +
383A VAL* 4.0 22.0 - - + -
405A PHE* 6.4 0.4 - - + -
407A VAL* 5.4 0.9 - - + -
411A ARG* 2.9 46.4 + - + +
412A ILE* 3.4 18.8 - - + +
414A GLN* 1.3 76.4 - - - +
416A GLU* 1.3 63.4 + - - +
418A LYS* 3.2 7.8 + - - +
419A ALA* 2.9 22.2 + - - +
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Residues in contact with GLU 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A VAL* 4.1 14.6 - - + -
384A LEU* 3.7 21.4 - - + +
387A ARG* 2.9 49.1 + - - +
388A LYS* 4.5 11.4 - - - -
398A LEU* 3.3 11.6 - - - +
412A ILE 2.7 19.4 + - - +
413A ARG* 3.8 4.3 - - - +
415A ILE* 1.3 72.4 - - - +
417A ASN* 1.3 66.0 + - - +
419A ALA* 3.2 4.3 + - - +
420A LEU* 3.0 38.5 + - + +
19C T 5.5 1.6 + - - -
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Residues in contact with ASN 417 (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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413A ARG* 3.0 44.2 + - - +
414A GLN* 3.2 6.9 + - - +
416A GLU* 1.3 83.7 - - - +
418A LYS* 1.3 61.0 + - - +
420A LEU* 3.5 9.5 + - - +
421A ARG* 3.0 30.9 + - - +
19C T 5.2 3.6 + - - -
20C C 5.7 0.8 + - - -
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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
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380A GLU* 4.0 13.7 - - - +
414A GLN 2.9 12.0 + - - +
415A ILE* 3.2 10.7 + - - +
417A ASN* 1.3 73.0 - - - +
419A ALA* 1.3 69.6 + - - +
421A ARG* 3.1 9.2 + - + +
422A LYS* 2.9 47.9 + - + +
1B C 6.2 2.6 - - - -
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Residues in contact with ALA 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A LEU* 3.9 14.3 - - + +
380A GLU* 4.1 27.5 + - + +
384A LEU* 4.1 24.0 - - + -
415A ILE 2.9 13.6 + - - +
416A GLU* 3.5 8.3 - - - +
418A LYS* 1.3 76.2 - - - +
420A LEU* 1.3 63.9 + - - +
422A LYS* 3.1 13.7 + - - +
423A LEU* 3.1 18.3 + - - +
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Residues in contact with LEU 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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384A LEU* 3.5 35.4 - - + -
388A LYS* 6.1 7.0 - - - -
416A GLU* 3.0 37.4 + - + +
417A ASN* 3.9 9.6 - - - +
419A ALA* 1.3 75.1 - - - +
421A ARG* 1.3 65.5 + - - +
423A LEU* 2.8 14.3 + - + +
424A LYS* 2.8 38.6 + - - +
389D GLY 4.9 3.6 - - - +
393D GLY* 4.6 18.2 - - - +
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Residues in contact with ARG 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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417A ASN* 3.0 24.3 + - - +
418A LYS* 3.3 10.3 - - + +
420A LEU* 1.3 77.6 - - - +
422A LYS* 1.3 63.0 - - + +
424A LYS* 4.0 11.0 - - - +
425A TYR* 3.0 28.4 + - + +
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Residues in contact with LYS 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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375A LYS 4.7 5.9 + - - +
376A LEU* 3.4 28.4 - - + +
377A SER* 4.6 1.8 - - - +
380A GLU* 2.8 37.3 + - - +
418A LYS* 2.9 38.0 + - + +
419A ALA* 3.3 7.0 - - - +
420A LEU 3.0 0.2 - - - -
421A ARG* 1.3 77.7 - - + +
423A LEU* 1.3 62.6 + - - +
425A TYR* 3.6 5.1 - - - +
426A HIS* 3.0 44.5 + - + +
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Residues in contact with LEU 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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372A ALA* 3.7 28.6 - - + +
373A LEU* 3.8 17.0 - - - +
376A LEU* 4.5 9.6 - - + -
384A LEU* 4.1 22.2 - - + -
419A ALA 3.1 11.2 + - - +
420A LEU* 2.8 9.6 + - + +
422A LYS* 1.3 77.7 - - - +
424A LYS* 1.3 61.5 + - - +
426A HIS* 3.4 3.4 + - - +
427A GLU* 3.0 24.6 + - - +
389D GLY 3.7 15.9 - - - +
390D LEU 3.5 20.0 - - - +
391D ILE 4.0 8.7 - - - +
392D ASP* 3.4 6.0 - - - -
393D GLY* 3.4 16.6 - - - +
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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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420A LEU* 2.8 32.3 + - - +
421A ARG* 4.0 9.4 - - - +
423A LEU* 1.3 70.7 - - - +
425A TYR* 1.3 59.1 + - - +
427A GLU* 3.1 5.0 + - - +
428A SER* 2.8 32.6 + - - -
392D ASP 3.4 14.8 + - - +
393D GLY* 3.9 18.4 - - - -
394D ARG* 3.9 40.0 - - - +
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Residues in contact with TYR 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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421A ARG* 3.0 20.6 + - + +
422A LYS* 3.6 5.2 - - - +
424A LYS* 1.3 77.1 - - - +
426A HIS* 1.3 84.9 + + - +
428A SER* 3.0 22.4 + - - -
429A ARG* 3.1 56.2 + - + +
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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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372A ALA* 3.6 34.3 - - + -
375A LYS* 5.6 7.1 - - - +
376A LEU* 6.2 0.4 - - + -
422A LYS* 3.0 37.2 + - + +
423A LEU 3.9 2.7 - - - +
425A TYR* 1.3 96.4 - + - +
427A GLU* 1.3 58.6 + - - +
429A ARG* 3.1 4.7 + - - +
430A THR* 2.9 41.2 + - + +
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Residues in contact with GLU 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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423A LEU 3.0 19.0 + - - +
424A LYS* 3.4 5.6 - - - +
426A HIS* 1.3 77.8 - - - +
428A SER* 1.3 56.2 + - - +
430A THR* 4.3 1.8 + - - -
431A ARG* 2.8 30.0 + - - -
432A LYS* 3.3 21.5 + - - +
433A LEU* 3.2 19.0 + - - +
434A ARG* 2.7 50.3 + - - +
392D ASP* 3.7 30.4 - - + +
394D ARG* 5.8 3.1 - - + -
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Residues in contact with SER 428 (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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424A LYS 2.8 17.6 + - - -
425A TYR* 3.0 22.2 + - - -
427A GLU* 1.3 73.1 - - - +
429A ARG* 1.3 62.3 + - - +
431A ARG* 4.4 3.4 + - - +
434A ARG* 4.5 21.2 + - - +
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Residues in contact with ARG 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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425A TYR* 3.1 59.3 + - + +
426A HIS* 3.7 5.6 - - - +
428A SER* 1.3 83.0 - - - +
430A THR* 1.3 64.7 + - + +
431A ARG* 5.1 0.4 - - - +
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Residues in contact with THR 430 (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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426A HIS* 2.9 22.9 + - + +
427A GLU* 4.2 1.6 + - - -
429A ARG* 1.3 81.8 - - + +
431A ARG* 1.3 74.2 + - - +
432A LYS* 3.4 28.6 + - - +
435A ASP* 3.9 4.2 - - - +
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Residues in contact with ARG 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A GLU* 2.8 25.6 + - - +
428A SER 5.1 2.2 - - - +
429A ARG 3.6 1.8 - - - -
430A THR* 1.3 82.2 + - - +
432A LYS* 1.3 65.4 + - - +
434A ARG* 3.0 36.0 + - + +
435A ASP* 2.8 47.1 + - - +
438A GLU* 3.2 29.3 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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