Contacts of the helix formed by residues 419 - 442 (chain A) in PDB entry 6DBV
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 419 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A SER 5.6 0.4 - - - +
418A LEU* 1.3 78.5 - - - +
420A ARG* 1.3 60.9 + - - +
421A ARG* 3.4 16.0 + - - +
422A ALA 3.6 5.5 + - - -
423A GLN* 3.1 27.0 + - - +
13H T 3.3 33.7 + - - +
14H G 4.9 13.2 + - - +
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Residues in contact with ARG 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A THR* 1.3 74.2 - - - +
421A ARG* 1.3 60.7 + - - +
423A GLN* 3.9 12.5 - - - +
424A LYS* 3.0 38.4 + - - +
455C LEU* 6.1 0.9 - - - -
456C LEU* 3.9 22.1 - - + +
459C ARG* 3.7 38.3 - - - +
464C HIS* 4.9 3.4 - - - -
471C GLU* 5.6 2.4 + - - -
42G G 4.1 5.3 + - - -
43G C 2.9 38.9 + - - -
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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
----------------------------------------------------------
419A THR* 3.3 9.7 + - - +
420A ARG* 1.3 76.8 - - - +
422A ALA* 1.3 58.4 + - - +
424A LYS* 4.1 3.7 - - - +
425A HIS* 2.9 59.1 + - - +
47G A 3.8 8.4 - - - +
48G C 3.4 14.5 - - - +
49G A 4.1 0.4 - - - +
13H T 3.6 42.4 + - + +
14H G 2.3 48.6 + - + +
15H T 4.3 6.5 + - - -
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Residues in contact with ALA 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A LEU* 4.3 10.3 - - + -
419A THR* 3.6 6.3 + - - +
421A ARG* 1.3 79.0 - - - +
423A GLN* 1.3 59.2 + - - +
425A HIS* 3.6 6.1 - - - +
426A ARG* 2.9 37.4 + - - +
12H T 3.5 50.0 - - + +
13H T 4.0 9.6 - - + +
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Residues in contact with GLN 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A LEU* 2.5 44.8 + - + +
416A LEU* 4.1 9.9 + - - +
418A LEU* 3.3 21.8 + - + +
419A THR 3.1 24.6 + - - +
420A ARG* 3.9 18.4 - - - +
421A ARG 3.3 0.2 - - - -
422A ALA* 1.3 77.4 - - - +
424A LYS* 1.3 57.3 + - - +
426A ARG* 3.3 2.9 + - - +
427A LEU* 2.9 34.6 + - - +
452C THR* 3.2 31.7 + - + +
455C LEU* 5.5 4.6 - - - +
456C LEU* 4.7 4.2 - - + +
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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
----------------------------------------------------------
420A ARG* 3.0 23.7 + - - +
421A ARG* 4.2 2.2 - - - +
423A GLN* 1.3 74.1 - - - +
425A HIS* 1.3 60.5 + - - +
427A LEU* 4.4 3.1 - - + +
428A ARG* 2.9 39.7 + - + +
431A LYS* 3.6 33.2 - - + +
456C LEU* 3.6 32.0 - - + +
43G C 5.7 1.0 - - - -
44G T 2.8 39.6 + - - +
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Residues in contact with HIS 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A ARG* 2.9 40.1 + - - +
422A ALA* 3.6 7.6 - - - +
423A GLN 3.3 0.2 - - - -
424A LYS* 1.3 77.9 - - - +
426A ARG* 1.3 61.0 + - + +
428A ARG* 4.1 14.0 + - - +
11H T 5.8 0.2 - - + -
12H T 3.8 36.6 - - + +
13H T 4.8 5.6 - - + -
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Residues in contact with ARG 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A ARG* 5.7 11.3 - - - +
413A GLN 3.2 20.2 + - - -
414A HIS* 5.5 0.2 - - - +
415A LEU* 3.6 33.8 - - - +
418A LEU* 3.1 26.9 - - - +
422A ALA 2.9 19.6 + - - +
423A GLN 3.7 4.0 - - - +
425A HIS* 1.3 80.7 - - + +
427A LEU* 1.3 62.5 + - + +
428A ARG 3.7 0.3 + - - -
429A ASP* 4.7 3.8 + - - +
437C PHE* 3.8 13.0 - - - -
441C GLU* 5.2 3.3 + - - +
442C GLU* 2.4 38.9 + - - +
11H T 4.7 3.4 - - - +
12H T 3.2 30.7 + - - +
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Residues in contact with LEU 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A LEU* 3.7 37.0 - - + -
423A GLN 2.9 17.2 + - - +
424A LYS* 3.7 3.1 - - + +
426A ARG* 1.3 77.2 - - + +
428A ARG* 1.3 65.4 + - - +
429A ASP 3.1 4.2 + - - -
430A LEU* 3.1 6.1 + - - +
431A LYS* 2.9 21.5 + - + +
437C PHE* 3.5 14.8 - - + -
442C GLU* 3.2 33.9 - - + +
449C VAL* 4.3 14.8 - - + +
452C THR* 3.8 20.0 - - + -
453C LEU* 4.3 17.3 - - + +
456C LEU* 5.5 3.8 - - + -
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Residues in contact with ARG 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A LYS* 2.9 22.2 + - + +
425A HIS* 4.1 12.2 + - - +
426A ARG 3.5 2.4 - - - -
427A LEU* 1.3 76.3 - - - +
429A ASP* 1.3 63.0 + - - +
431A LYS* 3.6 14.3 - - + +
432A ASN* 2.9 46.4 + - - +
46G T 4.1 28.4 + - - +
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Residues in contact with ASP 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A ARG 4.7 4.0 + - - +
427A LEU 3.1 0.8 + - - -
428A ARG* 1.3 78.1 - - - +
430A LEU* 1.3 58.4 + - - +
432A ASN* 3.4 4.0 + - - +
433A GLN* 2.9 35.6 + - - +
437C PHE* 3.7 18.0 - - + -
441C GLU* 4.8 9.4 - - - +
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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
----------------------------------------------------------
427A LEU 3.1 4.6 + - - +
429A ASP* 1.3 76.4 - - - +
431A LYS* 1.3 60.6 + - - +
433A GLN* 3.2 27.4 - - + +
434A VAL* 2.9 34.7 + - + +
430C LEU* 4.6 2.9 - - + -
434C VAL* 3.7 36.8 - - + +
437C PHE* 3.5 38.5 - - + -
449C VAL* 3.5 32.5 - - + -
453C LEU* 3.8 14.6 - - + -
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Residues in contact with LYS 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A LYS* 3.6 36.7 - - + +
427A LEU* 2.9 18.3 + - + +
428A ARG* 3.6 12.8 - - + +
429A ASP 3.3 0.2 - - - -
430A LEU* 1.3 76.8 - - - +
432A ASN* 1.3 66.6 + - - +
434A VAL* 3.5 5.0 + - - +
435A LYS* 2.9 32.8 + - + +
446A VAL* 5.7 1.4 - - - +
453C LEU* 4.4 15.1 - - + +
456C LEU* 5.1 16.2 + - + +
44G T 3.8 16.2 + - - -
45G G 4.7 12.8 + - - -
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Residues in contact with ASN 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A ARG* 2.9 47.4 + - - +
429A ASP* 4.1 3.5 - - - +
431A LYS* 1.3 83.8 - - - +
433A GLN* 1.3 60.8 + - - +
435A LYS* 3.4 13.1 - - + +
436A THR* 2.9 32.0 + - - +
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Residues in contact with GLN 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ASP* 2.9 30.0 + - - +
430A LEU* 3.2 26.4 - - + +
431A LYS 3.3 0.2 - - - -
432A ASN* 1.3 76.5 - - - +
434A VAL* 1.3 57.4 + - - +
436A THR* 3.1 11.2 - - + +
437A PHE* 3.0 30.0 + - - +
433C GLN* 3.1 40.0 + - - +
436C THR* 6.3 0.6 - - - +
437C PHE* 4.9 9.2 - - - +
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Residues in contact with VAL 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A LEU* 2.9 31.5 + - + +
431A LYS* 3.8 5.4 - - - +
433A GLN* 1.3 71.5 - - - +
435A LYS* 1.3 60.8 + - - +
437A PHE* 4.1 1.0 - - - +
438A ALA* 2.9 29.1 + - - +
446A VAL* 4.1 18.4 - - + +
449A VAL* 3.6 27.4 - - + -
450A CYS* 5.0 6.7 - - + +
453A LEU* 4.4 11.0 - - + -
430C LEU* 3.9 27.8 - - + -
453C LEU* 4.6 10.1 - - + -
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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
----------------------------------------------------------
431A LYS* 2.9 26.3 + - + +
432A ASN* 3.4 17.9 - - + +
433A GLN 3.2 0.2 - - - -
434A VAL* 1.3 75.9 - - - +
436A THR* 1.3 57.9 + - - +
438A ALA* 3.9 1.4 - - - +
439A GLU* 2.7 70.5 + - - +
444A GLY* 6.2 0.4 - - - -
446A VAL* 3.6 35.4 - - + +
45G G 6.1 0.9 - - - -
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Residues in contact with THR 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A ASN 2.9 17.9 + - - +
433A GLN* 3.1 23.3 - - + +
435A LYS* 1.3 75.4 - - - +
437A PHE* 1.3 58.2 + - + +
439A GLU* 3.4 7.8 + - - +
440A LYS* 2.9 55.0 + - - +
433C GLN* 6.4 0.2 - - - +
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Residues in contact with PHE 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A GLN 3.0 20.0 + - - +
434A VAL* 4.1 3.4 - - - +
436A THR* 1.3 78.5 - - + +
438A ALA* 1.3 61.0 + - - +
440A LYS* 3.2 19.4 + - + +
441A GLU* 3.0 58.3 + - + +
449A VAL* 5.1 3.4 - - + -
426C ARG 4.5 6.5 - - - -
427C LEU* 3.5 32.1 - - + -
429C ASP* 4.8 12.8 - - + -
430C LEU* 3.5 48.0 - - + -
433C GLN* 5.1 12.1 - - - +
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Residues in contact with ALA 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A VAL 2.9 19.5 + - - +
435A LYS 3.9 2.7 - - - +
437A PHE* 1.3 76.7 - - - +
439A GLU* 1.3 61.9 + - - +
441A GLU* 4.5 0.4 - - - +
442A GLU* 2.9 28.9 + - - +
443A GLY 3.2 6.4 + - - -
444A GLY 4.1 2.7 + - - -
445A ASP 3.7 22.0 - - - +
446A VAL* 4.0 15.9 - - + -
449A VAL* 3.7 21.1 - - + -
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Residues in contact with GLU 439 (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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435A LYS* 2.7 53.9 + - - +
436A THR* 3.9 6.2 - - - +
438A ALA* 1.3 76.9 - - + +
440A LYS* 1.3 59.7 + - - +
443A GLY* 4.4 9.2 + - - -
444A GLY* 4.3 19.5 - - - +
446A VAL* 5.4 0.9 - - + -
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Residues in contact with LYS 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A THR* 2.9 45.4 + - - +
437A PHE* 3.2 23.4 - - + +
438A ALA 3.1 0.2 - - - -
439A GLU* 1.3 80.2 - - - +
441A GLU* 1.3 66.9 + - + +
443A GLY 5.1 0.3 + - - -
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Residues in contact with GLU 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A PHE* 3.0 53.8 + - + +
438A ALA* 5.1 0.2 - - - -
440A LYS* 1.3 83.8 - - + +
442A GLU* 1.3 76.7 + - + +
443A GLY 3.5 1.2 + - - -
412C ARG* 2.6 42.4 + - - +
426C ARG* 4.4 22.8 + - + +
427C LEU* 5.5 1.6 - - + -
429C ASP* 5.5 1.9 - - - +
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Residues in contact with GLU 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A ALA 2.9 12.3 + - - +
441A GLU* 1.3 82.2 - - + +
443A GLY* 1.3 66.5 + - - +
444A GLY 3.8 0.2 - - - -
445A ASP* 4.1 28.2 - - + +
449A VAL* 3.6 24.9 - - + -
413C GLN 4.6 1.7 - - - +
414C HIS* 5.2 4.9 - - - -
415C LEU* 3.3 42.1 + - + +
426C ARG* 3.3 35.8 + - - +
427C LEU* 4.8 6.7 - - + +
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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) + - + + + + + -
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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