Contacts of the helix formed by residues 423 - 445 (chain A) in PDB entry 2KWH
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 LEU 423 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421A LYS 5.5 2.7 - - - -
422A ASP* 1.3 80.4 - - - +
424A SER* 1.3 63.9 + - - +
425A LYS 3.5 0.7 - - - -
426A GLU* 3.7 9.2 + - + +
427A GLU* 3.3 30.4 + - + +
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Residues in contact with SER 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A ASP* 2.8 14.0 + - - -
423A LEU* 1.3 76.5 - - - +
425A LYS* 1.3 65.8 + - - -
426A GLU 3.3 0.2 + - - -
427A GLU* 3.4 5.3 + - - +
428A ARG* 2.9 50.9 + - - +
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Residues in contact with LYS 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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412A LEU* 3.2 54.3 - - + +
415A ASP* 3.8 23.6 - - + -
416A LEU* 3.5 13.2 - - + -
422A ASP* 2.7 44.2 + - - +
424A SER* 1.3 79.4 - - - +
426A GLU* 1.3 56.4 + - - +
428A ARG* 3.2 13.1 + - - +
429A LEU* 2.8 26.1 + - - +
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Residues in contact with GLU 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A LEU* 3.7 29.9 - - + +
422A ASP 4.8 1.7 - - - +
423A LEU* 3.7 11.6 + - + +
424A SER 3.2 0.6 - - - -
425A LYS* 1.3 76.6 - - - +
427A GLU* 1.3 69.3 + - + +
428A ARG 3.1 1.3 - - - -
429A LEU* 3.1 33.5 - - + +
430A TRP* 3.2 9.5 + - - +
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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
----------------------------------------------------------
423A LEU* 3.3 20.7 + - + +
424A SER* 3.8 5.2 - - - +
426A GLU* 1.3 81.1 - - + +
428A ARG* 1.3 60.1 + - - +
430A TRP* 3.5 15.7 + - - +
431A GLU* 3.2 20.3 + - - +
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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
----------------------------------------------------------
408A LEU* 6.1 0.4 - - - -
412A LEU* 3.7 24.8 - - + +
424A SER* 2.9 37.0 + - - +
425A LYS* 3.4 13.6 - - - +
427A GLU* 1.3 74.2 - - - +
429A LEU* 1.3 59.6 + - - +
430A TRP 3.1 1.6 - - - -
431A GLU* 3.0 10.4 + - + +
432A VAL* 2.9 38.7 + - + +
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Residues in contact with LEU 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A LEU* 3.8 25.0 - - + +
412A LEU* 3.4 21.0 - - + +
413A HIS* 3.7 22.0 - - + +
416A LEU* 3.6 20.0 - - + -
425A LYS 2.8 11.1 + - - +
426A GLU* 3.1 38.4 - - + +
428A ARG* 1.3 73.3 - - - +
430A TRP* 1.3 63.7 + - + +
432A VAL* 3.7 3.5 - - - +
433A GLN* 2.7 43.0 + - + +
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Residues in contact with TRP 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 GLU 3.2 15.9 + - - +
427A GLU* 3.7 16.4 - - - +
428A ARG 3.1 0.8 - - - -
429A LEU* 1.3 83.2 - - + +
431A GLU* 1.3 60.6 + - - +
433A GLN* 3.5 15.6 - - + +
434A ARG* 2.9 64.3 + - + +
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Residues in contact with GLU 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A GLU 3.2 13.3 + - - +
428A ARG* 3.0 14.5 + - + +
430A TRP* 1.3 74.4 - - - +
432A VAL* 1.3 67.9 + - + +
434A ARG* 2.6 50.6 + - - +
435A ILE* 2.9 50.9 + - + +
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Residues in contact with VAL 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A GLN* 3.3 49.6 - - + +
408A LEU* 3.9 19.3 - - + -
409A LEU* 3.6 20.2 - - + -
412A LEU* 5.0 0.7 - - + -
428A ARG* 2.9 31.3 + - + +
429A LEU* 3.7 6.7 - - - +
431A GLU* 1.3 76.7 - - + +
433A GLN* 1.3 63.1 + - - +
435A ILE* 3.2 7.5 + - + -
436A LEU* 3.0 23.6 + - + +
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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
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406A GLU* 4.8 3.2 + - - -
409A LEU* 3.6 24.0 - - - +
429A LEU* 2.7 27.8 + - + +
430A TRP* 3.5 20.6 - - + +
432A VAL* 1.3 74.2 - - - +
434A ARG* 1.3 59.0 + - - +
436A LEU* 3.3 15.0 - - - +
437A THR* 2.7 43.0 + - - +
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Residues in contact with ARG 434 (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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430A TRP* 2.9 48.6 + - + +
431A GLU* 2.6 55.6 + - - +
433A GLN* 1.3 76.4 - - + +
435A ILE* 1.3 60.9 + - + +
437A THR* 4.0 4.2 - - - -
438A ALA* 2.9 33.0 + - + +
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Residues in contact with ILE 435 (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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405A GLN* 3.8 22.0 - - - +
431A GLU* 2.9 53.8 + - + +
432A VAL* 3.2 7.8 + - + +
434A ARG* 1.3 75.8 - - + +
436A LEU* 1.3 60.9 + - - +
438A ALA* 3.9 2.8 - - - +
439A LEU* 2.8 44.1 + - + +
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Residues in contact with LEU 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A ILE* 3.7 8.9 - - + +
402A ILE* 3.9 38.1 - - + -
405A GLN* 3.2 21.9 + - + +
406A GLU* 3.5 25.6 - - - +
409A LEU* 4.1 0.4 - - + -
432A VAL* 3.0 30.3 + - + +
433A GLN* 3.3 15.7 - - - +
435A ILE* 1.3 79.7 - - - +
437A THR* 1.3 90.1 + - - +
439A LEU* 4.0 2.0 - - - +
440A LYS* 3.3 32.3 + - - +
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Residues in contact with THR 437 (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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433A GLN* 2.7 31.6 + - - +
434A ARG* 4.0 5.4 - - - -
436A LEU* 1.3 91.7 - - - +
438A ALA* 1.3 62.4 + - - +
440A LYS* 3.3 12.4 - - - +
441A ARG* 2.9 41.8 + - + +
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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
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434A ARG 2.9 23.4 + - - +
435A ILE* 4.0 2.9 - - - +
437A THR* 1.3 75.4 - - - +
439A LEU* 1.3 58.1 + - - +
441A ARG* 3.4 4.4 + - - -
442A LYS* 2.8 54.4 + - + +
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Residues in contact with LEU 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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397A GLY 5.0 1.3 - - - -
398A ILE* 4.0 27.8 - - + +
401A GLU* 5.0 13.0 - - + -
405A GLN* 5.4 1.6 - - - +
435A ILE* 2.8 29.4 + - + +
436A LEU* 4.0 3.8 - - - +
438A ALA* 1.3 79.1 - - - +
440A LYS* 1.3 56.8 + - - +
442A LYS* 3.2 4.0 + - + +
443A LEU* 3.0 58.9 + - + +
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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
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395A GLN* 3.8 10.2 + - - +
398A ILE* 3.6 41.3 - - + +
402A ILE* 5.0 5.6 - - + -
436A LEU* 3.3 26.1 + - - +
437A THR* 3.3 18.8 - - - +
439A LEU* 1.3 79.8 - - - +
441A ARG* 1.3 71.9 + - + +
443A LEU* 4.6 1.3 - - - -
444A ARG* 3.1 46.2 + - - +
445A GLU* 4.0 1.3 + - - +
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Residues in contact with ARG 441 (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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437A THR* 2.9 36.3 + - + +
438A ALA* 3.7 5.6 - - - +
440A LYS* 1.3 92.7 - - + +
442A LYS* 1.3 66.2 + - + +
445A GLU* 2.8 75.6 + - + +
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Residues in contact with LYS 442 (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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438A ALA* 2.8 44.7 + - + +
439A LEU* 3.8 5.6 - - + +
441A ARG* 1.3 77.3 - - + +
443A LEU* 1.3 63.5 + - + +
446A ALA* 3.2 25.5 - - + +
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Residues in contact with LEU 443 (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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391A GLY* 6.1 0.9 - - - -
392A SER 3.2 31.6 - - - +
393A GLU* 4.1 23.0 - - + +
394A THR* 3.4 32.8 - - - +
395A GLN* 4.6 7.0 - - - +
397A GLY* 6.0 0.2 - - - -
398A ILE* 5.1 2.0 - - + -
439A LEU* 3.0 52.6 + - + +
440A LYS* 4.2 4.9 - - - +
442A LYS* 1.3 86.4 - - + +
444A ARG* 1.3 59.3 + - - +
446A ALA* 4.5 6.6 - - - +
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Residues in contact with ARG 444 (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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395A GLN* 2.8 44.6 + - + +
399A LYS* 5.9 2.4 - - - +
440A LYS* 3.1 23.2 + - - +
443A LEU* 1.3 75.3 - - - +
445A GLU* 1.3 99.1 + - - +
446A ALA* 3.1 11.2 + - - +
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Residues in contact with GLU 445 (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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440A LYS 4.3 2.2 - - - +
441A ARG* 2.8 72.9 + - + +
444A ARG* 1.3 116.5 + - - +
446A ALA* 1.3 59.1 + - - +
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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
------------------------------------------------------------
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