Contacts of the helix formed by residues 416 - 435 (chain A) in PDB entry 2PKG
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 LYS 416 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378A PRO* 3.9 29.6 - - + -
381A ARG* 4.4 4.5 - - - +
414A ASP* 3.1 11.9 + - - +
415A ALA* 1.3 83.8 - - + +
417A TRP* 1.3 67.5 + - + +
418A ARG* 3.2 6.0 + - + +
419A VAL* 3.2 14.7 + - + +
420A ARG* 3.1 23.7 + - - +
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Residues in contact with TRP 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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415A ALA 3.8 0.4 + - - -
416A LYS* 1.3 69.8 - - + +
418A ARG* 1.3 90.1 + - + +
420A ARG* 3.1 30.2 + - - +
421A LEU* 2.6 49.5 + - + +
455A VAL* 3.6 15.9 - - + -
457A ALA* 4.9 5.4 - - + -
458A ILE* 3.2 12.4 - - + +
417B TRP* 4.9 0.2 - + - -
421B LEU* 3.8 32.5 - - + -
456B TYR* 4.3 17.4 - + - -
457B ALA* 3.3 48.5 - - + -
460B GLU* 3.9 24.1 - - + +
461B ALA* 4.5 7.4 - - + -
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Residues in contact with ARG 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A PRO* 6.4 1.1 - - + -
382A LEU* 3.8 36.0 - - + +
416A LYS* 3.2 4.7 + - + +
417A TRP* 1.3 108.4 - - + +
419A VAL* 1.3 59.5 + - + +
421A LEU* 2.6 28.6 + - - +
422A ALA* 2.6 47.0 + - - +
425A GLU* 4.1 1.6 + - - -
418B ARG* 4.0 15.8 - - - +
421B LEU* 4.5 7.2 - - - +
425B GLU* 2.5 47.2 + - - -
461B ALA* 6.2 1.1 - - + -
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Residues in contact with VAL 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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378A PRO* 4.3 21.8 - - + +
381A ARG* 4.3 13.9 - - + +
382A LEU* 4.8 6.9 - - + +
385A ILE* 3.9 8.5 - - + -
411A LEU* 3.5 23.1 - - + +
414A ASP* 3.2 45.1 - - + +
416A LYS* 3.2 12.9 + - + +
418A ARG* 1.3 76.8 - - + +
420A ARG* 1.3 67.0 + - - +
422A ALA* 3.2 8.6 - - - +
423A ILE* 2.9 18.5 + - - +
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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
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411A LEU 4.5 6.7 - - - -
412A ALA* 4.1 16.8 - - - +
413A GLU* 4.9 1.8 - - - +
414A ASP 2.7 47.2 + - - +
415A ALA 3.0 19.0 + - - -
416A LYS 3.1 12.1 + - - -
417A TRP* 3.1 19.9 + - - +
418A ARG 3.0 0.8 - - - -
419A VAL* 1.3 75.8 - - - +
421A LEU* 1.3 56.2 + - - +
423A ILE* 2.6 31.6 + - - +
424A ILE* 3.0 12.8 + - - +
450A TRP* 4.8 7.2 - - - +
453A ASP* 2.6 45.0 + - - -
454A HIS* 5.3 4.4 - - - +
455A VAL* 3.2 17.0 - - - +
458A ILE* 3.6 11.1 - - + +
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Residues in contact with LEU 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 TRP* 2.6 31.9 + - + +
418A ARG* 2.6 24.8 + - - +
420A ARG* 1.3 71.5 - - - +
422A ALA* 1.3 66.7 + - - +
424A ILE* 3.0 6.7 + - + -
425A GLU* 3.0 46.2 + - + +
457A ALA* 5.7 0.2 - - + -
458A ILE* 3.2 12.9 - - + +
461A ALA* 3.9 25.4 - - + -
417B TRP* 3.7 33.2 - - + -
418B ARG* 4.5 1.3 - - - +
421B LEU* 4.2 4.5 - - + -
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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
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382A LEU* 4.4 17.7 - - + -
385A ILE* 3.9 26.7 - - + +
418A ARG* 2.6 25.6 + - - +
419A VAL* 3.2 12.6 - - - +
420A ARG 2.8 1.0 + - - -
421A LEU* 1.3 74.3 - - - +
423A ILE* 1.3 65.4 + - - +
425A GLU* 3.2 11.9 + - - +
426A TYR* 3.4 11.4 + - - +
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Residues in contact with ILE 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 ILE* 4.0 19.1 - - + -
408A ILE* 3.7 30.1 - - + +
411A LEU* 3.4 43.3 - - + -
412A ALA* 3.7 13.7 - - + -
419A VAL 2.9 14.8 + - - +
420A ARG 2.6 12.4 + - - +
422A ALA* 1.3 70.8 - - - +
424A ILE* 1.3 63.7 + - - +
426A TYR* 3.0 21.2 + - + +
427A MET* 3.0 15.7 + - - +
430A LEU* 6.5 0.4 - - + -
446A LEU* 5.9 1.1 - - + -
450A TRP* 3.6 24.5 - - + -
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Residues in contact with ILE 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 ARG 3.0 8.7 + - - +
421A LEU* 3.3 9.0 - - + +
423A ILE* 1.3 75.6 - - - +
425A GLU* 1.3 64.6 + - + +
426A TYR 3.1 0.7 + - - -
427A MET* 3.2 5.4 + - - +
428A PRO* 3.1 17.5 - - - +
450A TRP* 3.5 44.0 - - + -
458A ILE* 3.7 51.1 - - + +
461A ALA* 4.0 31.0 - - + +
462A ALA* 4.1 4.3 - - - +
465A ASN* 3.9 13.9 + - + -
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Residues in contact with GLU 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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418A ARG* 4.1 3.5 + - - -
421A LEU* 3.0 41.1 + - + +
422A ALA* 3.2 5.5 + - - +
424A ILE* 1.3 75.0 - - + +
426A TYR* 1.3 60.1 + - - +
428A PRO* 3.5 15.0 - - - +
429A LEU* 5.0 1.7 + - - +
461A ALA* 5.6 2.2 - - + -
379B GLU* 5.8 0.2 - - - +
382B LEU* 4.4 8.0 - - - +
418B ARG* 2.1 46.6 + - - -
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Residues in contact with TYR 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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385A ILE* 4.9 9.6 - - + +
388A LEU* 3.7 43.5 + - + +
389A ASP* 3.5 39.5 + - - +
392A ASN* 4.8 1.7 - - - +
400A LEU* 4.0 21.7 - - - +
408A ILE* 3.9 12.2 - - + +
422A ALA 3.4 9.4 + - - +
423A ILE* 3.0 14.5 + - + +
425A GLU* 1.3 80.6 - - - +
427A MET* 1.3 66.7 + - - +
428A PRO* 3.2 0.7 - - - -
429A LEU* 2.8 29.2 + - + +
430A LEU* 2.9 42.3 + - + +
433A GLN* 4.5 4.5 + - - -
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Residues in contact with MET 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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408A ILE* 5.7 1.3 - - + -
423A ILE* 3.0 14.7 + - - +
424A ILE 3.4 13.2 - - - +
426A TYR* 1.3 75.5 - - - +
428A PRO* 1.3 67.4 - - + +
430A LEU* 3.0 40.4 + - + +
431A ALA* 2.8 26.6 + - - +
439A PHE* 4.5 5.2 - - + -
443A LEU* 3.6 31.6 - - + -
446A LEU* 5.2 7.2 - - - -
447A CYS* 3.7 32.3 - - - -
450A TRP* 4.2 16.4 - - + -
465A ASN* 4.0 9.4 - - - +
469A LEU* 5.0 0.4 - - + -
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Residues in contact with PRO 428 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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424A ILE 3.1 16.2 - - - +
425A GLU* 3.5 13.7 - - - +
426A TYR 3.2 1.8 - - - -
427A MET* 1.3 90.0 - - - +
429A LEU* 1.3 67.8 + - + +
431A ALA* 3.8 1.7 - - - +
432A GLY 3.1 16.5 + - - -
465A ASN* 3.4 15.0 - - - +
468A LYS* 4.0 40.2 - - + +
469A LEU* 4.4 13.2 - - + +
472A LYS* 3.7 17.4 - - - +
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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
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389A ASP* 3.5 41.1 - - + +
425A GLU 5.4 1.3 - - - +
426A TYR* 2.8 21.3 + - + +
428A PRO* 1.3 78.6 - - + +
430A LEU* 1.3 61.6 + - - +
432A GLY* 3.3 1.6 + - - -
433A GLN* 2.6 46.6 + - + +
472A LYS* 4.3 17.3 - - - +
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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
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400A LEU* 4.9 11.9 - - + -
405A LEU* 4.4 11.2 - - + -
408A ILE* 4.1 29.8 - - + -
423A ILE* 6.5 0.2 - - + -
426A TYR* 2.9 39.7 + - + +
427A MET* 3.1 29.8 - - + +
429A LEU* 1.3 72.4 - - - +
431A ALA* 1.3 73.1 + - - +
433A GLN* 2.8 23.8 + - + +
434A LEU* 3.0 37.0 + - + -
443A LEU* 4.9 0.9 - - + -
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Residues in contact with ALA 431 (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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427A MET* 2.8 19.6 + - - +
428A PRO 3.8 0.4 - - - +
430A LEU* 1.3 70.2 - - - +
432A GLY* 1.3 70.7 + - - +
434A LEU* 2.6 22.3 + - - +
435A GLY 3.0 8.8 + - - +
439A PHE* 3.4 34.5 - - + -
443A LEU* 4.5 4.7 - - + -
469A LEU* 3.8 9.0 - - + -
473A PHE* 3.6 20.0 - - + -
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Residues in contact with GLY 432 (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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428A PRO 3.1 12.2 + - - -
429A LEU 3.6 5.2 - - - -
430A LEU 3.0 0.2 + - - -
431A ALA* 1.3 83.9 - - - +
433A GLN* 1.3 59.5 + - - +
435A GLY* 3.2 10.7 + - - -
472A LYS* 4.0 27.3 - - - +
473A PHE* 4.1 7.1 - - - -
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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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389A ASP 4.1 11.7 + - - -
392A ASN* 2.3 41.9 - - - +
393A GLU* 5.2 1.8 + - - -
397A ILE* 3.8 29.0 - - + +
400A LEU* 5.8 0.7 - - - -
426A TYR* 4.5 7.1 + - - -
429A LEU* 2.6 51.4 + - + +
430A LEU* 2.8 15.0 + - + +
431A ALA 2.8 2.4 + - - -
432A GLY* 1.3 71.2 - - - +
434A LEU* 1.3 61.7 + - - +
435A GLY* 3.3 1.2 + - - -
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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
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397A ILE* 3.9 21.5 - - + -
398A ARG* 6.1 0.2 - - - -
400A LEU* 6.2 0.4 - - + -
401A SER* 4.0 23.6 - - - -
405A LEU* 3.3 31.9 - - + -
430A LEU* 3.0 26.0 + - + -
431A ALA* 2.6 15.4 + - - +
433A GLN* 1.3 73.7 - - - +
435A GLY* 1.3 60.8 + - - +
437A GLU* 3.4 8.3 - - - +
438A PHE* 3.6 32.6 - - + +
439A PHE 5.3 0.2 - - - +
443A LEU* 4.0 17.3 - - + -
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Residues in contact with GLY 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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431A ALA 3.0 10.5 + - - +
432A GLY 3.2 10.1 + - - -
433A GLN 3.2 0.8 - - - -
434A LEU* 1.3 80.2 - - - +
436A VAL* 1.3 62.4 + - - -
437A GLU* 2.7 23.7 - - - +
438A PHE 3.2 0.2 + - - -
439A PHE* 3.2 18.2 + - - +
473A PHE* 4.3 1.6 - - - -
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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
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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