Contacts of the helix formed by residues 436 - 457 (chain A) in PDB entry 3IW4
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 436 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A LYS 3.7 3.0 + - - -
435A PHE* 1.3 71.3 - - - +
437A GLU* 1.3 69.4 + - - +
438A PRO* 3.3 12.6 - - + -
439A GLN* 2.9 27.3 + - + +
440A ALA 3.0 10.6 + - - -
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Residues in contact with GLU 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A PHE 3.6 2.0 + - - -
436A LYS* 1.3 73.7 - - - +
438A PRO* 1.3 67.3 - - + +
440A ALA* 3.6 7.9 - - - +
441A VAL* 2.8 45.3 + - + +
532A LEU* 4.2 10.6 - - + +
561A LEU* 5.5 0.7 - - - +
562A SER* 2.8 40.6 + - - -
564A GLU* 4.4 3.8 - - - +
565A ALA* 3.8 8.6 + - - +
596A PHE* 3.7 25.6 - - + +
598A ARG* 4.8 9.5 + - - -
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Residues in contact with PRO 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A LYS* 3.4 17.0 - - + -
437A GLU* 1.3 95.7 - - + +
439A GLN* 1.3 55.3 + - - +
441A VAL* 3.4 10.5 - - + +
442A PHE* 3.1 25.1 + - - +
613A PRO* 5.0 0.6 - - - +
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Residues in contact with GLN 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A VAL* 5.3 2.6 - - - +
435A PHE* 3.3 37.4 - - + +
436A LYS* 2.9 21.4 + - + +
438A PRO* 1.3 77.2 - - - +
440A ALA* 1.3 67.4 + - - +
442A PHE* 3.0 12.0 + - - +
443A TYR* 3.0 40.8 + - + -
613A PRO* 3.5 29.8 - - + -
614A PHE* 3.8 16.3 - - - -
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Residues in contact with ALA 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A PHE* 4.0 16.0 - - + +
436A LYS 3.0 10.7 + - - +
437A GLU 3.6 6.5 - - - +
439A GLN* 1.3 75.6 - - - +
441A VAL* 1.3 53.8 + - - +
442A PHE 3.1 0.3 + - - -
443A TYR* 3.1 2.1 + - - -
444A ALA* 2.7 36.3 + - - +
528A LEU* 4.9 2.7 - - + -
531A MET* 3.7 22.6 - - + +
532A LEU* 3.7 31.6 - - + -
596A PHE* 5.1 0.7 - - + -
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Residues in contact with VAL 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A GLU* 2.8 41.3 + - + +
438A PRO* 3.4 10.5 - - + +
440A ALA* 1.3 72.5 - - - +
442A PHE* 1.3 61.9 + - - +
444A ALA* 4.5 0.2 - - - -
445A ALA* 3.0 23.7 + - - +
596A PHE* 3.6 50.8 - - + +
597A PHE* 3.4 6.7 - - + -
599A ARG* 6.5 0.4 - - + -
600A ILE* 3.7 28.0 - - + -
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Residues in contact with PHE 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A PRO 3.1 13.8 + - - +
439A GLN 3.0 9.0 + - - +
441A VAL* 1.3 74.8 - - - +
443A TYR* 1.3 91.9 + + - +
445A ALA* 3.3 7.0 + - - +
446A GLU* 3.0 59.2 + - - +
475A GLY 3.8 7.0 - - - -
476A HIS* 3.5 10.1 - + - -
600A ILE* 5.1 7.4 - - + -
605A LEU* 4.3 12.3 - - + -
610A ILE* 4.2 24.7 - - + -
611A GLN 4.9 1.1 - - - -
612A PRO* 3.5 20.9 - - + -
613A PRO* 3.1 31.0 - - + -
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Residues in contact with TYR 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A LEU* 4.2 8.5 - - + -
435A PHE* 3.6 36.8 - + - -
439A GLN* 3.0 38.7 + - + -
440A ALA 3.7 0.9 - - - +
442A PHE* 1.3 104.5 - + - +
444A ALA* 1.3 64.7 + - - +
446A GLU* 3.0 4.1 + - - +
447A ILE* 2.9 30.8 + - + +
471A LEU* 3.8 15.6 - - + +
475A GLY 4.1 10.1 + - - -
477A ILE* 3.5 28.9 - - + -
531A MET* 3.7 16.2 - - - -
613A PRO* 4.3 5.0 - - + +
614A PHE* 3.6 30.7 + - - -
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Residues in contact with ALA 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A ALA 2.7 20.7 + - - +
441A VAL* 3.9 5.4 - - - +
443A TYR* 1.3 73.0 - - - +
445A ALA* 1.3 52.1 + - - +
447A ILE* 3.3 3.5 + - - -
448A SER 2.8 27.0 + - - -
524A TYR* 2.7 36.8 + - + +
527A LEU* 5.6 0.2 - - - -
528A LEU* 3.7 26.0 - - + -
531A MET* 3.9 6.1 - - + +
596A PHE* 4.6 1.6 - - + -
597A PHE* 4.0 8.3 - - + -
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Residues in contact with ALA 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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441A VAL 3.0 20.0 + - - +
442A PHE* 3.4 5.6 - - - +
443A TYR 3.2 0.2 - - - -
444A ALA* 1.3 76.2 - - - +
446A GLU* 1.3 63.4 + - - +
448A SER* 2.8 24.2 + - - -
449A ILE* 3.3 11.1 + - - +
597A PHE* 3.5 23.5 - - + -
600A ILE* 4.6 4.5 - - + -
602A TRP* 4.0 3.6 - - + -
605A LEU* 3.1 27.6 - - + -
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Residues in contact with GLU 446 (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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399A PHE* 3.4 39.2 - - + +
442A PHE* 3.0 38.7 + - + +
443A TYR 3.7 4.5 - - - +
445A ALA* 1.3 75.9 - - - +
447A ILE* 1.3 63.3 + - - +
449A ILE* 3.1 19.2 + - - +
450A GLY 3.6 2.6 + - - -
476A HIS* 2.8 26.9 + - - -
477A ILE* 3.0 41.5 + - + +
605A LEU* 3.8 22.3 - - + +
610A ILE* 5.8 0.2 - - - +
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Residues in contact with ILE 447 (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 LEU* 4.5 8.1 - - + -
443A TYR* 2.9 26.6 + - + +
444A ALA* 3.7 7.4 - - - +
446A GLU* 1.3 75.4 - - - +
448A SER* 1.3 64.0 + - - +
450A GLY* 2.8 14.6 + - - -
451A LEU* 3.1 11.3 + - + +
464A LEU* 4.0 22.0 - - + -
469A VAL* 4.4 13.5 - - + -
477A ILE* 3.7 23.8 - - + -
479A ILE* 3.6 18.8 - - + +
524A TYR* 4.2 13.0 - - + -
527A LEU* 3.7 33.9 - - + -
531A MET* 4.8 0.2 - - + -
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Residues in contact with SER 448 (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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444A ALA 2.8 18.7 + - - -
445A ALA* 2.8 16.3 + - - -
447A ILE* 1.3 73.8 - - - +
449A ILE* 1.3 57.0 + - - +
451A LEU* 2.9 7.7 + - - +
452A PHE* 2.8 62.8 + - - -
521A TRP* 4.5 3.8 - - - -
524A TYR* 3.6 21.8 - - - -
591A VAL* 4.9 2.9 - - - -
602A TRP* 3.5 10.8 - - - -
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Residues in contact with ILE 449 (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 PRO* 3.5 19.5 - - + -
399A PHE* 3.4 26.2 - - + -
445A ALA 3.5 4.9 - - - +
446A GLU 3.1 10.9 + - - +
448A SER* 1.3 83.5 + - - +
450A GLY* 1.3 61.1 + - - +
452A PHE* 3.3 16.8 + - + +
453A PHE* 3.1 23.2 + - - +
602A TRP* 3.4 39.0 - - + -
605A LEU* 4.7 2.7 - - + -
606A GLU* 3.6 36.1 - - + +
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Residues in contact with GLY 450 (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 PRO* 4.8 1.3 - - - -
399A PHE* 4.9 2.3 - - - +
400A LEU* 3.8 27.1 - - - -
446A GLU 3.6 2.8 + - - -
447A ILE 2.8 11.1 + - - -
449A ILE* 1.3 80.2 - - - +
451A LEU* 1.3 63.8 + - - -
452A PHE 3.2 0.2 + - - -
453A PHE* 3.2 6.0 + - - +
454A LEU* 3.1 29.1 + - - +
479A ILE* 4.4 5.2 - - - -
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Residues in contact with LEU 451 (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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447A ILE* 3.1 11.4 + - + +
448A SER 2.9 7.6 + - - +
450A GLY* 1.3 79.6 - - - +
452A PHE* 1.3 58.4 + - - +
454A LEU* 3.4 5.3 + - + -
455A HIS* 2.9 43.1 + - + +
461A TYR* 4.1 34.8 - - + -
464A LEU* 3.6 28.9 - - + -
479A ILE* 5.7 2.7 - - + -
520A ASP* 4.1 20.9 - - + +
521A TRP* 3.9 25.1 - - + -
524A TYR* 3.6 20.0 - - + -
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Residues in contact with PHE 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A SER* 2.8 45.6 + - - +
449A ILE* 3.5 23.3 - - + +
451A LEU* 1.3 74.9 - - - +
453A PHE* 1.3 65.6 + - - +
455A HIS* 3.4 3.9 + - - +
456A LYS* 3.0 34.5 + - - +
521A TRP* 3.5 29.6 - + - -
588A GLU* 3.6 42.0 - - + +
591A VAL* 4.4 8.1 - - + -
592A ARG* 3.8 37.9 - - + -
602A TRP* 4.2 2.2 - + - -
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Residues in contact with PHE 453 (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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393A LEU* 4.1 18.6 - - + -
394A LEU 3.5 19.7 - - - -
395A ASP 3.7 12.3 - - - -
396A LYS* 3.7 27.4 - - + -
397A PRO* 3.5 25.4 - - + -
400A LEU* 3.7 15.3 - - + -
449A ILE 3.1 13.4 + - - +
450A GLY 3.7 3.4 - - - +
452A PHE* 1.3 82.0 - - - +
454A LEU* 1.3 68.6 + - + +
456A LYS* 3.4 4.4 + - - +
457A ARG* 3.0 76.4 + - - +
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Residues in contact with LEU 454 (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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390A VAL* 4.1 15.7 - - + -
393A LEU* 4.1 9.4 - - + -
400A LEU* 4.9 9.0 - - + -
450A GLY 3.1 18.8 + - - +
451A LEU* 3.9 7.4 - - + +
453A PHE* 1.3 90.1 - - + +
455A HIS* 1.3 60.8 + - + +
457A ARG* 3.4 8.2 + - - +
459A ILE* 2.8 68.8 + - + +
461A TYR* 4.3 23.3 - - + -
482A PHE* 4.1 24.0 - - + -
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Residues in contact with HIS 455 (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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451A LEU* 2.9 29.0 + - + +
452A PHE* 4.1 3.6 - - - +
454A LEU* 1.3 77.6 - - + +
456A LYS* 1.3 65.2 + - - +
457A ARG 3.0 1.3 - - - -
458A GLY* 2.9 15.9 + - - -
459A ILE 3.0 21.8 - - - +
489A MET 4.7 3.1 - - - +
490A MET* 5.4 1.7 - - - +
517A LYS* 3.3 42.2 - - + +
520A ASP* 3.2 36.2 + - + +
521A TRP* 3.5 32.7 + + - -
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Residues in contact with LYS 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A PHE* 3.0 25.1 + - - +
453A PHE* 3.7 6.7 - - - +
455A HIS* 1.3 76.1 - - - +
457A ARG* 1.3 70.4 + - - +
458A GLY 3.5 2.8 + - - -
490A MET* 4.4 11.3 - - - +
588A GLU* 3.6 34.8 + - - +
592A ARG* 5.4 0.4 - - - +
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Residues in contact with ARG 457 (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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393A LEU* 4.4 17.9 - - + -
394A LEU 4.4 7.7 + - - -
395A ASP* 4.7 10.1 + - - +
453A PHE* 3.0 69.3 + - - +
454A LEU* 4.0 4.7 - - - +
455A HIS 3.0 1.2 - - - -
456A LYS* 1.3 93.5 - - - +
458A GLY* 1.3 61.1 + - - +
459A ILE* 3.3 16.6 + - + +
488A HIS* 5.1 1.7 + - - -
490A MET* 4.5 5.6 - - - +
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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
------------------------------------------------------------
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