Contacts of the helix formed by residues 418 - 441 (chain A) in PDB entry 5ZK3
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 PRO 418 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415A PRO 4.4 6.5 - - - +
416A CYS 3.7 7.6 - - - +
417A ILE* 1.3 91.7 - - - +
419A ASN* 1.3 66.7 + - - +
420A THR* 3.3 9.2 - - - +
421A VAL* 3.2 26.6 + - + +
422A TRP* 3.2 19.2 + - - -
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Residues in contact with ASN 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A TYR* 5.5 0.9 + - - -
84A THR* 6.4 0.2 - - - +
418A PRO* 1.3 73.0 - - - +
420A THR* 1.3 64.0 + - - +
422A TRP* 3.1 16.8 + - - +
423A THR* 2.9 28.2 + - - -
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Residues in contact with THR 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A PRO* 3.3 5.2 - - - +
419A ASN* 1.3 79.5 + - - +
421A VAL* 1.3 60.6 + - + +
423A THR* 3.1 11.6 + - + -
424A ILE* 2.9 43.6 + - + +
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Residues in contact with VAL 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A MET* 3.5 28.9 - - + +
417A ILE* 4.2 11.2 - - + -
418A PRO* 3.2 35.1 + - + +
420A THR* 1.3 74.4 - - - +
422A TRP* 1.3 67.6 + - - +
424A ILE* 3.1 19.0 + - + +
425A GLY 2.9 19.1 + - - -
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Residues in contact with TRP 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A TYR* 4.2 3.4 - - - +
403A TYR* 3.5 44.9 - + - -
406A MET* 3.7 39.9 - - + -
407A VAL* 3.9 11.0 - - + -
410A ASN* 3.8 26.4 + - + -
414A ALA 5.3 0.8 + - - -
417A ILE* 3.3 32.2 + - + +
418A PRO 3.2 27.4 + - - -
419A ASN* 3.1 16.7 + - - +
421A VAL* 1.3 75.7 - - - +
423A THR* 1.3 61.9 + - - +
425A GLY* 3.1 1.9 + - - -
426A TYR* 2.9 33.4 + + + -
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Residues in contact with THR 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A TYR* 3.3 25.5 + - + -
84A THR* 4.3 21.6 + - + +
419A ASN* 2.9 23.4 + - - -
420A THR* 3.3 13.9 - - + -
422A TRP* 1.3 75.0 - - - +
424A ILE* 1.3 58.9 + - + +
426A TYR* 3.5 1.0 + - - +
427A TRP* 2.9 56.7 + - + +
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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
----------------------------------------------------------
406A MET* 5.5 2.9 - - + -
420A THR* 2.9 33.5 + - + +
421A VAL* 3.1 22.6 + - + +
423A THR* 1.3 77.6 - - + +
425A GLY* 1.3 58.2 + - - +
427A TRP* 3.1 6.0 + - - +
428A LEU* 2.9 44.4 + - + +
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Residues in contact with GLY 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A THR 4.6 0.3 - - - +
403A TYR* 4.1 20.7 - - - +
406A MET* 3.9 16.8 - - - +
421A VAL 2.9 12.7 + - - -
422A TRP 3.1 2.6 + - - -
424A ILE* 1.3 74.0 - - - +
426A TYR* 1.3 64.9 + - - +
428A LEU* 3.2 10.4 + - - +
429A CYS* 3.0 25.5 + - - -
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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
----------------------------------------------------------
80A TYR* 3.4 45.8 - + + +
99A TRP* 5.0 6.5 - + - -
100A LEU* 5.4 6.6 - - - +
103A ASP* 4.7 1.6 - - - -
104A TYR* 4.2 13.2 + + - -
403A TYR* 3.4 40.2 + + - -
422A TRP* 2.9 19.4 + + + +
423A THR 3.6 8.7 - - - +
425A GLY* 1.3 73.9 - - - +
427A TRP* 1.3 58.8 + - - +
429A CYS* 3.3 5.2 + - - +
430A TYR* 3.0 54.1 + + + -
501A QNB 3.8 30.8 - - + +
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Residues in contact with TRP 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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26A ILE* 6.2 3.6 - - + +
30A ALA* 4.1 15.9 - - + -
33A LEU* 4.2 26.2 - - + -
77A MET* 4.0 39.9 - - + -
80A TYR* 3.5 25.4 - + - -
81A THR* 3.4 35.4 - - + +
84A THR* 5.2 2.0 + - - +
423A THR* 2.9 43.8 + - + +
424A ILE* 3.1 6.9 + - - +
426A TYR* 1.3 74.7 - - - +
428A LEU* 1.3 62.6 + - + +
430A TYR* 3.5 11.0 + + + +
431A ILE* 2.8 36.4 + - + +
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Residues in contact with LEU 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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398A ILE 5.2 2.0 - - - +
399A THR* 3.3 28.4 - - + +
402A PRO* 3.6 34.1 - - + -
406A MET* 5.9 0.2 - - + -
424A ILE* 2.9 33.9 + - + +
425A GLY* 3.6 6.5 - - - +
427A TRP* 1.3 75.1 - - + +
429A CYS* 1.3 65.3 + - - +
431A ILE* 2.9 24.3 + - + +
432A ASN 3.0 10.6 + - - -
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Residues in contact with CYS 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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72A ILE* 5.4 0.5 - - - +
399A THR 3.4 2.7 + - - -
400A TRP* 3.4 52.6 + - + +
403A TYR* 4.0 16.8 - - - -
425A GLY 3.0 16.0 + - - -
426A TYR 3.4 9.0 - - - +
428A LEU* 1.3 76.3 - - - +
430A TYR* 1.3 63.2 + - + +
432A ASN* 3.2 18.7 - - - +
433A SER* 4.1 3.3 + - - -
501A QNB 3.8 35.2 - - + -
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Residues in contact with TYR 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ILE* 3.6 19.3 - - + -
76A SER* 3.5 28.7 - - - -
77A MET* 3.3 44.1 - - + +
80A TYR* 4.0 26.9 - + + -
99A TRP* 3.8 13.3 - - - -
103A ASP* 3.5 25.6 + - - -
426A TYR* 3.0 40.0 + + - +
427A TRP* 3.8 18.2 - + + +
428A LEU 3.2 0.2 - - - -
429A CYS* 1.3 75.4 - - - +
431A ILE* 1.3 66.0 + - - +
433A SER* 3.1 16.8 + - - -
434A THR 3.7 0.2 + - - -
501A QNB 4.0 11.2 - - - -
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Residues in contact with ILE 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.6 43.5 - - + -
77A MET* 4.9 2.0 - - + -
399A THR* 4.5 9.2 - - + -
427A TRP* 2.8 29.0 + - + +
428A LEU* 2.9 17.4 + - + +
430A TYR* 1.3 73.5 - - - +
432A ASN* 1.3 67.5 + - - +
434A THR* 2.9 24.6 + - + +
435A ILE* 2.9 31.6 + - + +
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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
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110A ARG* 3.3 24.4 - - - +
395A ALA* 3.6 5.7 - - - +
396A PHE* 3.6 30.5 + - - +
399A THR* 3.1 29.6 + - - +
400A TRP* 3.1 17.0 - - - +
428A LEU 3.0 6.3 + - - -
429A CYS 3.2 14.6 - - - +
431A ILE* 1.3 76.2 - - - +
433A SER* 1.3 56.8 + - - +
435A ILE* 3.2 4.3 + - - +
436A ASN* 2.9 41.5 + - - +
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Residues in contact with SER 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A THR* 3.9 8.7 - - - -
41A ASN* 3.6 10.4 + - - -
69A ASP* 2.8 34.3 + - - +
72A ILE* 3.4 18.1 - - - +
110A ARG* 2.8 27.4 + - - -
429A CYS 4.8 1.7 + - - -
430A TYR 3.1 13.0 + - - -
432A ASN* 1.3 78.2 - - - +
434A THR* 1.3 61.7 + - - +
436A ASN* 3.7 0.3 + - - +
437A PRO* 3.2 18.4 - - - +
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Residues in contact with THR 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 4.0 16.4 + - + +
36A VAL* 3.8 28.1 - - + +
37A THR* 2.4 30.8 + - - +
77A MET* 3.6 14.9 - - - +
430A TYR 4.0 0.2 + - - -
431A ILE* 2.9 20.2 + - + +
433A SER* 1.3 78.0 - - - +
435A ILE* 1.3 70.0 + - + +
437A PRO* 3.4 11.1 - - - +
438A ALA* 4.7 3.8 + - - +
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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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395A ALA* 4.6 11.7 - - + -
399A THR* 5.3 4.9 - - + -
431A ILE* 2.9 33.7 + - + +
432A ASN* 3.9 5.6 - - - +
434A THR* 1.3 84.6 - - + +
436A ASN* 1.3 65.8 + - - +
438A ALA* 3.1 20.3 + - + +
439A CYS* 3.3 22.6 + - - -
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Residues in contact with ASN 436 (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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65A LEU* 4.1 16.9 - - - +
69A ASP* 2.9 30.5 + - - +
110A ARG* 3.1 24.5 - - - +
392A ILE* 4.2 16.3 - - - +
395A ALA* 4.3 8.1 - - - +
396A PHE* 5.8 0.2 - - - +
432A ASN* 2.9 30.3 + - - +
433A SER 3.9 0.4 - - - +
435A ILE* 1.3 75.5 - - - +
437A PRO* 1.3 66.8 - - + +
439A CYS* 2.9 17.7 + - - +
440A TYR* 3.2 22.6 - - + -
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Residues in contact with PRO 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A THR* 5.2 0.9 - - - +
40A GLY* 4.3 10.8 - - - -
41A ASN* 3.4 36.1 - - - +
44A VAL* 4.1 16.8 - - + -
433A SER 3.2 15.5 - - - +
434A THR* 3.4 12.3 - - - +
436A ASN* 1.3 91.2 - - + +
438A ALA* 1.3 55.8 + - - +
440A TYR* 4.1 11.4 - - + +
441A ALA* 2.9 36.7 + - + +
442A LEU* 3.5 3.1 + - - -
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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
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434A THR 4.7 3.0 + - - +
435A ILE* 3.1 17.7 + - + +
437A PRO* 1.3 78.2 - - - +
439A CYS* 1.3 60.8 + - - +
440A TYR 3.5 0.2 - - - -
442A LEU* 3.8 34.4 - - + +
443A CYS* 3.8 15.8 - - - -
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Residues in contact with CYS 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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388A THR* 3.8 13.7 + - - +
391A ALA* 4.2 23.7 - - + +
392A ILE* 4.1 17.9 - - + -
395A ALA* 4.1 18.4 - - - -
435A ILE* 3.3 34.5 - - - -
436A ASN* 2.9 13.8 + - - +
438A ALA* 1.3 79.7 - - - +
440A TYR* 1.3 58.1 + - - +
443A CYS* 4.0 15.0 - - - +
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Residues in contact with TYR 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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41A ASN* 4.4 3.3 + - - -
44A VAL* 3.6 30.8 - - + +
62A LEU* 3.6 43.7 + - + -
65A LEU* 4.6 7.2 - - + -
66A ALA* 3.6 28.8 + - - +
69A ASP* 4.8 2.1 + - - -
388A THR* 3.6 23.9 - - + +
392A ILE* 3.8 19.1 - - + -
436A ASN* 3.2 37.6 - - + -
437A PRO* 4.1 7.7 - - + +
439A CYS* 1.3 80.1 - - - +
441A ALA* 1.3 65.7 + - + +
442A LEU 3.7 0.7 - - - -
443A CYS* 4.2 5.7 - - - +
444A ASN* 3.7 19.8 + - - +
447A PHE* 3.9 8.7 - + - -
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Residues in contact with ALA 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 3.9 16.6 - - + -
437A PRO* 2.9 17.5 + - + +
440A TYR* 1.3 81.1 - - + +
442A LEU* 1.3 59.0 + - + +
443A CYS 3.1 8.7 + - - -
444A ASN 3.5 7.3 + - - +
447A PHE* 3.3 31.5 - - + +
448A LYS* 4.3 2.6 - - - +
451A PHE* 3.7 32.0 - - + -
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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