Contacts of the helix formed by residues 419 - 432 (chain A) in PDB entry 4Y5U
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 ASP 419 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282A VAL* 4.2 12.6 - - + +
413A ILE* 3.3 27.1 - - + -
417A ASN* 3.3 13.7 + - - +
418A GLN* 1.3 80.9 + - - +
420A ASN* 1.3 58.6 + - - -
421A ASN 3.5 2.2 - - - -
422A ALA* 3.9 7.0 - - - -
423A LYS* 3.1 52.1 + - - +
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Residues in contact with ASN 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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418A GLN* 3.5 30.8 - - + +
419A ASP* 1.3 76.0 + - - +
421A ASN* 1.3 75.8 + - - +
423A LYS* 3.6 9.9 + - - +
424A ALA 3.3 6.8 + - - -
503A ASN* 3.9 7.4 - - - +
515A TRP* 2.9 35.5 + - - +
516A GLN* 3.3 54.1 + - - +
519A ASP* 4.1 9.8 + - - +
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Residues in contact with ASN 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A GLU* 4.6 13.4 - - - +
418A GLN* 5.5 0.8 - - - +
419A ASP 3.5 0.2 - - - -
420A ASN* 1.3 91.4 + - - +
422A ALA* 1.3 62.6 + - - +
424A ALA* 3.5 2.6 + - - +
425A THR* 3.1 26.4 + - - +
499A TRP* 5.3 0.3 - - - -
503A ASN* 3.0 28.2 + - - +
504A LYS* 4.2 16.3 + - - -
516A GLN* 4.5 7.9 - - - +
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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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282A VAL* 3.7 15.7 - - + -
411A VAL* 3.6 30.2 - - + +
413A ILE* 3.9 17.3 - - + -
419A ASP* 3.7 10.9 - - - +
420A ASN 3.3 0.2 - - - -
421A ASN* 1.3 78.4 - - - +
423A LYS* 1.3 56.9 + - - +
425A THR* 3.5 7.2 + - - -
426A ILE* 3.1 31.5 + - - +
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Residues in contact with LYS 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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282A VAL* 4.2 16.6 - - + -
418A GLN* 5.8 1.0 - - - +
419A ASP* 3.1 42.5 + - - +
420A ASN* 3.8 4.7 - - - +
422A ALA* 1.3 75.3 - - - +
424A ALA* 1.3 58.2 + - - +
426A ILE* 3.9 3.6 - - - +
427A LEU* 3.0 27.4 + - - +
458A LYS* 5.7 8.9 - - - +
462A GLU* 5.7 5.3 + - - +
515A TRP* 4.0 13.2 - - + -
519A ASP* 3.1 37.9 + - - -
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Residues in contact with ALA 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 ASN 3.3 1.8 + - - -
421A ASN 3.7 3.4 - - - +
423A LYS* 1.3 77.1 - - - +
425A THR* 1.3 64.9 + - - +
427A LEU* 3.4 5.6 + - - +
428A TRP* 3.1 25.6 + - - +
499A TRP* 3.6 10.4 - - + -
502A PHE* 4.1 8.3 - - + -
503A ASN* 3.4 31.9 - - - +
515A TRP* 3.5 27.3 - - + +
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Residues in contact with THR 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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381A GLU* 4.1 26.0 + - + +
383A LYS* 3.9 34.3 + - + +
411A VAL* 4.0 16.2 - - + -
421A ASN 3.1 12.3 + - - -
422A ALA* 3.5 10.9 - - - -
424A ALA* 1.3 77.8 - - - +
426A ILE* 1.3 62.8 + - + +
428A TRP* 4.0 1.4 - - - +
429A ASP* 3.3 23.9 + - - +
499A TRP* 3.7 18.3 - - - -
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Residues in contact with ILE 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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212A GLY 5.7 1.3 - - - +
213A ASN* 5.1 1.8 - - - +
281A GLN* 3.5 54.1 - - + +
282A VAL* 4.2 5.4 - - + -
383A LYS* 4.8 3.4 - - + -
409A PRO* 3.4 33.7 - - + +
410A LEU 4.4 0.2 - - - -
411A VAL* 4.0 19.1 - - + -
422A ALA 3.1 16.5 + - - +
423A LYS* 4.1 4.3 - - - +
425A THR* 1.3 85.9 - - + +
427A LEU* 1.3 61.5 + - - +
429A ASP* 3.7 2.1 + - + +
430A ASN* 3.3 26.9 + - - +
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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
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213A ASN* 3.0 43.8 + - + +
423A LYS 3.0 18.3 + - - +
424A ALA* 3.8 4.0 - - - +
425A THR 3.4 0.4 - - - -
426A ILE* 1.3 77.2 - - - +
428A TRP* 1.3 62.6 + - + +
431A ALA* 3.2 10.4 + - - +
432A PHE* 5.9 0.9 - - + -
451A MET* 4.3 8.1 - - + -
454A THR* 4.0 18.2 - - + +
455A LEU* 5.1 2.2 - - + -
458A LYS* 3.5 47.8 - - + -
502A PHE* 3.9 28.3 - - + -
515A TRP* 4.7 11.7 - - + -
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Residues in contact with TRP 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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383A LYS* 5.9 0.9 - - - -
424A ALA 3.1 17.2 + - - +
425A THR* 4.0 2.5 - - - +
427A LEU* 1.3 73.2 - - + +
429A ASP* 1.3 60.0 + - - +
432A PHE* 2.9 69.2 + + - +
442A VAL* 3.8 20.1 - - + +
443A ALA 2.9 22.0 + - - -
444A GLU* 3.4 23.6 + - - -
446A VAL* 3.9 22.0 - - + -
451A MET* 4.5 7.4 - - + -
497A VAL* 4.0 4.3 - - + -
498A SER 3.5 14.4 - - - -
499A TRP* 3.4 49.9 - + + +
502A PHE* 4.0 21.8 - + + -
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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
----------------------------------------------------------
209A GLN* 3.8 2.9 + - - -
383A LYS* 3.3 31.0 + - - +
409A PRO* 3.1 17.1 - - + +
425A THR 3.3 16.5 + - - +
426A ILE* 4.0 5.6 - - + +
427A LEU 3.4 0.2 - - - -
428A TRP* 1.3 76.7 - - - +
430A ASN* 1.3 63.6 + - - +
431A ALA 3.5 0.2 + - - -
433A SER* 2.0 34.0 + - - -
437A ARG* 2.9 40.5 + - - -
440A PHE* 3.9 1.7 - - - +
442A VAL* 3.6 13.8 - - - +
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Residues in contact with ASN 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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206A ARG* 2.6 29.1 + - - -
209A GLN* 3.5 41.1 + - - +
210A LEU* 3.6 6.4 - - - +
212A GLY* 3.8 8.1 + - - -
213A ASN* 3.3 29.4 + - - +
281A GLN* 3.1 38.3 + - - +
408A LEU* 4.2 2.6 - - - +
426A ILE* 3.3 15.5 + - - +
429A ASP* 1.3 80.9 - - - +
431A ALA* 1.3 54.3 + - - +
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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
----------------------------------------------------------
206A ARG* 3.0 16.7 + - - -
210A LEU* 4.1 11.2 - - + +
213A ASN* 3.5 4.6 - - - +
427A LEU 3.2 15.9 + - - +
429A ASP 3.3 0.2 - - - -
430A ASN* 1.3 80.6 - - - +
432A PHE* 1.3 92.3 + - + +
433A SER 3.6 1.1 - - - -
450A LYS* 5.9 2.6 - - - -
454A THR* 3.8 19.7 - - + +
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Residues in contact with PHE 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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206A ARG* 4.6 0.2 - - - +
427A LEU* 5.9 0.7 - - + -
428A TRP* 2.9 61.4 + + - +
430A ASN 3.5 0.2 - - - -
431A ALA* 1.3 101.6 - - + +
433A SER* 1.3 63.5 + - - +
434A GLU* 5.4 2.0 - - - +
442A VAL* 3.5 17.7 - - + +
443A ALA* 4.0 12.1 + - + +
446A VAL* 3.7 42.4 - - + -
450A LYS* 4.2 20.2 - - + -
451A MET* 4.3 20.2 - - + -
454A THR* 3.9 15.7 - - + -
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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
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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