Contacts of the helix formed by residues 406 - 421 (chain A) in PDB entry 2Y4U
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 406 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402A LYS* 5.1 1.4 - - - +
404A ASN 3.8 2.0 + - - -
405A ALA* 1.3 71.1 - - - +
407A LYS* 1.3 69.1 + - + +
408A GLN* 3.0 12.9 + - + +
409A GLU* 3.1 40.7 + - + +
410A ILE* 3.3 12.8 + - - +
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Residues in contact with LYS 407 (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 ALA 3.6 3.2 + - - +
406A LYS* 1.3 76.6 - - - +
408A GLN* 1.3 57.3 + - - +
410A ILE* 3.8 14.4 - - + +
411A ILE* 3.0 29.7 - - + +
449A LEU* 3.7 20.1 - - + +
450A SER* 3.6 21.2 - - - +
451A ASP* 2.9 37.7 + - - +
454A MSE 5.2 8.7 - - - -
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Residues in contact with GLN 408 (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 LYS* 3.2 9.9 - - + +
407A LYS* 1.3 76.6 - - - +
409A GLU* 1.3 74.9 + - - +
410A ILE 3.2 1.9 + - - -
411A ILE* 3.4 18.0 + - + +
412A LYS* 3.5 10.0 + - - +
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Residues in contact with GLU 409 (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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401A VAL* 5.3 15.1 - - + +
405A ALA* 5.4 4.0 - - + -
406A LYS* 3.1 38.4 + - + +
408A GLN* 1.3 81.3 - - - +
410A ILE* 1.3 65.1 + - + +
412A LYS* 3.3 20.7 - - - +
413A ALA* 3.8 5.2 + - - +
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Residues in contact with ILE 410 (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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396A TYR* 5.6 1.3 - - + -
399A LEU* 4.7 7.3 - - + +
400A GLY* 6.4 1.6 - - - -
401A VAL* 6.2 2.2 - - - -
405A ALA* 3.6 37.0 - - + +
406A LYS 3.4 10.3 - - - +
407A LYS* 3.8 17.7 - - + +
409A GLU* 1.3 76.3 - - - +
411A ILE* 1.3 66.3 + - - +
412A LYS 3.1 0.9 + - - -
413A ALA* 3.4 4.0 + - - +
414A TYR* 3.1 19.0 + - + +
445A ALA* 6.2 0.2 - - + -
446A LYS* 3.4 19.1 - - + +
449A LEU* 3.8 40.4 - - + -
454A MSE 4.3 9.0 - - + -
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Residues in contact with ILE 411 (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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407A LYS* 3.0 24.9 - - + +
408A GLN* 3.7 11.7 - - + +
410A ILE* 1.3 74.9 - - + +
412A LYS* 1.3 54.9 + - - +
414A TYR* 3.1 5.1 + - + +
415A ARG* 2.8 77.2 + - + +
446A LYS* 3.2 38.6 - - - +
449A LEU* 5.7 4.3 - - + -
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Residues in contact with LYS 412 (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 GLN 3.5 6.4 + - - +
409A GLU* 3.3 18.6 + - - +
410A ILE 3.1 0.4 + - - -
411A ILE* 1.3 80.4 - - - +
413A ALA* 1.3 62.1 + - + +
415A ARG* 3.5 16.1 + - - +
416A LYS* 3.7 26.9 + - - +
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Residues in contact with ALA 413 (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 LEU* 3.7 28.3 - - + -
401A VAL* 4.8 12.6 - - + -
409A GLU 3.8 4.6 + - - +
410A ILE* 3.4 5.1 + - - +
412A LYS* 1.3 77.0 - - + +
414A TYR* 1.3 55.7 + - - +
416A LYS* 3.4 18.7 + - - +
417A LEU* 2.8 43.6 + - + +
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Residues in contact with TYR 414 (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 LEU* 3.9 10.8 - - + +
410A ILE* 3.1 9.3 + - + +
411A ILE* 3.1 16.3 + - + +
413A ALA* 1.3 74.4 - - - +
415A ARG* 1.3 77.3 + - - +
417A LEU* 4.3 2.0 - - - +
418A ALA* 2.4 54.4 + - + +
439A PHE* 6.0 1.2 - - - -
442A ILE* 3.7 37.7 - - + +
443A ALA* 4.3 9.8 - - - +
446A LYS* 3.4 59.8 - - + +
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Residues in contact with ARG 415 (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 ILE* 2.8 49.9 + - + +
412A LYS* 3.6 8.7 - - - +
413A ALA 3.3 0.2 - - - -
414A TYR* 1.3 87.7 - - - +
416A LYS* 1.3 54.0 + - + +
418A ALA* 3.5 4.3 + - - +
419A LEU* 2.8 34.6 + - - +
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Residues in contact with LYS 416 (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 LYS* 3.7 36.1 + - - +
413A ALA* 3.4 19.6 + - - +
414A TYR 3.2 0.4 - - - -
415A ARG* 1.3 79.3 - - + +
417A LEU* 1.3 53.9 + - + +
419A LEU* 3.0 17.0 + - + +
420A GLN* 2.4 60.7 + - - +
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Residues in contact with LEU 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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398A ILE* 5.0 5.8 - - + +
399A LEU* 2.9 44.9 - - + -
413A ALA* 2.8 29.8 + - + +
414A TYR* 3.9 4.3 - - - +
416A LYS* 1.3 72.2 - - + +
418A ALA* 1.3 59.6 + - - +
420A GLN* 3.3 17.3 - - - +
421A TRP* 2.8 64.5 + - + +
442A ILE* 4.5 15.9 - - + +
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Residues in contact with ALA 418 (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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414A TYR* 2.4 59.8 + - + +
415A ARG* 3.7 6.1 - - - +
417A LEU* 1.3 67.1 - - - +
419A LEU* 1.3 63.4 + - - +
422A HIS* 3.5 11.3 + - - +
439A PHE* 3.5 22.3 - - + -
442A ILE* 4.0 14.7 - - + +
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Residues in contact with LEU 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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415A ARG 2.8 17.9 + - - +
416A LYS* 3.2 22.4 - - + +
418A ALA* 1.3 72.7 - - - +
420A GLN* 1.3 60.2 + - + +
422A HIS* 4.3 2.3 - - - +
425A ASN* 2.7 38.6 + - - +
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Residues in contact with GLN 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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416A LYS* 2.4 47.1 + - - +
417A LEU* 3.3 32.1 - - - +
419A LEU* 1.3 83.7 - - + +
421A TRP* 1.3 67.6 + - + +
422A HIS 3.3 0.8 + - - -
425A ASN* 3.0 23.2 + - - +
426A PHE* 5.1 4.0 - - - -
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Residues in contact with TRP 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 LEU* 2.8 61.8 + - + +
420A GLN* 1.3 79.2 - - + +
422A HIS* 1.3 59.0 + - - +
423A PRO* 3.3 8.3 - - - +
426A PHE* 5.2 5.8 - + - -
434A LYS 5.8 0.2 - - - -
435A ALA* 3.9 29.1 - - + +
438A LYS* 3.7 55.6 - - + +
439A PHE* 3.1 25.4 - - + +
442A ILE* 4.6 11.4 - - + -
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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