Contacts of the helix formed by residues 434 - 449 (chain A) in PDB entry 4AY6
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 ASN 434 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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429A HIS* 2.9 58.5 + - - +
432A SER* 3.1 17.2 - - - +
433A GLY* 1.3 78.0 - - - +
435A ILE* 1.3 58.9 + - - +
436A PRO* 3.7 2.0 - - + -
437A GLU* 3.1 27.3 - - - +
438A ALA* 3.3 18.4 + - - +
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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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430A LYS* 4.2 24.7 - - + +
433A GLY* 3.5 19.2 + - - +
434A ASN* 1.3 73.9 - - - +
436A PRO* 1.3 77.8 - - + +
437A GLU 3.1 2.0 - - - -
438A ALA* 3.0 4.1 + - + -
439A ILE* 2.8 26.8 + - + +
462A CYS* 3.8 26.9 - - + +
465A ILE* 4.5 25.8 - - + -
466A VAL* 3.9 27.4 - - + -
869A PRO* 5.6 5.8 - - + -
871A VAL* 5.5 1.3 - - + -
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Residues in contact with PRO 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A ASN* 4.5 0.9 - - - -
435A ILE* 1.3 93.5 - - + +
437A GLU* 1.3 71.0 + - - +
439A ILE* 3.5 9.5 + - + +
440A ALA* 3.0 26.2 + - - +
466A VAL* 5.9 1.1 - - + -
871A VAL* 4.3 28.3 - - + -
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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
----------------------------------------------------------
429A HIS* 3.8 29.8 - - + +
434A ASN* 3.1 41.6 - - + +
436A PRO* 1.3 85.8 - - - +
438A ALA* 1.3 63.3 + - - +
440A ALA* 3.2 8.3 + - - +
441A SER* 3.2 24.4 + - - -
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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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426A ALA* 3.2 32.6 - - - +
429A HIS* 3.8 8.2 - - - +
430A LYS* 3.7 17.0 - - + +
434A ASN 3.3 14.3 + - - +
435A ILE* 3.0 11.9 + - - +
437A GLU* 1.3 76.7 - - - +
439A ILE* 1.3 62.9 + - - +
442A TYR* 3.0 28.0 + - + -
462A CYS* 4.6 6.1 - - - -
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Residues in contact with ILE 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A ILE* 2.8 23.9 + - + +
436A PRO* 3.6 11.0 - - + +
438A ALA* 1.3 73.0 - - - +
440A ALA* 1.3 68.1 + - - +
442A TYR* 3.1 4.4 + - - +
443A ARG* 2.9 49.9 + - - +
459A LEU* 3.9 16.4 - - + -
462A CYS* 3.6 31.0 - - + -
463A LEU* 3.9 23.1 - - + +
466A VAL* 4.4 9.6 - - + -
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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
----------------------------------------------------------
436A PRO 3.0 15.0 + - - +
437A GLU* 3.2 12.3 + - - +
439A ILE* 1.3 78.6 - - - +
441A SER* 1.3 58.4 + - - +
443A ARG* 3.1 10.8 + - - +
444A THR* 3.1 28.8 + - - -
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Residues in contact with SER 441 (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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422A HIS* 3.6 20.0 + - - +
425A LEU* 3.4 22.6 - - - +
426A ALA* 3.4 23.8 - - - -
429A HIS* 4.9 2.2 - - - -
437A GLU 3.2 9.8 + - - -
438A ALA 3.7 1.6 - - - -
440A ALA* 1.3 79.0 - - - +
442A TYR* 1.3 59.7 + - - +
444A THR* 3.5 8.3 + - - -
445A ALA* 3.1 27.2 + - - +
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Residues in contact with TYR 442 (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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423A SER* 3.5 23.6 - - - -
426A ALA* 3.6 23.6 - - + -
427A SER* 2.8 26.4 + - - -
430A LYS* 4.2 6.7 - - + +
438A ALA* 3.0 26.5 + - + -
439A ILE* 3.1 6.0 + - - +
441A SER* 1.3 73.2 - - - +
443A ARG* 1.3 65.5 - - - +
445A ALA* 3.2 5.5 + - - +
446A LEU* 3.0 27.7 + - - +
455A ALA* 3.9 23.3 - - + +
458A ASN* 3.2 34.8 + - + +
459A LEU* 4.1 28.7 - - + -
462A CYS* 4.0 17.7 - - - -
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Residues in contact with ARG 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A ILE* 2.9 35.1 + - + +
440A ALA* 3.3 11.4 - - - +
442A TYR* 1.3 74.9 - - - +
444A THR* 1.3 56.5 + - - +
446A LEU* 3.3 6.8 + - - +
447A LYS* 2.9 29.3 + - - +
459A LEU* 4.5 18.2 - - + +
463A LEU* 4.0 26.0 - - - +
468A ASP* 4.2 8.9 + - - -
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Residues in contact with THR 444 (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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422A HIS* 4.1 26.9 - - + +
440A ALA 3.1 15.8 + - - -
441A SER* 3.7 9.4 - - - -
442A TYR 3.3 0.2 - - - -
443A ARG* 1.3 72.4 - - - +
445A ALA* 1.3 66.3 + - - +
447A LYS* 3.2 11.5 + - + +
448A LEU* 3.1 30.7 + - + +
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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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419A ALA* 3.7 28.4 - - - +
422A HIS* 3.7 13.1 - - + +
423A SER* 3.8 16.4 - - - +
441A SER 3.1 12.2 + - - +
442A TYR* 3.2 10.1 + - - +
444A THR* 1.3 78.8 - - - +
446A LEU* 1.3 57.3 + - - +
448A LEU* 3.4 6.7 + - - +
449A LYS* 3.1 23.9 + - - +
452A PHE* 4.8 3.7 - - + -
455A ALA* 4.6 6.3 - - + -
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Residues in contact with LEU 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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442A TYR 3.0 16.1 + - - +
443A ARG* 3.8 5.6 - - - +
445A ALA* 1.3 73.2 - - - +
447A LYS* 1.3 67.9 + - - +
449A LYS 3.8 4.5 - - - +
450A PRO* 3.1 34.0 - - + +
452A PHE* 3.6 34.8 - - + +
455A ALA* 3.8 17.3 - - + -
456A TYR* 3.9 26.7 - - + +
459A LEU* 3.6 31.0 - - + -
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Residues in contact with LYS 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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443A ARG 2.9 14.1 + - - +
444A THR* 3.4 14.4 - - + +
446A LEU* 1.3 80.1 - - - +
448A LEU* 1.3 64.1 + - + +
449A LYS 3.5 0.2 + - - -
450A PRO* 3.7 12.6 - - - +
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Residues in contact with LEU 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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416A PRO 4.1 3.8 - - - +
417A ALA* 3.5 42.2 - - + +
419A ALA* 4.1 8.5 - - + -
422A HIS* 3.5 35.4 - - + +
444A THR* 3.1 21.9 + - + +
445A ALA* 3.6 6.1 - - - +
446A LEU 3.3 0.2 - - - -
447A LYS* 1.3 82.1 - - + +
449A LYS* 1.3 58.4 + - - +
450A PRO* 3.8 4.6 - - - +
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Residues in contact with LYS 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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419A ALA* 3.7 18.1 - - + +
420A ASP* 3.2 24.8 + - - -
445A ALA 3.1 5.8 + - - +
446A LEU* 3.2 9.9 - - - +
448A LEU* 1.3 77.7 - - - +
450A PRO* 1.4 60.4 - - + +
451A ASP* 3.0 25.7 + - + +
452A PHE* 3.6 44.2 - - + +
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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