Contacts of the helix formed by residues 438 - 448 (chain A) in PDB entry 2V9S
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 LEU 438 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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409A GLN 4.9 0.2 - - - +
410A THR* 4.0 6.7 - - - +
411A ILE* 3.6 37.0 - - + +
432A PHE* 3.8 31.9 - - + -
433A ILE 3.6 25.4 - - - +
434A CYS* 4.1 12.3 - - - -
435A ASP* 3.0 7.9 + - - +
437A HIS* 1.3 74.5 - - - +
439A LYS* 1.3 58.2 + - - +
440A TRP* 3.2 4.7 - - - +
441A LEU* 3.0 51.1 + - + +
442A ALA 3.4 4.7 + - - -
468A ILE* 4.3 4.9 - - + -
476A PHE* 3.9 12.8 - - + -
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Residues in contact with LYS 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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435A ASP 3.5 3.0 + - - -
436A CYS* 3.4 19.3 - - + +
437A HIS 3.5 0.8 - - - -
438A LEU* 1.3 74.2 - - - +
440A TRP* 1.3 66.1 + - - +
442A ALA* 3.1 12.7 + - - +
443A ASP* 3.1 29.3 + - - +
473A SER* 3.6 36.8 - - - +
474A LYS* 4.6 6.3 - - - +
476A PHE* 3.7 31.6 - - + +
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Residues in contact with TRP 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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411A ILE* 2.7 49.5 + - + -
412A ALA 3.8 5.6 - - - -
413A LYS* 3.3 52.7 - - + +
414A GLY 5.1 2.7 - - - -
416A PHE* 3.5 50.5 - + + -
436A CYS 5.0 0.6 + - - -
437A HIS 3.2 21.4 + - - -
438A LEU* 4.2 3.2 - - - +
439A LYS* 1.3 79.7 - - - +
441A LEU* 1.4 70.9 + - + +
443A ASP* 3.4 10.8 + - - +
444A TYR* 2.7 48.9 + + + +
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Residues in contact with LEU 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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411A ILE* 4.4 15.7 - - + -
416A PHE* 3.6 31.4 - - + -
427A LEU* 4.2 11.4 - - + -
432A PHE* 4.9 3.4 - - + -
438A LEU* 3.0 42.3 + - + +
440A TRP* 1.4 95.8 - - + +
442A ALA* 1.3 64.5 + - - +
444A TYR* 4.0 1.8 - - + -
445A LEU* 3.0 58.9 + - + +
468A ILE* 4.7 14.6 - - + -
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Residues in contact with ALA 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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438A LEU 3.4 3.4 + - - -
439A LYS 3.1 10.3 + - - +
441A LEU* 1.3 77.7 - - - +
443A ASP* 1.3 57.3 + - - +
445A LEU* 3.3 2.8 + - - +
446A HIS* 2.9 30.0 + - - +
468A ILE* 4.5 13.7 - - - +
469A GLY* 6.2 0.2 - - - -
471A ILE 4.4 7.0 - - - +
473A SER* 3.4 15.9 - - - +
476A PHE* 3.6 35.9 - - + -
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Residues in contact with ASP 443 (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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439A LYS* 3.1 28.9 + - - +
440A TRP* 3.5 10.5 - - - +
442A ALA* 1.3 71.5 - - - +
444A TYR* 1.3 67.3 + - - +
446A HIS* 3.6 8.2 - - - +
447A THR* 3.0 29.9 + - - +
473A SER* 2.3 33.7 + - - -
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Residues in contact with TYR 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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416A PHE* 3.6 43.6 + + + +
419A LEU 4.8 0.7 + - - -
422A ILE* 3.4 28.4 - - - +
425A MET* 4.0 5.6 - - + +
440A TRP* 2.7 40.1 + + + +
441A LEU* 3.6 5.6 - - + +
443A ASP* 1.3 74.4 - - - +
445A LEU* 1.3 68.5 + - + +
447A THR* 4.5 1.3 - - - -
448A ASN* 2.7 63.0 + - + +
450A ILE* 3.9 18.5 - - + +
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Residues in contact with LEU 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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425A MET* 5.2 1.8 - - - -
427A LEU* 4.9 4.0 - - + -
441A LEU* 3.0 45.8 + - + +
442A ALA* 3.9 3.1 - - - +
444A TYR* 1.3 88.3 - - + +
446A HIS* 1.3 64.0 - - - +
448A ASN 3.7 14.6 - - - +
449A PRO* 3.1 29.1 - - + +
450A ILE* 4.4 3.4 - - + +
451A GLU* 3.7 40.2 - - + +
455A ALA* 6.2 1.3 - - + -
468A ILE* 4.3 18.6 - - + -
469A GLY* 5.4 13.7 - - - +
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Residues in contact with HIS 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 ALA 2.9 17.5 + - - +
443A ASP* 3.6 9.2 - - - +
445A LEU* 1.3 76.3 - - - +
447A THR* 1.3 73.4 + - - +
449A PRO* 3.9 8.4 - - - +
473A SER* 5.8 0.9 - - - +
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Residues in contact with THR 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 ASP* 3.0 14.5 + - - +
444A TYR* 3.4 8.3 - - - -
446A HIS* 1.3 87.8 - - - +
448A ASN* 1.3 76.0 + - - +
449A PRO* 3.4 7.3 - - - +
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Residues in contact with ASN 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 TYR* 2.7 61.8 + - + +
445A LEU* 3.3 14.1 - - - +
447A THR* 1.3 92.2 - - - +
449A PRO* 1.4 53.4 - - - +
450A ILE* 2.6 41.3 + - + +
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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