Contacts of the helix formed by residues 436 - 450 (chain A) in PDB entry 1IR1
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 436 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392A GLU* 5.7 1.6 - - - +
434A GLY 3.9 1.8 + - - +
435A ARG* 1.3 69.8 - - - +
437A LEU* 1.3 59.0 + - - +
438A ALA* 3.4 15.3 + - - +
439A ARG* 3.1 32.1 + - + +
440A GLU* 2.7 49.7 + - - +
444A ILE* 5.1 0.2 - - - -
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Residues in contact with LEU 437 (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 PRO* 3.9 33.8 - - + +
389A ALA 5.3 0.2 + - - -
391A THR* 3.7 31.6 - - + -
392A GLU* 4.1 17.5 - - + +
427A CYS* 3.7 21.8 - - + +
431A ARG* 4.0 31.9 - - + +
435A ARG 3.4 4.3 + - - +
436A ASP* 1.3 73.4 + - - +
438A ALA* 1.3 58.0 + - - +
441A GLY* 3.0 29.5 + - - +
444A ILE* 3.9 20.9 - - + -
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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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389A ALA* 6.4 2.0 - - - +
392A GLU* 4.6 21.7 - - + +
436A ASP* 3.2 13.6 + - - +
437A LEU* 1.3 79.7 - - - +
439A ARG* 1.3 63.4 + - - +
441A GLY* 4.5 1.4 + - - -
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Residues in contact with ARG 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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436A ASP* 3.1 25.5 + - + +
438A ALA* 1.3 83.9 - - - +
440A GLU* 1.3 66.0 + - + +
441A GLY 3.5 0.8 + - - -
442A ASN 5.3 0.9 + - - -
443A THR* 5.2 1.2 + - - -
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Residues in contact with GLU 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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435A ARG* 3.0 43.1 + - - +
436A ASP* 2.7 37.7 + - - +
439A ARG* 1.3 78.7 - - + +
441A GLY* 1.3 64.4 + - - +
442A ASN 3.4 2.0 - - - -
443A THR* 3.1 14.8 + - + +
444A ILE* 2.9 33.9 + - + +
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Residues in contact with GLY 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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388A PRO* 3.6 29.8 - - - +
437A LEU 3.0 22.9 + - - -
438A ALA 4.4 1.9 + - - -
439A ARG 3.5 3.0 + - - -
440A GLU* 1.3 77.6 - - - +
442A ASN* 1.3 62.6 + - - +
444A ILE* 3.3 7.8 + - - +
445A ILE* 3.2 18.1 + - - +
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Residues in contact with ASN 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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385A TRP* 3.5 31.4 - - + +
439A ARG 5.3 0.8 + - - -
440A GLU 3.4 0.6 - - - -
441A GLY* 1.3 74.1 - - - +
443A THR* 1.3 63.1 + - - +
445A ILE* 3.5 3.1 + - - +
446A ARG* 3.0 55.6 + - - +
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Residues in contact with THR 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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435A ARG* 4.2 8.1 - - - +
439A ARG 5.2 1.0 + - - -
440A GLU* 3.1 18.7 + - + +
442A ASN* 1.3 76.5 - - - +
444A ILE* 1.3 59.7 + - - +
446A ARG* 3.2 14.7 + - + +
447A GLU* 2.9 53.5 + - + +
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Residues in contact with ILE 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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426A ALA* 3.9 33.8 - - + +
427A CYS* 4.3 12.1 - - - +
430A ALA* 3.5 21.8 - - + -
435A ARG* 3.7 25.6 - - + +
437A LEU* 3.9 21.1 - - + -
440A GLU* 2.9 32.1 + - + +
441A GLY* 3.6 9.2 - - - +
443A THR* 1.3 76.3 - - - +
445A ILE* 1.3 61.9 + - - +
447A GLU* 3.4 14.4 + - - +
448A ALA* 3.3 19.4 + - - +
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Residues in contact with ILE 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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384A VAL 4.0 18.4 - - - +
385A TRP* 3.9 22.7 - - + +
388A PRO* 3.9 14.4 - - + -
423A ALA* 4.0 25.6 - - + +
426A ALA* 5.5 2.2 - - + -
427A CYS* 4.3 19.1 - - - -
441A GLY 3.2 14.1 + - - +
442A ASN* 3.9 6.5 - - - +
444A ILE* 1.3 75.1 - - + +
446A ARG* 1.3 68.0 + - - +
448A ALA* 3.2 12.4 + - - +
449A THR* 3.1 14.3 + - + +
455A LEU* 3.9 6.7 - - + +
459A CYS* 3.6 29.6 - - - -
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Residues in contact with ARG 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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385A TRP* 4.1 21.6 - - + -
442A ASN* 3.0 62.0 + - - +
443A THR* 3.2 14.6 + - + +
445A ILE* 1.3 74.0 - - - +
447A GLU* 1.3 64.8 + - - +
449A THR* 2.5 30.7 + - + +
450A LYS* 3.3 20.7 + - - +
463A LYS* 5.7 5.1 - - - +
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Residues in contact with GLU 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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435A ARG* 2.9 43.5 + - - -
443A THR* 2.9 35.0 + - + +
444A ILE* 3.6 12.3 - - - +
446A ARG* 1.3 75.6 - - - +
448A ALA* 1.3 62.5 + - - +
450A LYS* 3.2 28.1 - - - +
451A TRP* 3.8 9.2 - - - -
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Residues in contact with ALA 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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422A VAL* 4.5 2.2 - - + -
426A ALA* 4.2 20.6 - - + -
444A ILE 3.3 9.2 + - - +
445A ILE* 3.2 7.0 + - - +
447A GLU* 1.3 75.5 - - - +
449A THR* 1.3 60.6 + - - +
450A LYS 3.0 5.7 + - - -
451A TRP* 3.3 24.9 + - + +
452A SER* 3.1 24.3 + - - -
455A LEU* 3.4 23.8 - - + -
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Residues in contact with THR 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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385A TRP* 5.7 1.3 - - + -
445A ILE 3.1 16.1 + - - +
446A ARG* 2.5 25.6 + - + +
448A ALA* 1.3 76.2 - - - +
450A LYS* 1.3 69.4 + - - +
451A TRP 3.3 0.6 + - - -
452A SER 3.5 20.0 + - - +
453A PRO* 5.1 0.2 - - - +
455A LEU* 4.0 8.7 - - + -
456A ALA* 3.8 22.4 - - - +
459A CYS* 3.8 29.4 - - + -
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Residues in contact with LYS 450 (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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446A ARG* 3.3 33.4 + - - +
447A GLU* 3.2 16.8 + - - +
448A ALA 3.0 0.4 - - - -
449A THR* 1.3 87.4 + - - +
451A TRP* 1.3 60.3 + - + +
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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