Contacts of the helix formed by residues 441 - 455 (chain A) in PDB entry 3IAD
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 441 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393A SER* 4.4 17.5 + - - -
435A LEU* 4.3 11.2 - - - +
436A ALA* 4.6 12.3 - - - +
438A ASP* 2.9 32.4 + - + +
440A SER* 1.3 82.2 - - - +
442A HIS* 1.3 57.7 + - - +
443A MET 3.5 2.5 - - - -
444A ASN* 3.3 18.4 + - + +
445A LEU* 2.8 35.4 + - + +
606A ASP* 5.2 9.2 + - - +
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Residues in contact with HIS 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A ASP 4.2 0.6 + - - -
439A MET 2.9 18.2 + - - +
440A SER 3.3 1.6 - - - -
441A LYS* 1.3 78.2 - - - +
443A MET* 1.3 76.7 + - + +
445A LEU* 3.1 6.6 + - - +
446A LEU* 2.7 49.5 + - + +
481A HIS* 3.0 33.9 + - + +
485A LEU* 4.2 0.4 - - - +
541A TYR 5.1 0.2 + - - -
542A ILE* 3.6 42.9 + - + +
546A LEU* 4.1 20.2 - - + -
604A PHE* 3.9 22.0 + + + +
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Residues in contact with MET 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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440A SER 5.1 0.4 + - - -
442A HIS* 1.3 95.0 - - + +
444A ASN* 1.3 62.4 + - - +
446A LEU* 3.8 14.6 - - + +
447A ALA* 2.8 31.5 + - - +
541A TYR 4.6 14.6 - - - +
542A ILE* 5.0 3.1 - - + -
600A ILE* 5.6 5.6 - - + -
604A PHE* 3.6 23.7 + - + +
605A LEU* 3.7 25.8 - - + -
606A ASP 6.2 0.2 - - - +
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Residues in contact with ASN 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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440A SER 4.7 6.7 + - - -
441A LYS* 3.3 18.4 + - + +
442A HIS 3.3 0.6 - - - -
443A MET* 1.3 79.3 - - - +
445A LEU* 1.3 64.2 + - + +
447A ALA* 3.6 6.1 + - - +
448A ASP* 3.1 31.4 + - - +
606A ASP* 4.4 25.3 + - - +
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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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436A ALA* 3.3 44.9 - - + +
441A LYS* 2.8 21.9 + - + +
442A HIS* 3.1 6.3 + - - +
444A ASN* 1.3 77.9 - - + +
446A LEU* 1.3 63.6 + - - +
448A ASP* 3.6 8.2 + - + +
449A LEU 3.2 16.8 + - - -
474A GLN* 6.3 0.2 - - + -
477A GLN* 4.2 22.4 - - + +
478A ASN* 3.2 33.1 + - - +
481A HIS* 3.9 31.2 - - + +
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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 HIS* 2.7 40.4 + - + +
443A MET* 3.8 18.2 - - + +
445A LEU* 1.3 72.4 - - - +
447A ALA* 1.3 58.9 + - - +
449A LEU* 3.3 3.6 + - + +
450A LYS* 2.9 49.0 + - + +
478A ASN* 4.4 1.5 + - - -
541A TYR 6.0 0.9 - - - +
545A PRO* 3.9 22.4 - - + +
546A LEU* 3.8 32.0 - - + +
549A THR* 3.9 22.4 - - + +
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Residues in contact with ALA 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 MET 2.8 17.7 + - - +
444A ASN* 3.8 9.2 - - - +
446A LEU* 1.3 76.7 - - - +
448A ASP* 1.3 64.0 + - - +
450A LYS* 3.4 11.6 + - - +
451A THR* 3.0 27.6 + - - -
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Residues in contact with ASP 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 ASN 3.1 19.1 + - - +
445A LEU* 3.8 10.9 - - + +
446A LEU 3.3 0.2 - - - -
447A ALA* 1.3 78.3 - - - +
449A LEU* 1.3 59.0 + - - +
451A THR* 3.3 8.6 + - - -
452A MET* 3.0 31.6 + - - +
474A GLN* 2.7 44.3 + - + +
477A GLN* 5.7 0.5 + - - -
478A ASN* 5.0 3.8 - - - +
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Residues in contact with LEU 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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445A LEU 3.2 14.7 + - - +
446A LEU* 3.3 6.0 + - + +
448A ASP* 1.3 80.2 - - - +
450A LYS* 1.3 62.1 + - - +
452A MET* 3.1 10.4 + - + +
453A VAL* 3.0 27.5 + - + +
474A GLN 5.0 2.0 - - - +
475A VAL* 5.2 4.5 - - + -
478A ASN* 3.7 35.0 - - + +
482A CYS* 5.5 0.4 - - - -
546A LEU* 4.3 13.2 - - + +
549A THR* 3.4 30.7 - - + +
550A TRP* 3.9 23.6 - - + +
553A LEU* 4.2 23.8 - - + -
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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 LEU* 2.9 38.7 + - + +
447A ALA* 3.5 12.3 - - - +
449A LEU* 1.3 75.9 - - - +
451A THR* 1.3 58.0 + - - +
453A VAL* 3.1 5.2 + - - +
454A GLU* 2.8 47.2 + - - +
545A PRO* 5.6 3.7 - - - +
549A THR* 3.8 24.4 - - + +
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Residues in contact with THR 451 (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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447A ALA 3.0 16.1 + - - -
448A ASP* 3.5 11.2 - - - -
449A LEU 3.3 0.2 - - - -
450A LYS* 1.3 75.0 - - - +
452A MET* 1.3 65.2 + - + +
454A GLU* 3.5 12.4 + - - +
455A THR* 3.0 44.8 + - + +
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Residues in contact with MET 452 (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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448A ASP 3.0 12.3 + - - +
449A LEU* 3.1 15.5 + - + +
451A THR* 1.3 81.4 - - + +
453A VAL* 1.3 60.9 + - - +
455A THR* 3.7 7.7 + - - +
456A LYS* 3.2 24.8 + - - +
464A LEU* 6.2 1.3 - - + -
466A LEU* 4.6 7.4 - - + -
471A ASP* 3.2 54.3 - - - +
474A GLN* 3.8 20.9 - - - +
475A VAL* 4.5 13.2 - - + -
553A LEU* 4.2 17.4 - - + +
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Residues in contact with VAL 453 (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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449A LEU* 3.0 18.7 + - + +
450A LYS* 3.1 8.0 + - - +
452A MET* 1.3 74.1 - - - +
454A GLU* 1.3 70.2 + - + +
455A THR 3.0 2.8 + - - -
456A LYS* 3.1 25.1 + - + +
549A THR* 3.6 32.3 - - + +
552A ASP* 3.9 26.0 - - + +
553A LEU* 4.1 19.1 - - + +
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Residues in contact with GLU 454 (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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450A LYS* 2.8 39.4 + - - +
451A THR* 3.9 10.6 + - - +
453A VAL* 1.3 76.5 - - + +
455A THR* 1.3 63.4 + - + +
456A LYS 3.6 0.4 + - - -
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Residues in contact with THR 455 (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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451A THR* 3.0 32.3 + - + +
452A MET* 3.8 10.4 + - - +
453A VAL 3.0 0.8 - - - -
454A GLU* 1.3 84.8 - - + +
456A LYS* 1.3 62.9 + - - +
457A LYS* 3.7 6.9 + - - +
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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