Contacts of the helix formed by residues 440 - 451 (chain A) in PDB entry 1B3U
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 GLU 440 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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439A ASP* 1.3 99.3 - - - +
441A LYS* 1.3 64.6 + - - +
443A ASN* 3.1 3.0 + - - +
444A SER* 2.9 23.3 + - - -
480A THR* 5.7 0.6 - - - +
484A LYS* 2.9 37.2 - - - +
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Residues in contact with LYS 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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404A LEU* 3.7 30.7 - - + -
408A VAL* 3.5 34.9 - - + +
439A ASP* 3.4 4.9 - - - +
440A GLU* 1.3 81.1 + - - +
442A LEU* 1.3 64.9 + - - +
444A SER* 2.6 30.6 + - - +
445A LEU* 3.3 19.1 + - - +
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Residues in contact with LEU 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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404A LEU* 4.1 21.5 - - + +
407A ILE* 4.7 7.4 - - + -
426A MET* 3.5 24.7 - - + -
437A PHE* 3.5 43.7 - - + +
438A PHE* 3.4 29.8 - - + -
439A ASP* 3.2 21.1 + - - +
441A LYS* 1.3 77.6 - - - +
443A ASN* 1.3 61.8 + - - +
445A LEU* 3.2 32.8 + - + +
446A CYS* 3.3 9.8 + - - -
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Residues in contact with ASN 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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438A PHE* 3.0 38.3 + - - +
439A ASP 2.7 29.0 + - - +
440A GLU* 3.6 5.3 - - - +
442A LEU* 1.3 73.0 - - - +
444A SER* 1.3 66.0 + - - +
446A CYS* 3.3 10.2 + - - +
447A MET* 3.1 29.5 + - + +
468A LEU* 5.7 0.9 - - - +
476A TRP* 4.0 12.2 - - - -
480A THR* 3.4 23.3 - - - +
481A ILE* 4.8 11.6 - - + +
484A LYS* 4.1 13.0 - - + +
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Residues in contact with SER 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 GLU 2.9 12.6 + - - -
441A LYS* 2.6 32.6 + - - +
443A ASN* 1.3 76.7 - - - +
445A LEU* 1.3 60.7 + - - +
447A MET* 3.1 20.3 + - - +
448A ALA* 2.8 31.6 + - - +
484A LYS* 5.8 1.1 - - - -
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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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404A LEU* 5.2 0.9 - - + -
407A ILE* 3.9 17.3 - - + -
408A VAL* 3.8 40.2 - - + -
411A ALA* 3.7 30.5 - - + -
412A GLU* 5.7 2.0 - - - +
441A LYS* 3.9 20.2 - - - +
442A LEU* 3.2 21.3 + - + +
444A SER* 1.3 84.0 + - - +
446A CYS* 1.3 64.1 + - - +
447A MET 3.2 0.9 + - - -
448A ALA* 3.3 15.8 + - + +
449A TRP* 3.5 27.7 + - + -
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Residues in contact with CYS 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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426A MET* 4.2 27.8 - - - -
438A PHE* 4.8 2.5 - - - -
442A LEU* 3.3 17.5 + - - -
443A ASN* 3.3 11.1 + - - +
445A LEU* 1.3 79.3 - - - +
447A MET* 1.3 62.7 + - + +
449A TRP* 3.6 25.9 + - - +
450A LEU* 4.5 3.5 - - - +
461A ALA* 4.3 11.4 - - - +
464A ASN* 3.9 21.9 - - - +
465A LEU* 5.3 14.0 - - + +
468A LEU* 4.5 13.0 - - + -
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Residues in contact with MET 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 ASN* 3.1 12.3 - - + +
444A SER* 3.1 36.0 + - - +
445A LEU 3.1 0.4 - - - -
446A CYS* 1.3 79.4 - - + +
448A ALA* 1.3 65.0 + - - +
449A TRP 3.2 0.4 - - - -
450A LEU* 3.1 25.8 + - - +
451A VAL 4.5 0.2 + - - -
465A LEU* 5.5 8.7 - - + -
481A ILE* 4.4 15.7 - - + +
484A LYS* 4.2 25.6 - - + -
485A VAL* 4.0 26.9 - - - -
488A MET* 4.6 13.2 - - + -
499A THR* 3.7 15.1 - - + +
503A CYS* 3.7 20.9 - - - -
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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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444A SER 2.8 16.1 + - - +
445A LEU* 3.3 8.5 + - - +
447A MET* 1.3 76.4 - - - +
449A TRP* 1.3 63.5 + - + +
451A VAL* 3.1 25.6 + - + +
452A ASP* 4.0 1.4 + - - -
499A THR* 4.7 9.9 - - - -
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Residues in contact with TRP 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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407A ILE* 6.1 0.2 - - + -
411A ALA* 3.1 47.7 + - + +
419A ARG* 4.5 8.8 + - + +
422A ILE* 4.2 14.8 - - + -
423A ILE* 3.6 44.1 - - + +
426A MET* 4.5 9.9 - - - -
445A LEU* 3.5 16.1 + - + -
446A CYS* 3.6 40.2 - - + +
447A MET 3.2 0.8 - - - -
448A ALA* 1.3 78.9 - - + +
450A LEU* 1.3 56.5 + - - +
451A VAL 3.0 0.2 - - - -
452A ASP* 2.8 36.4 + - - +
457A ILE* 3.9 18.8 - - + +
458A ARG* 3.7 5.5 - - - +
461A ALA* 3.6 21.5 - - + -
464A ASN* 4.6 7.2 - - - -
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Residues in contact with LEU 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 CYS 4.5 2.7 - - - +
447A MET* 3.1 15.6 + - - +
449A TRP* 1.3 76.5 - - - +
451A VAL* 1.3 56.4 + - + +
452A ASP 3.4 0.4 - - - -
458A ARG* 3.3 22.4 - - + +
461A ALA* 3.9 9.9 - - + -
462A THR* 3.5 41.7 - - - +
465A LEU* 4.4 14.8 - - + -
499A THR* 5.4 2.2 - - + -
502A PHE* 3.1 33.2 - - + +
503A CYS* 3.6 46.0 - - - +
506A VAL* 4.6 6.1 - - + -
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Residues in contact with VAL 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 MET 4.5 0.2 + - - -
448A ALA* 3.1 15.3 + - + +
449A TRP 3.0 1.4 - - - -
450A LEU* 1.3 76.6 - - - +
452A ASP* 1.3 67.5 + - - +
453A HIS 3.7 0.9 + - - -
458A ARG* 4.6 0.7 - - - +
495A LEU* 4.1 47.1 - - + +
498A MET* 4.2 18.8 - - + -
499A THR* 4.0 15.9 - - - +
502A PHE* 4.3 13.5 - - + -
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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