Contacts of the helix formed by residues 445 - 459 (chain A) in PDB entry 4BU2
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 THR 445 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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443A LEU* 3.7 0.6 - - - +
444A THR* 1.3 90.7 - - + +
446A ASP* 1.3 66.6 + - - +
447A GLU* 3.6 10.0 + - - +
448A GLU* 2.7 34.9 + - - +
449A LYS* 3.1 24.6 + - - +
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Residues in contact with ASP 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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360A LEU* 3.8 27.9 - - + +
445A THR* 1.3 73.2 - - - +
447A GLU* 1.3 60.1 + - - +
449A LYS* 3.1 32.1 + - - +
450A GLU* 2.8 31.2 + - - +
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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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445A THR* 3.3 7.2 + - - +
446A ASP* 1.3 78.6 - - - +
448A GLU* 1.3 52.8 + - - +
450A GLU* 3.3 5.5 + - - +
451A SER* 2.6 39.3 + - - -
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Residues in contact with GLU 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A HIS* 4.1 27.3 + - + -
443A LEU* 3.9 7.9 - - + +
444A THR* 3.2 17.6 + - - +
445A THR* 2.7 56.3 + - - +
447A GLU* 1.3 70.6 - - - +
449A LYS* 1.3 64.7 + - - +
450A GLU 3.1 1.6 - - - -
451A SER* 3.7 9.6 - - - -
452A LEU* 2.9 27.7 + - - +
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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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360A LEU* 5.6 3.1 - - + +
438A VAL* 3.0 41.0 - - + +
439A LYS* 2.8 46.3 + - - +
441A LEU* 3.3 25.6 - - + +
443A LEU* 3.4 28.5 - - + +
444A THR 5.9 0.2 - - - -
445A THR 3.1 20.2 + - - +
446A ASP* 3.1 36.2 + - - +
448A GLU* 1.3 77.5 - - - +
450A GLU* 1.3 58.1 + - - +
452A LEU* 4.2 0.5 - - - +
453A VAL* 3.3 16.1 + - - +
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Residues in contact with GLU 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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358A PRO* 2.7 25.3 - - - +
359A ARG* 3.0 6.9 - - - +
360A LEU* 2.9 36.1 + - + +
438A VAL* 4.3 4.7 - - - +
446A ASP 2.8 14.8 + - - +
447A GLU* 3.6 5.4 - - + +
449A LYS* 1.3 76.4 - - - +
451A SER* 1.3 67.3 + - - +
452A LEU 3.2 1.6 - - - -
453A VAL* 3.1 5.6 + - - +
454A LEU* 2.8 43.0 + - + +
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Residues in contact with SER 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 GLU* 2.6 26.2 + - - -
448A GLU* 3.7 10.5 - - - -
450A GLU* 1.3 73.3 - - - +
452A LEU* 1.3 65.2 + - - +
454A LEU* 3.0 12.3 + - - +
455A SER* 2.8 26.6 + - - -
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Residues in contact with LEU 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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419A PHE* 3.7 26.0 - - + -
423A HIS* 4.5 18.6 - - + +
426A ALA* 4.2 15.7 - - + -
427A LEU* 4.6 7.4 - - + -
430A ILE* 4.3 13.5 - - + -
441A LEU* 4.6 6.3 - - + -
443A LEU* 3.8 22.7 - - + -
448A GLU 2.9 17.7 + - - +
449A LYS 4.2 2.0 - - - +
451A SER* 1.3 74.7 - - - +
453A VAL* 1.3 64.2 + - + +
455A SER* 2.7 26.0 + - - -
456A LEU* 3.1 40.7 + - + +
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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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358A PRO* 4.3 16.2 - - + -
364A VAL* 3.9 26.7 - - + -
430A ILE* 5.9 3.1 - - + -
438A VAL* 3.8 14.6 - - + -
441A LEU* 3.4 23.1 - - + -
449A LYS 3.3 18.6 - - - +
450A GLU* 3.1 8.3 + - - +
452A LEU* 1.3 79.5 - - + +
454A LEU* 1.3 55.7 + - - +
456A LEU* 3.9 7.8 - - + +
457A TRP* 3.0 27.4 + - - +
462A ILE* 4.0 18.6 - - + +
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Residues in contact with LEU 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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357A LEU* 3.9 33.7 - - + -
358A PRO* 4.4 7.6 - - + +
450A GLU* 2.8 34.2 + - + +
451A SER* 3.2 16.8 - - - +
452A LEU 2.9 0.2 - - - -
453A VAL* 1.3 76.7 - - - +
455A SER* 1.3 65.0 + - - +
457A TRP* 3.4 5.8 + - + +
458A THR* 3.1 30.4 + - + +
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Residues in contact with SER 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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417A LEU* 4.1 13.5 - - - +
419A PHE* 4.0 26.8 - - - -
451A SER* 2.8 14.0 + - - -
452A LEU* 2.7 14.9 + - - -
454A LEU* 1.3 71.0 - - - +
456A LEU* 1.3 63.3 + - - -
458A THR* 2.7 27.1 + - - -
459A GLU* 3.3 5.7 + - - +
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Residues in contact with LEU 456 (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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366A LEU* 4.8 7.4 - - + -
393A ILE* 5.5 2.7 - - + -
417A LEU* 3.7 12.1 - - + -
419A PHE* 3.4 22.9 - - + -
427A LEU* 4.9 7.0 - - + -
430A ILE* 4.4 17.9 - - + -
431A TRP* 6.3 2.0 - - + -
452A LEU* 3.1 38.9 + - + +
453A VAL* 4.0 5.8 - - + +
455A SER* 1.3 79.9 - - - +
457A TRP* 1.3 61.8 + - - +
459A GLU* 3.1 7.6 + - - +
461A LEU* 3.1 37.0 + - + +
462A ILE* 3.3 33.7 - - + -
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Residues in contact with TRP 457 (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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356A LYS 4.0 12.0 + - - +
357A LEU* 3.9 28.9 - - + -
358A PRO* 3.5 33.3 - - + +
453A VAL 3.0 19.9 + - - +
454A LEU* 3.5 7.4 - - + +
455A SER 3.0 0.4 + - - -
456A LEU* 1.3 76.7 - - - +
458A THR* 1.3 77.4 + - + +
460A CYS* 3.0 20.3 + - - -
462A ILE* 3.9 32.6 + - + +
463A GLN* 5.3 1.5 - - - +
464A VAL* 5.3 2.8 - - + +
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Residues in contact with THR 458 (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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398A LYS* 4.5 4.7 + - - -
417A LEU* 5.4 0.7 - - - +
454A LEU* 3.1 19.5 - - + +
455A SER* 2.7 21.2 + - - -
457A TRP* 1.3 96.2 - - + +
459A GLU* 1.3 67.2 + - - +
460A CYS* 3.1 8.4 + - - -
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Residues in contact with GLU 459 (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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395A HIS* 2.9 42.6 + - + +
397A LEU* 3.7 5.0 - - - +
398A LYS* 3.9 15.6 + - - +
415A HIS* 5.1 1.9 - - - +
416A GLY 3.6 13.5 + - - +
417A LEU* 3.3 34.9 - - + +
455A SER 3.3 4.2 + - - +
456A LEU 3.1 9.3 + - - +
457A TRP 3.1 1.0 - - - -
458A THR* 1.3 87.7 + - - +
460A CYS* 1.3 69.9 + - - +
461A LEU* 3.2 19.8 - - + +
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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