Contacts of the helix formed by residues 445 - 460 (chain A) in PDB entry 6DBT
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 445 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438A ALA* 4.1 1.8 - - - +
442A GLU* 3.4 17.6 + - + +
443A GLY 3.2 3.6 - - - +
444A GLY* 1.3 71.7 - - - +
446A VAL* 1.3 61.9 + - - +
447A LYS* 3.2 13.2 + - - +
448A SER* 2.5 40.1 + - - -
449A VAL* 3.1 27.0 + - + +
414C HIS* 4.0 11.2 + - + +
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Residues in contact with VAL 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A LYS* 5.8 1.6 - - + +
434A VAL* 4.9 13.7 - - + -
435A LYS* 3.6 41.1 - - + -
438A ALA* 4.9 2.9 - - + -
444A GLY 2.8 16.1 + - - +
445A ASP* 1.3 71.2 - - - +
447A LYS* 1.3 63.2 + - - +
449A VAL* 4.4 5.6 - - - +
450A CYS* 2.9 32.2 + - + -
457C ALA* 4.2 22.4 - - + -
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Residues in contact with LYS 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A ASP* 3.1 9.6 - - - +
446A VAL* 1.3 79.9 - - - +
448A SER* 1.3 61.4 + - - +
450A CYS* 3.2 9.5 - - - -
451A LEU* 2.9 34.0 + - + +
474A MET* 4.3 20.3 - - - +
454C PHE* 4.2 10.0 - - + -
457C ALA* 5.5 5.6 - - + +
458C LEU* 3.8 21.5 - - - +
461C GLY* 5.7 1.2 - - - -
463C GLU* 3.3 31.1 + - - -
466C GLN* 4.3 4.9 - - - +
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Residues in contact with SER 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A ASP* 2.5 30.7 + - - -
447A LYS* 1.3 79.9 - - - +
449A VAL* 1.3 57.5 + - - +
451A LEU* 3.5 7.5 - - - +
452A THR* 2.9 34.8 + - - -
414C HIS* 4.0 8.4 + - - -
415C LEU* 4.0 8.3 - - - -
416C LEU* 3.4 33.2 - - - +
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Residues in contact with VAL 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A VAL* 3.8 24.9 - - + -
437A PHE* 4.8 6.7 - - + -
438A ALA* 3.8 21.1 - - + -
442A GLU* 4.4 15.0 - - + -
445A ASP* 3.1 19.8 + - + +
446A VAL* 3.8 5.2 - - - +
448A SER* 1.3 77.9 - - - +
450A CYS* 1.3 58.8 + - - +
452A THR* 3.8 1.9 - - - -
453A LEU* 2.9 46.1 + - + +
415C LEU* 3.8 19.7 - - + +
427C LEU* 4.8 2.0 - - + +
430C LEU* 4.0 10.3 - - + -
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Residues in contact with CYS 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A VAL* 5.6 4.3 - - + -
446A VAL* 2.9 30.3 + - + +
447A LYS* 3.2 18.6 - - - -
449A VAL* 1.3 77.1 - - + +
451A LEU* 1.3 63.1 + - - +
453A LEU* 3.7 11.7 - - + +
454A PHE* 2.9 26.2 + - - +
450C CYS* 5.2 3.1 - - + +
453C LEU* 4.8 12.3 - - + -
454C PHE* 3.4 32.6 - - + +
457C ALA* 4.0 21.5 - - + -
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Residues in contact with LEU 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A LYS* 2.9 23.5 + - + +
448A SER* 3.5 6.7 - - - +
449A VAL 3.2 0.2 - - - -
450A CYS* 1.3 79.1 - - - +
452A THR* 1.3 63.7 + - - +
454A PHE* 3.2 2.0 + - - +
455A LEU* 2.9 40.3 + - + +
470A LEU* 4.2 22.2 - - + -
471A GLU* 5.0 9.6 - - - +
474A MET* 5.0 20.9 - - + -
475A GLN* 6.5 0.2 - - + -
416C LEU* 4.2 24.9 - - + -
454C PHE* 3.5 32.3 - - + -
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Residues in contact with THR 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 SER 2.9 19.7 + - - -
449A VAL 3.9 2.5 - - - -
451A LEU* 1.3 72.4 - - - +
453A LEU* 1.3 57.3 + - - +
455A LEU* 3.3 13.1 + - + +
456A LEU* 2.9 34.8 + - + +
415C LEU* 3.6 12.1 + - + +
416C LEU* 3.4 19.8 - - - +
423C GLN* 4.0 32.5 - - + +
427C LEU* 3.7 24.0 - - + -
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Residues in contact with LEU 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A VAL* 4.7 9.6 - - + -
449A VAL* 2.9 30.0 + - + +
450A CYS* 3.7 8.7 - - - +
452A THR* 1.3 76.8 - - - +
454A PHE* 1.3 57.7 + - - +
456A LEU* 3.4 7.1 + - + +
457A ALA* 2.9 29.2 + - - +
427C LEU* 3.8 30.5 - - + +
430C LEU* 3.6 31.4 - - + -
431C LYS* 4.8 20.6 - - + -
434C VAL* 5.0 8.5 - - + -
450C CYS* 4.7 10.5 - - + -
453C LEU* 5.8 5.4 - - + -
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Residues in contact with PHE 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 CYS 2.9 18.3 + - - +
451A LEU* 3.8 3.8 - - - +
453A LEU* 1.3 75.2 - - - +
455A LEU* 1.3 63.7 + - - +
457A ALA* 3.3 1.4 + - - +
458A LEU* 2.9 66.7 + - + +
470A LEU* 3.5 29.2 - - + -
447C LYS* 3.8 9.2 - - + -
450C CYS* 3.4 30.7 - - - +
451C LEU* 3.5 45.5 - - + -
454C PHE* 5.0 9.9 - + + -
470C LEU* 5.1 7.0 - - + -
473C MET* 5.8 2.7 - - + -
474C MET* 4.2 14.6 - - + -
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Residues in contact with LEU 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 LEU* 2.9 38.7 + - + +
452A THR* 3.5 18.8 - - + +
454A PHE* 1.3 76.7 - - - +
456A LEU* 1.3 59.6 + - + +
458A LEU* 3.1 7.5 + - - +
459A ARG* 2.9 35.7 + - + +
467A ALA* 4.3 20.8 - - + +
470A LEU* 3.9 25.4 - - + -
471A GLU* 3.2 30.3 - - - +
416C LEU* 5.4 4.0 - - + -
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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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452A THR* 2.9 27.4 + - + +
453A LEU* 3.9 6.1 - - + +
455A LEU* 1.3 78.7 - - + +
457A ALA* 1.3 62.4 + - - +
459A ARG* 3.4 9.2 + - + +
460A ALA* 3.2 23.0 + - - +
420C ARG* 4.7 15.5 - - + +
423C GLN* 4.2 23.3 - - + +
424C LYS* 3.7 59.5 - - + +
427C LEU* 4.6 8.5 - - + -
431C LYS* 5.1 19.7 + - + +
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Residues in contact with ALA 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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453A LEU 2.9 18.3 + - - +
454A PHE 3.5 5.6 - - - +
455A LEU 3.2 0.2 - - - -
456A LEU* 1.3 77.8 - - - +
458A LEU* 1.3 64.6 + - + +
460A ALA* 3.6 11.4 + - - +
461A GLY* 3.6 6.9 + - - -
463A GLU* 4.3 2.3 - - - +
431C LYS* 5.8 5.6 - - - +
446C VAL* 5.4 7.2 - - + -
447C LYS* 4.8 12.6 - - + +
450C CYS* 3.7 23.8 - - - -
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Residues in contact with LEU 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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454A PHE* 2.9 60.4 + - + +
455A LEU* 3.6 6.5 - - - +
457A ALA* 1.3 81.2 - - + +
459A ARG* 1.3 58.1 + - - +
461A GLY* 2.9 18.7 + - - -
463A GLU* 3.2 41.9 + - + +
466A GLN* 3.9 16.2 - - + +
467A ALA* 3.7 38.6 - - + +
470A LEU* 5.2 1.3 - - + -
447C LYS* 3.9 17.5 - - + -
473C MET* 5.4 1.3 - - + -
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Residues in contact with ARG 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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455A LEU* 2.9 24.1 + - + +
456A LEU* 3.9 12.8 - - + +
457A ALA 3.4 0.2 - - - -
458A LEU* 1.3 76.1 - - - +
460A ALA* 1.3 60.8 + - - +
461A GLY 3.4 0.3 + - - -
462A ASN* 3.4 13.1 + - - +
463A GLU 3.8 3.2 + - - +
464A HIS* 3.0 43.7 - - - +
467A ALA* 3.1 27.7 + - + +
468A ASP* 2.7 27.9 + - - +
471A GLU* 6.1 1.2 - - - +
420C ARG* 3.1 39.9 - - - +
424C LYS* 6.0 3.8 - - - +
32E T 3.3 40.6 + - - +
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Residues in contact with ALA 460 (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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456A LEU 3.2 16.1 + - - +
457A ALA* 3.9 7.6 - - - +
458A LEU 3.2 0.2 - - - -
459A ARG* 1.3 77.0 - - - +
461A GLY* 1.3 57.2 + - - +
462A ASN* 3.3 7.4 - - - -
424C LYS* 6.6 0.2 - - - -
431C LYS* 5.2 10.1 + - - -
32E T 5.5 2.7 - - - -
33E G 4.4 20.0 + - - +
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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