Contacts of the helix formed by residues 445 - 461 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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414A HIS* 3.7 17.7 + - - -
438C ALA* 4.1 2.7 - - - +
442C GLU* 3.6 25.3 + - + +
443C GLY 3.2 3.3 - - - +
444C GLY* 1.3 72.5 - - - +
446C VAL* 1.3 61.0 + - - +
447C LYS* 3.8 6.6 + - - +
448C SER* 2.9 37.8 + - - -
449C VAL* 3.2 23.4 + - - +
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Residues in contact with VAL 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A ALA* 5.4 7.0 - - + -
431C LYS* 5.7 4.5 - - + +
434C VAL* 3.6 31.9 - - + +
435C LYS* 3.6 32.3 - - + +
438C ALA* 3.6 17.3 - - + -
444C GLY 2.8 20.7 + - - +
445C ASP* 1.3 71.9 - - - +
447C LYS* 1.3 63.5 + - - +
449C VAL* 3.3 3.3 + - - +
450C CYS* 3.0 32.0 + - - -
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Residues in contact with LYS 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A PHE* 3.8 1.7 - - + -
457A ALA* 4.8 8.7 - - + +
458A LEU* 3.9 16.8 - - + -
463A GLU* 1.9 46.5 + - - +
466A GLN* 3.5 6.2 + - - +
445C ASP* 3.1 6.9 - - - +
446C VAL* 1.3 77.9 - - - +
448C SER* 1.3 62.4 + - - +
450C CYS* 3.2 12.2 - - - -
451C LEU* 2.9 28.8 + - - +
474C MET* 3.6 28.7 - - + +
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Residues in contact with SER 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A HIS* 4.3 3.4 + - - -
415A LEU* 4.9 4.9 - - - -
416A LEU* 3.5 34.7 - - - +
445C ASP* 2.9 31.4 + - - -
447C LYS* 1.3 80.9 - - - +
449C VAL* 1.3 54.2 + - - +
451C LEU* 3.4 8.7 + - - +
452C THR* 2.6 38.4 + - - -
474C MET* 5.8 1.2 - - - +
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Residues in contact with VAL 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A LEU* 4.5 9.9 - - + -
427A LEU* 4.0 19.6 - - + +
430A LEU* 4.3 24.2 - - + -
434C VAL* 4.7 6.1 - - + -
437C PHE* 5.0 5.8 - - + -
438C ALA* 4.7 9.4 - - + -
442C GLU* 4.2 25.8 - - + -
445C ASP* 3.2 18.6 + - + +
446C VAL* 3.6 9.9 - - - +
447C LYS 3.2 0.8 - - - -
448C SER* 1.3 77.2 - - - +
450C CYS* 1.3 59.3 + - - +
452C THR* 3.1 7.4 + - - -
453C LEU* 2.9 34.7 + - + +
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Residues in contact with CYS 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A CYS* 5.2 2.9 - - + +
453A LEU* 4.7 8.3 - - + -
454A PHE* 3.4 34.0 - - + +
457A ALA* 3.7 23.6 - - - -
434C VAL* 5.4 4.9 - - + -
446C VAL* 3.0 32.4 + - + +
447C LYS* 3.2 13.5 - - - -
449C VAL* 1.3 77.9 - - - +
451C LEU* 1.3 55.8 + - - +
453C LEU* 3.3 17.6 + - + +
454C PHE* 2.9 28.4 + - - +
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Residues in contact with LEU 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A LEU* 4.0 29.2 - - + -
454A PHE* 3.5 23.8 - - + -
447C LYS 2.9 18.5 + - - +
448C SER* 3.4 3.6 - - - +
450C CYS* 1.3 78.8 - - - +
452C THR* 1.3 56.8 + - - +
454C PHE* 3.2 4.3 + - + +
455C LEU* 2.9 47.6 + - + +
470C LEU* 4.1 18.8 - - + -
474C MET* 3.6 49.1 - - + -
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Residues in contact with THR 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415A LEU* 3.8 6.3 - - + +
416A LEU* 3.3 15.6 - - - +
423A GLN* 3.4 48.2 - - + +
427A LEU* 3.9 13.5 - - + -
448C SER 2.6 24.7 + - - -
449C VAL 3.6 4.3 - - - -
451C LEU* 1.3 72.2 - - - +
453C LEU* 1.3 66.5 + - - +
455C LEU* 3.6 12.7 - - + +
456C LEU* 3.0 33.0 + - + +
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Residues in contact with LEU 453 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A LEU* 3.8 36.6 - - + +
430A LEU* 4.5 20.9 - - + -
431A LYS* 5.0 11.9 - - + +
434A VAL* 4.7 14.1 - - + -
450A CYS* 4.8 13.2 - - + -
453A LEU* 5.8 4.5 - - + -
434C VAL* 5.4 4.9 - - + -
449C VAL* 2.9 24.3 + - + +
450C CYS* 3.4 20.9 - - + +
452C THR* 1.3 76.9 - - - +
454C PHE* 1.3 56.7 + - - +
456C LEU* 3.9 2.4 - - - +
457C ALA* 2.9 31.9 + - - +
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Residues in contact with PHE 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A LYS* 4.2 12.1 - - + -
450A CYS* 3.4 29.3 - - + +
451A LEU* 3.5 52.9 - - + -
454A PHE* 5.0 9.6 - + + -
470A LEU* 4.5 16.4 - - + -
473A MET* 4.8 5.8 - - + -
474A MET* 5.3 4.9 - - + -
450C CYS 2.9 13.9 + - - +
451C LEU* 3.5 10.1 - - - +
453C LEU* 1.3 75.9 - - - +
455C LEU* 1.3 57.5 - - - +
457C ALA* 3.4 1.0 + - - +
458C LEU* 2.9 57.7 + - + +
470C LEU* 3.5 27.6 - - + -
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Residues in contact with LEU 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A LEU* 5.3 3.6 - - + -
423A GLN* 5.4 3.8 - - - +
451C LEU* 2.9 40.6 + - + +
452C THR* 3.2 20.8 + - + +
454C PHE* 1.3 77.1 - - - +
456C LEU* 1.3 65.0 + - + +
458C LEU* 3.4 4.8 + - - +
459C ARG* 2.9 33.0 + - + +
467C ALA* 4.2 20.4 - - + +
470C LEU* 3.7 27.1 - - + -
471C GLU* 4.3 23.1 - - + +
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Residues in contact with LEU 456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A ARG* 4.2 31.4 - - + +
423A GLN* 4.3 16.2 - - + +
424A LYS* 3.9 44.6 - - + +
427A LEU* 6.1 3.1 - - + -
452C THR* 3.0 22.8 + - + +
453C LEU* 4.2 2.5 - - - +
455C LEU* 1.3 81.1 - - + +
457C ALA* 1.3 60.9 + - - +
459C ARG* 3.7 8.7 - - + +
460C ALA* 2.9 29.8 + - - +
44G T 4.3 9.7 + - - +
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Residues in contact with ALA 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A VAL* 4.2 18.4 - - + -
447A LYS* 5.5 5.7 - - - +
450A CYS* 4.0 21.5 - - - -
453C LEU 2.9 19.2 + - - +
454C PHE 3.9 2.7 - - - +
456C LEU* 1.3 76.3 - - - +
458C LEU* 1.3 60.0 + - - +
460C ALA* 3.6 8.0 + - - +
461C GLY* 3.3 15.6 + - - -
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Residues in contact with LEU 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447A LYS* 3.8 18.2 - - - +
473A MET* 4.6 4.5 - - + -
474A MET* 5.9 0.4 - - + -
454C PHE* 2.9 43.7 + - + +
455C LEU* 3.6 4.7 - - - +
457C ALA* 1.3 73.6 - - - +
459C ARG* 1.3 58.5 + - - +
460C ALA 3.0 1.8 - - - -
461C GLY* 2.7 27.3 + - - -
462C ASN 3.3 4.3 + - - -
463C GLU* 3.3 29.3 + - - +
466C GLN* 3.3 48.9 - - + +
467C ALA* 3.7 20.4 - - + +
470C LEU* 5.1 3.6 - - + -
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Residues in contact with ARG 459 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420A ARG* 3.8 37.0 - - - +
455C LEU* 2.9 21.4 + - + +
456C LEU* 3.3 11.4 + - + +
458C LEU* 1.3 74.9 - - - +
460C ALA* 1.3 60.0 + - - +
462C ASN* 3.7 0.3 + - - -
464C HIS* 2.7 84.8 + - - +
467C ALA* 3.2 23.1 + - + +
468C ASP* 2.6 25.9 + - - +
471C GLU* 5.4 6.3 + - - +
43G C 4.1 20.0 - - - +
44G T 5.2 1.1 - - - +
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Residues in contact with ALA 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456C LEU 2.9 17.6 + - - +
457C ALA* 3.6 9.2 - - - +
458C LEU 3.0 0.2 - - - -
459C ARG* 1.3 77.4 - - - +
461C GLY* 1.3 59.6 + - - +
462C ASN* 3.2 4.9 + - - +
43G C 4.0 15.3 + - - +
44G T 4.0 25.0 - - - +
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Residues in contact with GLY 461 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447A LYS* 5.7 1.1 - - - -
457C ALA 3.3 7.3 + - - -
458C LEU* 2.7 15.5 + - - -
460C ALA* 1.3 72.9 - - - +
462C ASN* 1.3 60.5 + - - +
463C GLU* 2.9 31.7 - - - +
22H A 5.2 1.0 - - - +
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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
------------------------------------------------------------
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