Contacts of the helix formed by residues 463 - 474 (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 GLU 463 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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457A ALA 4.3 2.6 - - - +
458A LEU* 3.2 39.0 + - + +
459A ARG* 4.1 2.7 + - - -
461A GLY* 3.1 18.2 - - - +
462A ASN* 1.3 72.5 - - - +
464A HIS* 1.3 64.1 + - - +
465A LYS* 3.1 4.3 + - - +
466A GLN* 2.7 38.0 + - - +
467A ALA* 3.2 22.0 + - - +
447C LYS* 1.9 43.6 + - - +
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Residues in contact with HIS 464 (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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459A ARG* 3.0 25.4 + - - +
462A ASN* 3.0 41.0 + - - +
463A GLU* 1.3 72.3 - - - +
465A LYS* 1.3 58.8 + - + +
468A ASP* 2.9 38.4 + - - +
420C ARG* 6.2 1.6 - - - -
31E C 3.2 36.3 + - + -
32E T 3.6 11.3 + - - -
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Residues in contact with LYS 465 (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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463A GLU* 3.1 1.4 - - - +
464A HIS* 1.3 79.9 - - + +
466A GLN* 1.3 64.3 + - + +
468A ASP* 3.3 5.0 + - - +
469A GLU* 3.0 32.4 + - - +
479C PHE* 3.8 33.3 - - + -
514C GLN* 3.4 38.8 - - - +
517C GLN* 6.1 0.2 - - - +
518C PRO* 5.6 4.5 - - - +
521C THR* 5.8 5.7 - - - +
22F C 5.9 0.4 - - - -
23F T 3.3 30.0 + - - -
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Residues in contact with GLN 466 (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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458A LEU* 3.9 13.8 - - + +
463A GLU* 2.7 50.9 + - + +
465A LYS* 1.3 75.2 - - + +
467A ALA* 1.3 58.5 + - - +
469A GLU* 3.3 3.0 + - - -
470A LEU* 2.9 28.9 + - - +
447C LYS* 3.5 9.0 + - - +
473C MET* 3.6 34.8 - - + +
474C MET* 4.6 3.5 - - - +
478C GLY 5.1 3.4 - - - +
479C PHE* 4.4 26.1 - - + -
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Residues in contact with ALA 467 (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* 4.3 19.4 - - + +
458A LEU* 3.7 24.6 - - + +
459A ARG* 3.1 34.8 - - + +
463A GLU 3.2 7.9 + - - +
466A GLN* 1.3 78.4 - - - +
468A ASP* 1.3 55.8 + - - +
470A LEU* 3.6 4.9 - - - +
471A GLU* 2.9 30.1 + - - +
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Residues in contact with ASP 468 (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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459A ARG* 2.7 29.9 + - - +
464A HIS* 2.9 23.4 + - - +
465A LYS* 3.6 5.6 - - - +
466A GLN 3.3 0.2 - - - -
467A ALA* 1.3 77.3 - - - +
469A GLU* 1.3 58.4 + - + +
471A GLU* 3.4 5.8 + - - +
472A ALA* 2.9 28.1 + - - +
508C LYS* 6.1 0.7 - - - +
512C GLY 4.3 9.1 - - - +
513C ARG* 6.2 0.9 - - - -
514C GLN* 6.2 4.3 - - + +
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Residues in contact with GLU 469 (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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465A LYS 3.0 17.3 + - - +
466A GLN 3.9 4.0 - - - +
468A ASP* 1.3 73.5 - - + +
470A LEU* 1.3 61.2 + - - +
472A ALA* 3.2 10.4 + - - +
473A MET* 2.9 25.1 + - - +
473C MET* 4.8 7.7 - - + +
478C GLY 2.8 25.5 - - - +
479C PHE* 2.6 36.5 - - - +
480C GLY* 3.5 6.3 + - - -
513C ARG* 4.7 18.8 - - + +
514C GLN* 3.3 25.9 - - + +
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Residues in contact with LEU 470 (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* 4.2 16.4 - - + -
454A PHE* 3.5 36.6 - - + -
455A LEU* 3.9 20.2 - - + -
458A LEU* 5.2 0.9 - - + -
466A GLN 2.9 17.6 + - - +
467A ALA* 3.6 5.2 - - - +
468A ASP 3.3 0.2 - - - -
469A GLU* 1.3 76.1 - - - +
471A GLU* 1.3 58.9 + - - +
473A MET* 2.8 44.8 + - + +
474A MET* 3.3 7.9 + - + +
454C PHE* 4.5 11.4 - - + -
470C LEU* 3.7 25.8 - - + -
473C MET* 4.7 8.2 - - - -
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Residues in contact with GLU 471 (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* 5.0 10.8 - - - +
455A LEU* 3.2 39.0 - - + +
459A ARG* 6.1 1.1 - - - +
467A ALA 2.9 16.1 + - - +
468A ASP* 3.8 6.3 - - - +
470A LEU* 1.3 77.7 - - - +
472A ALA* 1.3 56.9 + - - +
474A MET* 2.7 36.7 - - - +
475A GLN* 4.3 6.6 - - - +
476A GLY 3.7 2.8 + - - +
416C LEU* 5.7 3.3 - - - +
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Residues in contact with ALA 472 (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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468A ASP 2.9 14.5 + - - +
469A GLU* 3.4 11.0 - - - +
470A LEU 3.1 0.4 - - - -
471A GLU* 1.3 74.5 - - - +
473A MET* 1.3 57.5 + - - +
476A GLY 2.7 21.8 - - - +
477A ARG* 3.3 11.1 - - - -
479A PHE* 4.8 1.4 - - - -
512C GLY* 3.7 18.4 - - - +
513C ARG* 3.6 37.2 + - - +
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Residues in contact with MET 473 (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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469A GLU 2.9 10.3 + - - +
470A LEU* 2.8 33.6 + - + +
472A ALA* 1.3 78.9 - - - +
474A MET* 1.3 90.0 + - + +
477A ARG* 3.2 31.5 + - + +
479A PHE* 5.6 8.1 - - + -
454C PHE* 4.8 4.3 - - + -
458C LEU* 4.6 8.7 - - + -
466C GLN* 3.7 28.3 - - + +
469C GLU* 3.4 34.8 - - + +
470C LEU* 4.6 7.6 - - + -
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Residues in contact with MET 474 (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 LYS* 4.3 21.3 - - - +
451A LEU* 5.0 22.0 - - + -
470A LEU* 3.3 12.2 + - + +
471A GLU* 2.7 30.8 - - - +
472A ALA 3.3 0.2 - - - -
473A MET* 1.3 113.4 - - + +
475A GLN* 1.3 90.2 + - + +
476A GLY 3.6 1.1 - - - -
477A ARG* 5.1 4.0 - - - +
454C PHE* 5.3 7.2 - - + -
458C LEU* 6.0 0.2 - - - -
466C GLN* 3.8 27.8 - - - +
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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