Contacts of the helix formed by residues 452 - 468 (chain A) in PDB entry 1DGB
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 ASN 452 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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450A VAL 4.0 0.2 + - - -
451A LEU* 1.3 70.9 - - - +
453A GLU* 1.3 65.6 + - - +
454A GLU* 2.9 20.1 + - - +
455A GLN* 2.8 51.6 + - - +
456A ARG* 3.0 31.8 + - - +
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Residues in contact with GLU 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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452A ASN* 1.3 76.6 + - - +
454A GLU* 1.3 65.6 + - - +
456A ARG* 3.0 23.0 + - + +
457A LYS* 2.9 22.7 + - + +
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Residues in contact with GLU 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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452A ASN* 2.9 24.4 + - - +
453A GLU* 1.3 76.9 - - - +
455A GLN* 1.3 56.3 + - - +
457A LYS* 3.3 20.3 + - - +
458A ARG* 2.8 65.9 + - - +
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Residues in contact with GLN 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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201A SER* 5.8 0.9 - - - -
202A ASP* 4.1 12.9 + - - +
450A VAL 4.1 3.3 - - - +
451A LEU* 3.4 28.7 - - + +
452A ASN* 2.8 51.5 + - - +
454A GLU* 1.3 73.6 - - - +
456A ARG* 1.3 67.0 + - - +
458A ARG* 3.3 26.5 + - - +
459A LEU* 2.9 23.7 + - - +
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Residues in contact with ARG 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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447A TYR* 2.8 61.9 + - + +
448A VAL* 2.7 33.5 + - - +
451A LEU* 2.8 25.5 + - + +
452A ASN* 3.0 14.6 + - - +
453A GLU* 3.0 38.0 + - - +
455A GLN* 1.3 74.8 - - - +
457A LYS* 1.3 65.3 + - - +
459A LEU* 3.1 10.3 + - - +
460A CYS* 3.0 27.7 + - - -
492A HIS* 5.1 1.6 - - + -
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Residues in contact with LYS 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 GLU* 2.9 15.2 + - + +
454A GLU* 3.3 23.1 - - - +
456A ARG* 1.3 78.5 - - - +
458A ARG* 1.3 79.5 + - - +
460A CYS* 3.2 3.3 + - - +
461A GLU* 3.0 57.7 + - - +
492A HIS* 4.0 25.4 + - + +
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Residues in contact with ARG 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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202A ASP* 2.9 45.1 + - - +
454A GLU* 2.8 52.7 + - - +
455A GLN* 3.5 25.7 - - - +
457A LYS* 1.3 89.3 - - - +
459A LEU* 1.3 65.4 + - - +
461A GLU* 2.9 14.5 + - - +
462A ASN* 2.9 34.1 + - - +
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Residues in contact with LEU 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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197A SER* 3.3 18.6 - - - +
200A PHE* 3.3 45.1 - - + +
201A SER* 3.6 5.8 - - - +
446A PHE* 4.6 4.3 - - + -
447A TYR* 4.2 13.0 - - + -
451A LEU* 3.8 24.5 - - + -
455A GLN 2.9 13.8 + - - +
456A ARG* 3.2 8.3 - - - +
458A ARG* 1.3 76.8 - - - +
460A CYS* 1.3 62.9 + - - +
462A ASN* 3.2 3.8 + - - +
463A ILE* 3.1 26.8 + - + +
489A TYR* 3.5 35.4 - - + +
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Residues in contact with CYS 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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447A TYR* 4.5 9.0 - - - -
456A ARG 3.0 19.3 + - - -
457A LYS 3.6 6.1 - - - +
459A LEU* 1.3 77.5 - - - +
461A GLU* 1.3 58.2 + - - +
463A ILE* 3.2 4.6 + - - +
464A ALA* 2.9 32.6 + - - +
489A TYR* 4.1 24.9 - - - -
492A HIS* 3.8 39.3 - - + -
493A ILE* 4.0 17.3 - - + +
496A LEU* 3.8 7.1 - - + +
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Residues in contact with GLU 461 (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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457A LYS* 3.0 49.1 + - + +
458A ARG* 2.9 22.3 + - - +
460A CYS* 1.3 75.8 - - - +
462A ASN* 1.3 61.2 + - - +
464A ALA* 3.8 0.9 - - - +
465A GLY* 2.8 27.0 + - - -
492A HIS* 5.4 1.4 - - + -
496A LEU* 3.8 25.7 - - + +
500A TYR* 4.2 9.5 + - - +
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Residues in contact with ASN 462 (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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127A ARG* 2.9 34.8 + - - +
200A PHE* 2.9 44.9 + - + +
201A SER 4.2 3.6 + - - -
202A ASP* 5.0 2.8 + - - +
247A VAL* 3.7 17.2 - - - +
458A ARG* 2.9 24.8 + - - +
459A LEU 3.5 6.1 - - - +
461A GLU* 1.3 77.3 - - - +
463A ILE* 1.3 66.6 + - - +
465A GLY* 3.5 2.1 + - - -
466A HIS* 3.5 12.1 + - - +
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Residues in contact with ILE 463 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A TRP* 4.0 20.0 - - + -
196A VAL* 4.8 3.4 - - + -
200A PHE* 3.5 29.6 - - + -
459A LEU* 3.1 19.9 + - + +
460A CYS 3.6 5.8 - - - +
462A ASN* 1.3 76.2 - - - +
464A ALA* 1.3 59.4 + - - +
466A HIS* 3.1 5.2 + - - +
467A LEU* 2.9 38.4 + - + +
482A PHE* 3.9 18.8 - - + -
489A TYR* 3.3 39.0 - - + +
493A ILE* 3.8 17.0 - - + -
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Residues in contact with ALA 464 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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460A CYS 2.9 16.2 + - - +
461A GLU 4.0 2.2 - - - +
463A ILE* 1.3 78.9 - - - +
465A GLY* 1.3 62.0 + - - +
467A LEU* 4.4 1.8 - - - -
468A LYS* 3.0 29.5 + - - +
493A ILE* 4.3 8.7 - - + +
496A LEU* 3.6 30.5 - - + -
497A LEU* 4.0 17.8 - - + +
500A TYR* 3.7 11.0 - - + -
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Residues in contact with GLY 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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461A GLU 2.8 18.6 + - - -
462A ASN* 3.5 3.6 + - - -
463A ILE 3.2 0.6 - - - -
464A ALA* 1.3 78.2 - - - +
466A HIS* 1.3 54.8 + - - +
468A LYS* 3.1 30.4 + - - +
469A ASP* 4.3 0.3 - - - +
500A TYR* 4.1 15.0 - - - -
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Residues in contact with HIS 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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179A PRO* 4.2 20.7 - - + +
182A VAL* 3.8 28.0 - - + +
183A TRP* 2.7 35.1 + + - +
186A TRP* 5.7 0.4 - + - -
200A PHE* 4.2 16.9 - + + -
462A ASN 3.5 9.1 + - - +
463A ILE 3.1 6.7 + - - +
465A GLY* 1.3 76.6 - - - +
467A LEU* 1.3 64.4 + - - +
468A LYS 3.0 3.5 + - - -
469A ASP* 3.2 23.5 + - - +
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Residues in contact with LEU 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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183A TRP* 3.4 49.1 - - + +
463A ILE* 2.9 33.1 + - + +
464A ALA* 4.2 1.8 - - - +
466A HIS* 1.3 78.5 - - - +
468A LYS* 1.3 61.8 + - - +
470A ALA* 2.8 26.2 + - + +
475A GLN* 3.6 25.8 + - + +
478A ALA* 4.1 21.3 - - + -
479A VAL* 4.9 0.9 - - + -
482A PHE* 4.9 1.8 - - + -
493A ILE* 4.4 7.9 - - + -
497A LEU* 4.0 22.2 - - + -
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Residues in contact with LYS 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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464A ALA 3.0 14.1 + - - +
465A GLY* 3.1 26.2 + - - +
467A LEU* 1.3 76.4 - - - +
469A ASP* 1.3 92.7 + - - +
470A ALA 3.3 1.7 - - - +
475A GLN* 3.3 21.2 + - - +
497A LEU* 4.0 7.8 - - + +
500A TYR* 3.8 48.5 - - + +
501A ASN* 4.0 8.8 - - - +
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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