Contacts of the helix formed by residues 452 - 468 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451D LEU* 1.3 75.5 - - - +
453D GLU* 1.3 65.9 + - - +
454D GLU* 3.0 11.3 + - - +
455D GLN* 2.8 46.8 + - - +
456D ARG* 2.9 29.9 + - - +
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Residues in contact with GLU 453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452D ASN* 1.3 73.3 - - - +
454D GLU* 1.3 72.1 + - + +
456D ARG* 3.2 33.9 + - - +
457D LYS* 3.1 22.9 + - - +
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Residues in contact with GLU 454 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452D ASN* 3.0 10.7 + - - +
453D GLU* 1.3 86.8 - - + +
455D GLN* 1.3 62.1 + - - +
457D LYS* 3.2 24.7 + - - +
458D ARG* 3.0 51.4 + - - +
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Residues in contact with GLN 455 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D SER* 5.5 4.3 - - - -
202D ASP* 3.8 27.1 + - - +
450D VAL 3.9 4.9 + - - +
451D LEU* 3.1 32.8 - - + +
452D ASN* 2.8 55.2 + - - +
454D GLU* 1.3 69.7 - - - +
456D ARG* 1.3 60.9 + - - +
458D ARG* 3.4 13.3 + - - +
459D LEU* 2.8 30.8 + - - +
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Residues in contact with ARG 456 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447D TYR* 2.7 59.1 + - + +
448D VAL* 2.8 28.3 + - - +
451D LEU* 2.9 28.8 + - + +
452D ASN* 2.9 17.6 + - - +
453D GLU* 3.2 46.2 + - - +
455D GLN* 1.3 75.8 - - - +
457D LYS* 1.3 64.0 + - - +
459D LEU* 3.3 7.1 + - - +
460D CYS* 2.9 29.8 + - - -
492D HIS* 5.2 0.9 - - - +
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Residues in contact with LYS 457 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453D GLU 3.1 13.6 + - - +
454D GLU* 3.4 29.1 + - - +
456D ARG* 1.3 76.6 - - - +
458D ARG* 1.3 58.4 + - + +
460D CYS* 3.2 5.5 + - - +
461D GLU* 2.9 55.7 + - - +
492D HIS* 3.8 24.7 - - + -
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Residues in contact with ARG 458 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D SER* 6.3 0.4 - - - -
202D ASP* 2.6 45.9 + - - +
452D ASN* 6.0 0.2 - - - +
454D GLU* 3.0 51.8 + - - +
455D GLN* 3.7 7.4 - - - +
457D LYS* 1.3 75.8 - - + +
459D LEU* 1.3 56.4 + - - +
461D GLU* 3.1 19.0 + - + +
462D ASN* 2.7 51.3 + - - +
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Residues in contact with LEU 459 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D SER* 3.5 19.7 - - - +
200D PHE* 3.2 44.8 + - + +
201D SER* 4.7 4.0 - - - +
446D PHE* 4.8 0.9 - - + -
447D TYR* 4.2 9.4 - - + -
451D LEU* 3.8 24.5 - - + -
455D GLN 2.8 19.8 + - - +
456D ARG 3.4 3.8 - - - +
458D ARG* 1.3 76.1 - - - +
460D CYS* 1.3 62.9 + - - +
462D ASN* 3.3 1.4 + - - +
463D ILE* 3.1 40.4 + - + +
489D TYR* 3.5 31.9 - - + +
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Residues in contact with CYS 460 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447D TYR* 4.2 7.4 - - - -
456D ARG 2.9 16.5 + - - +
457D LYS 3.5 7.6 - - - +
459D LEU* 1.3 76.3 - - - +
461D GLU* 1.3 58.3 + - - +
463D ILE* 3.3 4.4 + - - +
464D ALA* 2.9 28.8 + - - +
489D TYR* 3.8 21.5 - - - -
492D HIS* 3.7 39.5 - - + +
493D ILE* 3.7 29.2 - - + +
496D LEU* 3.8 2.8 - - + +
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Residues in contact with GLU 461 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457D LYS* 2.9 52.8 + - - +
458D ARG* 3.2 27.5 - - + +
460D CYS* 1.3 72.1 - - - +
462D ASN* 1.3 62.3 + - - +
464D ALA* 3.8 1.1 - - - +
465D GLY* 2.8 26.7 + - - -
492D HIS* 4.6 5.9 + - - -
496D LEU* 3.5 21.7 - - + +
500D TYR* 4.3 7.6 + - + +
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Residues in contact with ASN 462 (chain D).
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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127D ARG* 3.4 24.5 + - - +
200D PHE* 3.1 41.4 + - + +
201D SER* 4.9 4.8 - - - +
202D ASP* 5.3 1.8 + - - +
247D VAL* 3.8 16.9 - - - +
458D ARG* 2.7 41.6 + - - +
459D LEU 3.6 4.0 - - - +
461D GLU* 1.3 73.3 - - - +
463D ILE* 1.3 67.1 + - - +
465D GLY* 3.1 10.3 + - - -
466D HIS* 3.1 10.7 + - - +
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Residues in contact with ILE 463 (chain D).
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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183D TRP* 4.0 21.2 - - + -
196D VAL* 5.3 3.6 - - + -
200D PHE* 3.6 30.1 - - + -
459D LEU* 3.1 36.3 + - + +
460D CYS 3.6 3.8 - - - +
462D ASN* 1.3 76.2 - - - +
464D ALA* 1.3 53.0 + - - +
466D HIS* 3.0 3.5 + - - +
467D LEU* 2.6 51.3 + - + +
482D PHE* 4.1 11.9 - - + -
489D TYR* 3.7 15.3 - - + +
493D ILE* 4.0 27.4 - - + -
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Residues in contact with ALA 464 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460D CYS 2.9 17.0 + - - +
461D GLU 3.8 3.1 - - - +
463D ILE* 1.3 76.1 - - - +
465D GLY* 1.3 66.3 + - - +
467D LEU* 4.4 6.3 - - - -
468D LYS* 2.9 29.8 + - - +
493D ILE* 4.4 9.8 - - + +
496D LEU* 3.5 32.1 - - + -
497D LEU* 4.4 7.9 - - + +
500D TYR* 3.7 12.1 - - + -
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Residues in contact with GLY 465 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461D GLU 2.8 22.9 + - - -
462D ASN* 3.1 4.2 + - - -
464D ALA* 1.3 73.8 - - - +
466D HIS* 1.3 55.8 + - - +
468D LYS* 2.9 27.4 + - - -
469D ASP* 4.3 0.9 - - - +
500D TYR* 3.7 19.0 - - - -
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Residues in contact with HIS 466 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D PRO* 3.9 26.1 - - + +
182D VAL* 4.0 20.1 - - + +
183D TRP* 2.6 38.6 + + - +
200D PHE* 4.1 19.9 - + + -
462D ASN 3.1 9.3 + - - +
463D ILE 3.0 5.8 + - - +
465D GLY* 1.3 76.3 - - - +
467D LEU* 1.3 64.9 + - - +
468D LYS 3.2 3.2 + - - -
469D ASP* 3.4 18.1 + - - +
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Residues in contact with LEU 467 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D TRP* 3.5 46.9 - - + +
463D ILE* 2.6 37.4 + - + +
464D ALA 4.2 1.1 - - - +
466D HIS* 1.3 74.0 + - - +
468D LYS* 1.3 61.2 + - - +
469D ASP 3.0 1.7 + - - -
470D ALA* 3.1 17.1 + - + +
475D GLN* 3.4 20.8 - - + +
478D ALA* 4.0 24.2 - - + -
479D VAL* 4.8 1.3 - - + -
482D PHE* 5.0 2.5 - - + -
493D ILE* 4.4 8.5 - - + -
497D LEU* 4.0 27.4 - - + -
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Residues in contact with LYS 468 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464D ALA 2.9 21.7 + - - +
465D GLY* 2.9 21.1 + - - +
467D LEU* 1.3 76.4 - - - +
469D ASP* 1.3 93.2 + - - +
470D ALA 3.2 2.6 - - - +
475D GLN* 3.0 19.1 - - - +
497D LEU* 3.6 9.8 - - + +
500D TYR* 3.7 50.3 - - + +
501D ASN* 4.0 10.9 + - - +
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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