Contacts of the helix formed by residues 452 - 468 (chain C) in PDB entry 1DGH
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451C LEU* 1.3 71.7 - - - +
453C GLU* 1.3 63.2 + - - +
454C GLU* 3.0 20.4 + - - +
455C GLN* 2.9 51.3 + - - +
456C ARG* 3.0 32.8 + - - +
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Residues in contact with GLU 453 (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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452C ASN* 1.3 76.2 - - - +
454C GLU* 1.3 75.9 + - - +
456C ARG* 3.2 35.0 + - - +
457C LYS* 3.0 29.3 + - - +
492C HIS* 5.4 5.4 + - - -
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Residues in contact with GLU 454 (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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452C ASN* 3.0 21.6 + - - +
453C GLU* 1.3 87.8 + - - +
455C GLN* 1.3 62.2 + - - +
457C LYS* 3.5 14.9 + - - +
458C ARG* 3.2 49.9 + - - +
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Residues in contact with GLN 455 (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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201C SER* 5.6 3.3 - - - -
202C ASP* 3.9 14.0 + - - +
450C VAL 4.0 4.2 - - - +
451C LEU* 3.2 33.3 - - + +
452C ASN* 2.9 48.5 + - - +
454C GLU* 1.3 75.2 - - - +
456C ARG* 1.3 60.7 + - - +
458C ARG* 3.6 25.7 + - - +
459C LEU* 3.0 28.1 + - - +
3001C NDP 5.6 5.8 + - - -
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Residues in contact with ARG 456 (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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447C TYR* 2.9 59.4 + - + +
448C VAL* 2.7 33.1 + - - +
451C LEU* 2.9 23.3 + - + -
452C ASN* 3.0 15.2 + - - +
453C GLU* 3.2 53.2 + - - +
455C GLN* 1.3 73.6 - - - +
457C LYS* 1.3 65.8 + - - +
459C LEU* 3.2 7.7 + - - +
460C CYS* 3.0 29.2 + - - -
492C HIS* 5.1 2.0 - - + -
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Residues in contact with LYS 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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453C GLU* 3.0 22.3 + - - +
454C GLU* 3.7 12.6 - - - +
456C ARG* 1.3 78.3 - - - +
458C ARG* 1.3 67.2 + - - +
460C CYS* 3.4 2.3 + - - +
461C GLU* 3.0 66.0 + - + +
492C HIS* 3.9 26.0 + - + +
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Residues in contact with ARG 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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201C SER 6.3 0.2 - - - -
202C ASP* 2.6 47.9 + - - +
454C GLU* 3.2 33.5 + - - +
455C GLN* 3.6 26.4 - - - +
457C LYS* 1.3 82.1 - - - +
459C LEU* 1.3 61.0 + - - +
461C GLU* 3.2 14.3 + - - +
462C ASN* 2.8 44.9 + - - +
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Residues in contact with LEU 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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197C SER* 3.5 25.6 - - - +
200C PHE* 3.5 30.7 + - + +
201C SER* 4.0 5.5 - - - +
446C PHE* 4.8 4.5 - - + -
447C TYR* 4.0 12.3 - - + -
451C LEU* 3.9 24.2 - - + -
455C GLN 3.0 18.5 + - - +
456C ARG 3.2 3.8 + - - +
458C ARG* 1.3 75.5 - - - +
460C CYS* 1.3 58.5 + - - +
462C ASN* 3.2 2.6 + - - +
463C ILE* 2.9 43.0 + - + +
489C TYR* 3.5 33.0 - - + +
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Residues in contact with CYS 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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447C TYR* 4.2 6.7 - - - -
456C ARG 3.0 16.7 + - - +
457C LYS 3.7 3.6 - - - +
459C LEU* 1.3 78.1 - - - +
461C GLU* 1.3 59.5 + - - +
463C ILE* 3.3 3.1 + - - +
464C ALA* 2.8 32.4 + - - +
489C TYR* 4.0 20.6 - - - -
492C HIS* 3.8 28.5 - - + -
493C ILE* 3.7 27.9 - - + +
496C LEU* 3.6 16.8 - - + +
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Residues in contact with GLU 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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457C LYS* 3.0 59.0 + - + +
458C ARG* 3.6 12.8 - - - +
460C CYS* 1.3 75.0 - - - +
462C ASN* 1.3 61.8 + - - +
464C ALA* 4.0 1.0 - - - +
465C GLY* 2.9 27.7 + - - -
496C LEU* 3.8 27.1 - - + +
500C TYR* 4.3 10.6 + - - +
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Residues in contact with ASN 462 (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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127C ARG* 3.3 26.2 + - - +
200C PHE* 2.8 49.5 + - + +
201C SER 4.2 5.7 + - - -
202C ASP* 5.2 2.0 + - - +
247C VAL* 3.7 18.6 - - - +
458C ARG* 2.8 31.0 + - - +
459C LEU 3.4 0.7 - - - +
461C GLU* 1.3 77.5 - - - +
463C ILE* 1.3 66.1 + - - +
465C GLY* 3.5 7.3 + - - -
466C HIS* 3.5 8.3 + - - +
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Residues in contact with ILE 463 (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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183C TRP* 4.0 21.0 - - + -
196C VAL* 4.7 2.9 - - + -
200C PHE* 3.5 28.9 - - + -
459C LEU* 2.9 29.1 + - + +
460C CYS 3.7 3.6 - - - +
462C ASN* 1.3 75.7 - - - +
464C ALA* 1.3 59.5 + - - +
466C HIS* 3.1 5.2 + - - +
467C LEU* 2.9 30.9 + - + +
482C PHE* 3.9 21.5 - - + -
489C TYR* 3.5 26.0 - - + +
493C ILE* 3.9 28.5 - - + -
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Residues in contact with ALA 464 (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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460C CYS 2.8 20.0 + - - +
461C GLU 4.0 1.6 - - - +
463C ILE* 1.3 74.5 - - - +
465C GLY* 1.3 62.8 + - - +
467C LEU* 4.4 1.3 - - - -
468C LYS* 3.0 28.8 + - - +
493C ILE* 4.2 7.6 - - + +
496C LEU* 3.6 29.4 - - + -
497C LEU* 3.7 20.3 - - + +
500C TYR* 3.6 10.2 - - + -
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Residues in contact with GLY 465 (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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461C GLU 2.9 19.0 + - - -
462C ASN* 3.5 3.3 + - - -
463C ILE 3.2 0.6 - - - -
464C ALA* 1.3 77.3 - - - +
466C HIS* 1.3 57.6 + - - +
468C LYS* 3.0 31.6 + - - +
469C ASP* 4.3 0.2 - - - +
500C TYR* 3.7 13.2 - - - -
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Residues in contact with HIS 466 (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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179C PRO* 4.1 22.6 - - + +
182C VAL* 3.9 26.2 - - + +
183C TRP* 2.9 33.3 + + - +
200C PHE* 4.2 17.4 - + + -
462C ASN 3.5 9.7 + - - +
463C ILE 3.1 6.5 + - - +
465C GLY* 1.3 76.9 - - - +
467C LEU* 1.3 64.1 + - - +
468C LYS 3.2 2.9 + - - -
469C ASP* 3.3 19.5 + - - +
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Residues in contact with LEU 467 (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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183C TRP* 3.5 48.4 - - + +
463C ILE* 2.9 31.9 + - + +
466C HIS* 1.3 74.7 - - - +
468C LYS* 1.3 64.5 + - - +
470C ALA* 2.9 17.2 + - + +
475C GLN* 3.6 32.6 - - + +
478C ALA* 3.8 22.2 - - + -
479C VAL* 4.8 0.9 - - + -
482C PHE* 4.8 2.2 - - + -
493C ILE* 4.5 7.6 - - + -
497C LEU* 4.1 22.9 - - + -
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Residues in contact with LYS 468 (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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464C ALA 3.0 14.6 + - - +
465C GLY* 3.0 26.6 + - - +
467C LEU* 1.3 77.2 - - - +
469C ASP* 1.3 96.0 + - - +
470C ALA 3.6 1.9 - - - +
475C GLN* 3.2 18.8 - - - +
497C LEU* 3.8 8.0 - - + +
500C TYR* 3.9 38.8 - - + +
501C ASN* 4.0 11.6 + - - +
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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