Contacts of the helix formed by residues 420 - 424 (chain B) in PDB entry 3DHF
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 420 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314A SER* 4.2 19.9 - - - -
315A GLY* 4.3 7.6 + - - +
417B PRO* 3.2 14.5 + - - +
419B ALA* 1.3 80.8 - - - +
421B PRO* 1.3 62.2 - - - +
422B ASN* 2.8 45.1 + - - +
423B LYS* 2.8 40.6 + - + +
424B ARG 3.9 1.6 + - - -
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Residues in contact with PRO 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B ASP* 4.9 5.4 - - - +
417B PRO 4.0 3.8 - - - +
418B VAL 4.6 5.8 - - - +
419B ALA 3.9 4.7 - - - +
420B ASP* 1.3 88.4 - - - +
422B ASN* 1.3 61.0 + - + +
423B LYS 3.1 0.9 - - - -
424B ARG* 3.1 31.5 + - + +
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Residues in contact with ASN 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ARG* 3.2 22.5 + - - +
41B GLU 3.2 11.3 - - - +
396B ASN* 2.5 36.4 + - - +
420B ASP* 2.8 28.5 + - - +
421B PRO* 1.3 82.8 - - - +
423B LYS* 1.3 64.7 + - - +
424B ARG 3.3 0.7 - - - -
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Residues in contact with LYS 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A ASP* 2.9 24.5 + - - +
314A SER* 4.0 11.4 - - - -
354A ASP* 2.7 31.5 + - - -
503A NMN 4.1 1.2 + - - -
40B ARG* 3.8 20.7 + - - +
415B LYS* 3.5 24.8 - - - +
417B PRO* 4.0 14.6 - - + -
420B ASP* 2.8 31.8 + - - +
422B ASN* 1.3 84.8 - - - +
424B ARG* 1.3 64.6 + - - +
425B SER* 3.4 2.8 + - - -
501B MG 4.0 1.9 - - - -
504B POP 3.0 37.3 + - - +
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Residues in contact with ARG 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B GLU* 4.7 2.3 - - - +
40B ARG* 4.2 14.8 - - - +
414B PHE* 5.1 3.1 - - + -
415B LYS 3.4 12.6 - - - +
416B ASP* 3.5 35.4 - - + +
417B PRO* 4.2 0.2 - - - +
420B ASP 3.9 1.8 + - - -
421B PRO* 3.1 22.8 + - + +
422B ASN 3.3 0.7 - - - +
423B LYS* 1.3 78.3 - - - +
425B SER* 1.3 75.9 + - - +
426B LYS* 5.5 2.0 - - - +
427B LYS* 6.2 4.9 - - - +
444B GLU* 5.2 9.7 + - - -
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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