Contacts of the helix formed by residues 420 - 426 (chain R) in PDB entry 1HI0
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 PRO 420 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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415R LEU 3.6 8.7 - - - +
416R ASP 5.2 2.7 - - - +
417R HIS 5.2 0.9 - - - -
418R THR* 3.5 7.9 - - - +
419R ALA* 1.3 89.0 - - - +
421R HIS* 1.3 60.7 + - + +
422R LEU 2.9 6.0 + - - -
423R ASN* 3.0 39.8 + - - +
424R SER 4.5 0.9 + - - -
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Residues in contact with HIS 421 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418R THR 4.0 2.2 + - - -
419R ALA* 2.9 25.1 + - + +
420R PRO* 1.3 81.9 - - + +
422R LEU* 1.3 77.7 + - + +
424R SER* 3.9 12.6 + - - -
425R ARG* 5.0 1.9 - - - +
445R GLU* 2.8 29.1 + - - -
463R ARG* 3.6 62.0 + - + +
464R ALA 3.8 7.4 - - - -
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Residues in contact with LEU 422 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415R LEU* 4.0 11.4 - - + -
419R ALA* 2.7 34.5 + - + +
421R HIS* 1.3 98.1 - - + +
423R ASN* 1.3 54.7 + - - +
424R SER 3.1 3.1 - - - -
425R ARG* 2.7 69.6 + - + +
426R ILE* 4.1 5.4 + - - +
435R PHE* 4.2 14.8 - - + -
444R GLU* 4.3 6.1 - - + +
445R GLU* 4.9 9.2 - - + +
446R ILE* 4.0 24.7 - - + -
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Residues in contact with ASN 423 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122R ARG* 2.5 44.1 + - - +
415R LEU* 4.1 7.6 + - - +
416R ASP* 6.2 0.2 - - - +
419R ALA 4.8 1.1 - - - -
420R PRO* 3.0 40.3 + - - +
422R LEU* 1.3 77.8 - - - +
424R SER* 1.3 56.0 + - - +
426R ILE* 3.0 35.4 + - - +
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Residues in contact with SER 424 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420R PRO 4.5 1.6 + - - -
421R HIS 3.9 13.4 + - - -
422R LEU 4.6 0.2 - - - +
423R ASN* 1.3 77.5 - - - +
425R ARG* 1.3 65.8 + - - +
426R ILE 3.2 0.8 + - - -
427R LYS* 2.9 40.4 + - - +
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Residues in contact with ARG 425 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421R HIS 5.0 1.3 - - - +
422R LEU* 2.7 50.8 + - + +
424R SER* 1.3 85.3 - - - +
426R ILE* 1.3 61.8 + - + +
427R LYS* 3.8 1.3 - - - -
431R SER* 3.2 30.6 - - - +
434R ARG* 5.5 0.2 + - - -
435R PHE* 3.5 26.8 - - + +
438R SER* 4.7 3.4 + - - -
444R GLU* 3.4 31.3 + - - -
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Residues in contact with ILE 426 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122R ARG* 4.1 29.0 - - + +
125R LEU* 4.4 14.0 - - + +
126R LEU* 4.2 14.1 - - + -
415R LEU* 3.9 26.9 - - + -
422R LEU 4.2 10.5 - - - +
423R ASN* 3.0 16.9 + - - +
424R SER 3.2 0.2 - - - -
425R ARG* 1.3 81.9 - - - +
427R LYS* 1.3 59.8 + - - +
431R SER* 3.8 1.8 - - - -
432R ALA* 3.8 26.7 - - + +
435R PHE* 3.8 33.2 - - + -
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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