Contacts of the helix formed by residues 408 - 416 (chain G) in PDB entry 1R4N
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 408 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396G ARG* 3.7 30.0 - - - +
401G GLU* 5.4 0.6 - - - +
406G THR 2.9 7.4 + - - -
407G ILE* 1.3 70.5 - - - +
409G LYS* 1.3 56.8 + - - +
410G ASP* 3.2 8.1 + - - +
411G GLU* 2.9 34.2 + - - +
412G ILE* 3.7 12.8 + - - +
533G GLN* 4.1 27.3 - - - +
534G LEU* 5.3 4.0 - - - +
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Residues in contact with LYS 409 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404G LEU 5.9 1.9 + - - -
407G ILE* 2.4 45.2 + - + +
408G ASN* 1.3 64.4 - - - +
410G ASP* 1.3 64.9 + - - +
412G ILE* 3.9 6.1 - - - -
413G ILE* 3.3 31.8 + - + +
468G TYR 3.5 25.4 + - - +
469G GLY* 3.7 16.2 + - - +
470G LEU* 3.4 18.4 - - + -
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Residues in contact with ASP 410 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408G ASN* 3.2 6.8 - - - +
409G LYS* 1.3 80.6 - - - +
411G GLU* 1.3 59.1 + - - +
413G ILE* 3.9 3.3 - - - +
414G SER* 2.9 33.3 + - - -
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Residues in contact with GLU 411 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408G ASN* 2.9 25.3 + - - +
410G ASP* 1.3 78.2 - - - +
412G ILE* 1.3 65.6 + - + +
414G SER* 4.0 10.5 + - - -
415G SER* 3.1 38.7 + - - -
423G ILE* 6.3 0.4 - - + -
532G PHE* 4.0 16.2 - - + -
533G GLN* 3.6 35.5 + - + +
534G LEU 4.6 1.9 + - - -
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Residues in contact with ILE 412 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407G ILE* 3.4 29.2 - - + -
408G ASN 3.7 11.6 + - - +
409G LYS* 4.1 6.5 - - - +
410G ASP 3.3 0.6 - - - -
411G GLU* 1.3 81.1 - - + +
413G ILE* 1.3 64.2 + - + +
415G SER* 3.3 2.9 + - - -
416G MET* 3.1 32.0 + - + +
423G ILE* 4.4 20.6 - - + +
426G TYR* 4.8 13.5 - - + -
427G LEU* 4.1 27.1 - - + -
464G PHE* 5.7 1.6 - - + -
470G LEU* 4.0 23.8 - - + -
472G VAL* 5.1 3.4 - - + -
533G GLN* 5.5 6.3 - - - +
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Residues in contact with ILE 413 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409G LYS* 3.3 24.2 + - + +
410G ASP* 3.5 3.0 + - - +
411G GLU 3.4 0.2 - - - -
412G ILE* 1.3 71.9 - - - +
414G SER* 1.3 70.0 + - - +
415G SER 3.0 0.9 + - - -
416G MET* 3.1 20.7 + - + +
417G ASP* 3.6 12.5 + - - +
469G GLY 5.2 2.2 - - - +
470G LEU* 4.2 18.8 - - + -
471G SER* 4.6 23.3 - - - +
472G VAL* 4.1 20.4 - - + -
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Residues in contact with SER 414 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410G ASP* 2.9 22.8 + - - -
411G GLU* 3.5 17.3 + - - -
412G ILE 3.3 0.2 - - - -
413G ILE* 1.3 77.1 - - - +
415G SER* 1.3 59.4 + - - +
417G ASP* 2.5 26.3 + - - +
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Residues in contact with SER 415 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411G GLU* 3.1 26.4 + - - -
412G ILE 3.7 3.4 - - - -
414G SER* 1.3 74.6 - - - +
416G MET* 1.3 54.1 + - - +
417G ASP* 2.5 20.8 + - - +
418G ASN* 3.4 8.5 + - - +
421G ASN* 3.9 28.6 + - - +
423G ILE* 3.8 19.7 - - - -
532G PHE* 3.8 14.8 - - - -
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Residues in contact with MET 416 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412G ILE* 3.1 17.2 + - + +
413G ILE* 3.1 11.5 + - + +
415G SER* 1.3 73.1 - - - +
417G ASP* 1.3 54.7 + - - +
418G ASN 2.8 19.2 + - - +
419G PRO* 4.0 9.2 - - + +
421G ASN 4.9 0.2 - - - +
423G ILE* 3.3 24.5 - - + -
424G VAL* 4.0 22.4 - - + -
427G LEU* 3.8 26.7 - - + -
472G VAL* 3.8 31.0 - - + -
473G MET 3.7 26.0 + - - +
474G VAL* 4.2 11.4 - - + -
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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