Contacts of the helix formed by residues 408 - 416 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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396E ARG* 3.7 29.5 - - - +
401E GLU* 5.8 0.4 - - - +
406E THR 2.9 7.0 + - - -
407E ILE* 1.3 69.6 - - - +
409E LYS* 1.3 56.7 + - - +
410E ASP* 3.1 8.4 + - - +
411E GLU* 2.9 34.8 + - - +
412E ILE* 3.7 12.6 + - - +
533E GLN* 4.1 26.7 + - - +
534E LEU* 5.4 4.0 - - - +
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Residues in contact with LYS 409 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404E LEU 5.9 1.9 + - - -
407E ILE* 2.4 44.6 + - + +
408E ASN* 1.3 64.4 - - - +
410E ASP* 1.3 65.9 + - - +
411E GLU 3.4 0.2 - - - -
412E ILE* 3.9 6.3 - - - -
413E ILE* 3.3 30.5 + - + +
468E TYR 3.4 26.1 + - - +
469E GLY* 3.7 16.2 + - - +
470E LEU* 3.4 18.6 - - + -
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Residues in contact with ASP 410 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408E ASN* 3.1 6.8 - - - +
409E LYS* 1.3 82.2 - - - +
411E GLU* 1.3 57.9 + - - +
413E ILE* 3.9 2.7 - - - +
414E SER* 2.9 33.5 + - - -
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Residues in contact with GLU 411 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408E ASN* 2.9 26.6 + - - +
410E ASP* 1.3 76.7 - - - +
412E ILE* 1.3 65.9 + - + +
414E SER* 3.4 11.0 + - - -
415E SER* 3.1 37.3 + - - -
423E ILE* 6.3 0.4 - - + -
532E PHE* 4.1 16.5 - - + -
533E GLN* 3.6 35.8 + - + +
534E LEU 4.6 2.1 + - - -
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Residues in contact with ILE 412 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407E ILE* 3.5 28.9 - - + -
408E ASN 3.7 11.1 + - - +
409E LYS* 4.1 6.3 - - - +
410E ASP 3.3 0.6 - - - -
411E GLU* 1.3 80.9 - - + +
413E ILE* 1.3 66.3 + - + +
415E SER* 3.3 2.8 + - - -
416E MET* 3.1 31.4 + - + +
423E ILE* 4.5 20.6 - - + +
426E TYR* 4.8 14.6 - - + -
427E LEU* 4.2 26.0 - - + -
464E PHE* 5.7 1.3 - - + -
470E LEU* 4.0 24.7 - - + -
472E VAL* 5.1 3.4 - - + -
532E PHE* 6.6 0.2 - - - -
533E GLN* 5.5 6.5 - - - +
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Residues in contact with ILE 413 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409E LYS* 3.3 23.3 + - + +
410E ASP* 3.4 3.0 + - - +
411E GLU 3.4 0.2 - - - -
412E ILE* 1.3 71.9 - - - +
414E SER* 1.3 71.1 + - - +
415E SER 3.1 0.5 + - - -
416E MET* 3.1 14.3 + - - +
417E ASP* 3.6 14.2 + - - +
469E GLY 5.3 2.5 - - - +
470E LEU* 4.2 19.3 - - + -
471E SER* 4.6 23.6 - - - +
472E VAL* 4.1 25.1 - - + -
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Residues in contact with SER 414 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410E ASP* 2.9 22.8 + - - -
411E GLU* 3.5 16.6 + - - -
413E ILE* 1.3 77.7 - - - +
415E SER* 1.3 58.3 + - - +
417E ASP* 2.5 26.8 + - - +
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Residues in contact with SER 415 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411E GLU* 3.1 25.5 + - - -
412E ILE 3.6 4.5 - - - -
413E ILE 3.1 0.4 - - - -
414E SER* 1.3 73.9 - - - +
416E MET* 1.3 52.1 + - - +
417E ASP* 2.5 20.3 + - - +
418E ASN* 3.4 8.5 + - - +
421E ASN* 3.9 27.0 + - - +
423E ILE* 3.8 19.7 - - - -
532E PHE* 3.7 14.7 - - - -
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Residues in contact with MET 416 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412E ILE* 3.1 15.9 + - + +
413E ILE 3.1 11.3 + - - +
415E SER* 1.3 74.1 - - - +
417E ASP* 1.3 54.6 - - - +
418E ASN* 2.8 20.0 + - - +
419E PRO* 3.9 10.2 - - + +
423E ILE* 3.4 24.2 - - + -
424E VAL* 4.0 23.6 - - + -
427E LEU* 3.8 26.0 - - + -
472E VAL* 3.8 29.4 - - + -
473E MET 3.7 25.6 + - - +
474E VAL* 4.2 11.9 - - + -
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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