Contacts of the helix formed by residues 404 - 415 (chain A) in PDB entry 3N51
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 GLU 404 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377A ARG* 4.0 14.1 + - - +
381A ILE* 3.8 41.1 - - + +
384A TYR* 6.2 1.4 - - - +
385A LYS* 5.3 4.5 + - - -
405A HIS* 1.3 62.4 + - - +
406A GLU* 3.1 11.7 - - - +
407A VAL* 3.1 24.3 + - - +
408A ASP* 2.9 31.7 + - - +
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Residues in contact with HIS 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A GLU* 1.3 79.8 - - - +
406A GLU* 1.3 64.0 + - - +
408A ASP* 3.4 11.6 + - - +
409A GLN* 3.1 53.7 + - + +
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Residues in contact with GLU 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A TYR* 5.1 18.2 - - + +
404A GLU 3.1 7.5 - - - +
405A HIS* 1.3 86.1 - - - +
407A VAL* 1.3 64.2 + - - +
409A GLN* 3.3 5.6 + - - +
410A VAL* 3.0 32.3 + - + +
431A ALA 4.8 6.4 - - - +
434A ARG* 2.5 38.0 + - - +
435A LYS* 5.1 7.5 + - + +
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Residues in contact with VAL 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377A ARG* 4.4 7.2 - - + -
380A LEU* 4.3 9.6 - - + +
381A ILE* 3.9 39.9 - - + +
384A TYR* 4.4 10.3 - - + -
404A GLU 3.1 18.6 + - - +
406A GLU* 1.3 77.7 - - + +
408A ASP* 1.3 57.2 + - - +
410A VAL* 3.1 3.8 + - - +
411A LEU* 2.9 49.2 + - + +
427A PHE* 3.8 32.1 - - + -
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Residues in contact with ASP 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ARG* 2.9 44.3 + - - +
404A GLU* 2.9 15.7 + - - +
405A HIS* 3.7 12.7 - - - +
406A GLU 3.3 0.2 - - - -
407A VAL* 1.3 76.4 - - - +
409A GLN* 1.3 63.1 + - - +
411A LEU* 3.9 9.6 - - - +
412A ASP* 3.0 27.5 + - - +
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Residues in contact with GLN 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405A HIS* 3.1 47.0 + - + +
406A GLU* 3.3 12.1 + - - +
408A ASP* 1.3 76.6 - - - +
410A VAL* 1.3 65.4 + - - +
412A ASP* 3.2 27.8 + - - +
413A ALA* 3.6 6.8 + - - +
434A ARG* 3.8 32.2 + - - +
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Residues in contact with VAL 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A TYR* 5.5 0.2 - - + -
406A GLU* 3.0 21.5 + - + +
407A VAL 3.1 6.5 + - - +
409A GLN* 1.3 74.9 - - - +
411A LEU* 1.3 58.6 + - - +
413A ALA* 3.0 8.3 + - - +
414A VAL* 2.9 33.9 + - + +
427A PHE* 3.3 39.7 - - + +
430A VAL* 3.4 37.0 - - + -
431A ALA* 4.1 15.9 - - + -
434A ARG* 4.2 10.1 - - - +
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Residues in contact with LEU 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377A ARG* 4.0 28.3 - - + -
380A LEU* 3.7 13.5 - - + -
407A VAL* 2.9 37.6 + - + +
408A ASP* 4.0 12.8 - - - +
410A VAL* 1.3 70.4 - - - +
412A ASP* 1.3 62.1 + - - +
414A VAL* 4.1 4.7 - - + +
415A ASP 2.8 39.5 + - - +
418A LYS* 5.5 11.9 - - + -
422A ILE* 3.4 42.2 - - + -
427A PHE* 4.3 7.6 - - + -
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Residues in contact with ASP 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A ASP 3.0 14.9 + - - +
409A GLN* 3.2 29.1 + - - +
411A LEU* 1.3 77.8 - - - +
413A ALA* 1.3 60.8 - - - +
416A PHE* 3.6 43.0 - - - +
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Residues in contact with ALA 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409A GLN 3.6 5.1 + - - +
410A VAL 3.0 9.9 + - - +
412A ASP* 1.3 81.4 + - - +
414A VAL* 1.3 64.4 + - - +
415A ASP* 4.7 0.2 - - - -
416A PHE 4.9 1.0 + - - -
430A VAL* 4.5 18.2 - - + -
434A ARG* 5.7 2.7 - - - -
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Residues in contact with VAL 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410A VAL* 2.9 37.6 + - + +
411A LEU* 4.1 6.3 - - - +
413A ALA* 1.3 78.3 - - - +
415A ASP* 1.3 61.1 + - + +
422A ILE* 3.8 31.6 - - + -
423A GLU 5.0 1.3 - - - +
426A GLU* 3.9 34.6 - - + +
427A PHE* 4.5 3.6 - - - -
430A VAL* 4.0 17.5 - - + -
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Residues in contact with ASP 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A LEU* 2.8 23.7 + - - +
414A VAL* 1.3 76.0 - - + +
416A PHE* 1.3 70.4 + - - +
417A ASP* 3.4 14.2 + - - +
418A LYS* 3.2 19.6 + - - +
419A ASN* 3.0 26.8 + - - +
420A GLY 3.9 7.1 + - - -
421A TYR 4.9 3.8 - - - +
422A ILE* 3.8 22.2 - - + +
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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