Contacts of the helix formed by residues 403 - 415 (chain N) in PDB entry 3L73
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 403 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351N GLU* 3.6 20.3 - - - +
354N VAL* 4.0 11.0 - - - -
401N ALA 4.2 7.3 - - - +
402N VAL* 1.3 76.7 - - - +
404N ALA* 1.3 64.7 + - - +
405N ARG* 3.1 30.2 + - - +
406N MET* 3.0 23.2 + - - +
407N VAL* 2.8 21.9 + - - +
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Residues in contact with ALA 404 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349N THR* 3.8 13.5 - - - +
350N THR 4.1 2.0 - - - -
351N GLU* 3.2 37.0 + - + +
354N VAL* 3.7 15.0 - - - +
403N ASP* 1.3 71.8 - - - +
405N ARG* 1.3 66.4 + - - +
407N VAL* 2.8 15.9 + - - +
408N ARG* 3.0 31.9 + - - +
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Residues in contact with ARG 405 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351N GLU* 4.3 0.6 + - - +
403N ASP* 3.1 14.6 + - - +
404N ALA* 1.3 78.2 - - - +
406N MET* 1.3 61.4 + - - +
408N ARG* 3.4 33.6 + - - +
409N ASP* 3.2 66.3 + - - +
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Residues in contact with MET 406 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269N VAL* 3.3 22.7 - - + -
398N ARG 5.1 1.1 - - - +
401N ALA* 4.1 13.0 - - + +
402N VAL* 3.1 45.8 - - + +
403N ASP* 3.0 23.7 + - - +
404N ALA 2.8 1.6 + - - -
405N ARG* 1.3 78.5 - - - +
407N VAL* 1.3 65.7 + - - +
409N ASP* 3.2 8.1 + - + +
410N VAL* 3.0 30.9 + - + +
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Residues in contact with VAL 407 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269N VAL* 3.6 12.8 - - + -
272N VAL* 4.3 8.7 - - + -
273N ALA* 4.2 15.9 - - + -
276N ILE* 4.6 4.5 - - + -
345N LEU* 4.6 2.2 - - + +
349N THR* 4.4 17.3 - - + +
354N VAL* 3.7 21.8 - - + -
402N VAL* 3.7 20.0 - - + -
403N ASP 2.8 17.5 + - - +
404N ALA 2.8 11.5 + - - +
406N MET* 1.3 72.5 - - - +
408N ARG* 1.3 61.4 + - - +
410N VAL* 3.4 0.7 + - - +
411N CYS* 2.9 41.3 + - - -
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Residues in contact with ARG 408 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345N LEU 3.4 21.3 - - - +
346N CYS 3.6 7.7 - - - +
347N THR* 3.5 32.5 + - - +
348N SER* 3.9 1.7 - - - +
349N THR* 3.0 34.8 + - - +
404N ALA* 3.0 20.4 + - - +
405N ARG* 3.4 45.0 + - - +
407N VAL* 1.3 78.8 - - - +
409N ASP* 1.3 61.5 + - - +
411N CYS* 3.9 0.5 - - - +
412N SER* 2.7 34.5 + - - -
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Residues in contact with ASP 409 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405N ARG* 3.2 51.2 + - - +
406N MET* 3.2 9.7 + - + +
408N ARG* 1.3 78.9 - - - +
410N VAL* 1.3 64.3 + - + +
412N SER* 3.8 5.2 - - - -
413N LYS* 3.1 23.4 + - - +
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Residues in contact with VAL 410 (chain N).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266N ASP* 4.3 19.7 - - + +
269N VAL* 3.6 38.6 - - + -
270N LEU* 3.6 28.3 - - + -
406N MET* 3.0 20.0 + - + +
409N ASP* 1.3 77.7 - - + +
411N CYS* 1.3 64.5 + - - +
413N LYS* 2.9 20.8 + - + +
414N TYR* 3.0 25.5 + - + -
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Residues in contact with CYS 411 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269N VAL* 5.6 0.2 - - - -
270N LEU* 5.1 7.9 - - - -
273N ALA* 3.8 20.2 - - - -
320N PHE* 5.5 0.9 - - - -
345N LEU* 4.0 18.2 - - + -
346N CYS* 4.0 17.3 - - - +
407N VAL* 2.9 42.8 + - - +
408N ARG 4.0 2.0 - - - +
410N VAL* 1.3 78.9 - - - +
412N SER* 1.3 54.9 + - - +
414N TYR* 4.5 1.6 - - - +
415N ILE* 2.6 53.9 + - + +
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Residues in contact with SER 412 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346N CYS* 3.3 25.9 + - - +
408N ARG 2.7 22.5 + - - -
409N ASP* 3.8 6.1 - - - -
411N CYS* 1.3 77.5 - - - +
413N LYS* 1.3 63.3 + - - +
416N TYR* 3.2 29.8 + - - +
418N LYS* 5.5 0.2 - - - -
15W ARG* 3.2 28.8 + - - -
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Residues in contact with LYS 413 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264N ASP* 5.0 2.4 + - - -
266N ASP* 2.9 26.1 + - - +
409N ASP 3.1 11.7 + - - +
410N VAL* 2.9 15.1 + - + +
412N SER* 1.3 82.4 - - - +
414N TYR* 1.3 84.1 + - + +
418N LYS* 3.6 19.8 + - - -
15W ARG* 4.5 5.3 + - - +
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Residues in contact with TYR 414 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257N VAL* 3.5 20.6 - - + +
258N GLU 3.6 21.4 - - - +
259N GLY* 4.4 0.7 - - - -
260N PRO* 3.2 47.2 - - + +
264N ASP* 3.7 5.2 + - - -
266N ASP* 3.3 29.1 + - + -
270N LEU* 4.4 15.0 - - + -
320N PHE* 6.0 1.8 - - + -
410N VAL* 3.0 28.3 + - + +
411N CYS 4.3 1.3 - - - +
413N LYS* 1.3 108.7 + - + +
415N ILE* 1.3 64.5 + - + +
418N LYS* 3.5 18.3 - - - +
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Residues in contact with ILE 415 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257N VAL* 4.4 7.2 - - + -
270N LEU* 6.2 0.4 - - + -
320N PHE* 3.9 31.0 - - + -
342N TRP* 3.5 44.6 - - + -
343N MET* 4.2 13.7 - - + -
345N LEU* 4.7 3.1 - - + -
346N CYS* 4.2 7.4 - - - -
411N CYS* 2.6 41.1 + - + +
412N SER 3.7 0.2 + - - -
414N TYR* 1.3 81.7 - - + +
416N TYR* 1.3 67.2 + - - +
417N ASP 3.2 0.9 + - - -
418N LYS* 3.1 15.3 + - - +
441N MET* 3.4 18.2 - - + +
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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