Contacts of the helix formed by residues 385 - 394 (chain Y) in PDB entry 5MG3
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 CYS 385 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270Y ASN* 3.4 31.2 - - - -
273Y GLY 4.1 10.3 - - - +
274Y VAL* 3.9 21.8 - - + -
277Y ALA* 5.5 3.1 - - + -
321Y TYR* 4.9 0.2 + - - -
381Y ILE 3.9 14.1 - - - -
382Y THR 3.5 8.0 + - - +
383Y PHE 3.1 0.4 - - - -
384Y ILE* 1.4 66.5 - - - +
386Y LEU* 1.3 60.3 + - - +
387Y ILE 3.6 0.7 - - - -
388Y PRO* 3.6 14.2 - - - +
389Y GLU* 3.6 19.1 - - - +
407Y LEU* 4.3 16.4 - - + +
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Residues in contact with LEU 386 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277Y ALA* 5.6 2.9 - - + -
321Y TYR* 3.4 46.7 - - + +
322Y ALA* 4.1 31.4 - - + +
325Y ILE* 4.1 25.8 - - + -
382Y THR 3.9 9.9 - - - +
383Y PHE* 3.0 21.4 + - + +
385Y CYS* 1.3 79.0 - - - +
387Y ILE* 1.4 57.4 + - - +
388Y PRO 3.6 0.2 - - - -
389Y GLU* 3.5 5.5 + - + +
390Y PHE* 2.9 33.3 + - - +
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Residues in contact with ILE 387 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460E VAL* 4.2 16.4 - - + -
461E ARG* 6.3 0.4 - - - +
464E ILE* 4.5 9.6 - - + -
236Y PHE* 4.5 15.5 - - + -
383Y PHE 3.8 11.7 - - - +
384Y ILE* 3.9 27.8 - - + +
386Y LEU* 1.4 75.9 - - - +
388Y PRO* 1.3 67.5 - - + +
390Y PHE* 3.5 12.2 + - + +
391Y MET* 3.2 20.4 + - + +
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Residues in contact with PRO 388 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233Y PHE* 5.4 0.6 - - - +
236Y PHE* 3.8 26.9 - - + +
237Y VAL* 4.2 37.5 - - + -
384Y ILE 3.2 26.2 - - - +
385Y CYS* 3.6 16.6 - - - +
387Y ILE* 1.3 81.5 - - + +
389Y GLU* 1.3 63.6 + - - +
391Y MET* 3.3 1.6 + - - +
392Y ARG* 3.2 29.1 + - - +
407Y LEU* 4.7 4.5 - - + -
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Residues in contact with GLU 389 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318Y VAL* 6.0 3.6 - - + -
321Y TYR* 2.6 37.0 + - + +
385Y CYS 3.6 16.2 - - - +
386Y LEU* 3.5 9.5 + - + +
388Y PRO* 1.3 75.6 - - - +
390Y PHE* 1.3 63.7 + - - +
392Y ARG* 2.6 49.2 + - - +
393Y ASP* 3.0 28.5 + - - +
403Y GLY* 5.3 0.2 - - - -
404Y THR* 2.8 33.2 + - - +
407Y LEU* 3.4 18.2 - - + +
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Residues in contact with PHE 390 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386Y LEU 2.9 20.5 + - - +
387Y ILE* 3.9 13.9 - - + +
389Y GLU* 1.3 74.4 - - - +
391Y MET* 1.4 60.7 + - + +
393Y ASP* 5.0 2.0 - - - -
394Y ALA* 2.9 52.5 + - + +
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Residues in contact with MET 391 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232Y PHE* 3.8 30.5 - - + -
233Y PHE* 3.7 10.1 - - + -
236Y PHE* 3.6 46.4 - - + -
387Y ILE* 3.2 10.2 + - + +
388Y PRO 3.3 2.6 + - - +
390Y PHE* 1.4 81.8 - - + +
392Y ARG* 1.3 62.3 + - - +
394Y ALA* 4.5 1.7 - - - -
395Y MET* 3.2 57.9 + - + +
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Residues in contact with ARG 392 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233Y PHE* 3.5 42.7 - - + +
237Y VAL* 5.8 3.0 - - - +
388Y PRO* 3.2 13.3 + - - +
389Y GLU* 2.6 48.3 + - - +
391Y MET* 1.3 81.0 - - - +
393Y ASP* 1.3 91.9 + - - +
395Y MET 3.8 0.2 - - - -
396Y LYS* 2.9 31.5 + - - +
397Y VAL* 4.3 12.1 - - + -
402Y GLY* 4.4 9.6 - - - -
403Y GLY 3.6 10.2 + - - -
406Y LEU* 3.2 42.2 + - + +
407Y LEU* 3.6 5.5 - - - +
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Residues in contact with ASP 393 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318Y VAL* 6.0 7.0 - - + -
389Y GLU* 3.0 16.3 + - - +
390Y PHE* 4.4 1.8 - - - +
392Y ARG* 1.3 102.5 + - - +
394Y ALA* 1.4 60.8 + - - +
395Y MET 3.3 2.0 + - - -
396Y LYS* 2.6 51.2 + - - +
402Y GLY* 3.1 7.4 - - - -
403Y GLY* 2.8 23.2 + - - -
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Residues in contact with ALA 394 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390Y PHE* 2.9 41.3 + - + +
391Y MET* 4.5 3.8 - - - +
393Y ASP* 1.4 76.1 - - - +
395Y MET* 1.3 65.1 + - + +
396Y LYS* 5.5 0.7 - - - -
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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