Contacts of the helix formed by residues 373 - 387 (chain A) in PDB entry 1YNU
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 THR 373 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369A LEU* 4.7 0.3 - - - +
371A SER* 2.8 25.6 + - - +
372A ASN* 1.3 78.9 - - - +
374A PHE* 1.3 62.9 + - - +
375A GLU* 3.4 12.0 + - - +
376A ALA* 3.1 24.4 + - - +
377A GLU 3.2 14.6 + - - -
403A PRO* 3.4 15.3 - - - +
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Residues in contact with PHE 374 (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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373A THR* 1.3 72.3 - - - +
375A GLU* 1.3 57.1 + - - +
376A ALA 3.1 0.4 - - - -
377A GLU* 2.9 29.1 + - - +
378A MET* 2.7 39.4 + - + +
395A GLY 5.0 0.4 - - - -
396A SER* 3.6 29.6 + - - -
400A CYS 3.2 26.5 - - - -
401A THR* 3.8 15.5 - - - -
402A GLU 4.1 1.3 - - - -
403A PRO* 3.6 24.0 - - + -
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Residues in contact with GLU 375 (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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373A THR* 3.5 11.6 - - - +
374A PHE* 1.3 78.7 - - - +
376A ALA* 1.3 56.9 + - - +
378A MET* 3.4 11.3 + - - +
379A GLU* 3.1 26.0 + - - +
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Residues in contact with ALA 376 (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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369A LEU* 3.8 5.5 - - + +
370A ARG* 4.1 13.3 + - + +
371A SER* 3.2 43.7 - - - +
373A THR* 3.1 11.0 + - - +
374A PHE 3.1 0.2 - - - -
375A GLU* 1.3 78.3 - - - +
377A GLU* 1.3 64.0 + - - +
379A GLU* 3.3 11.5 + - - +
380A LEU* 3.0 23.7 + - - +
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Residues in contact with GLU 377 (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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369A LEU* 3.6 14.7 - - + +
373A THR 3.2 7.9 + - - +
374A PHE* 2.9 24.1 + - - +
376A ALA* 1.3 74.0 - - - +
378A MET* 1.3 66.7 + - - +
380A LEU* 3.1 4.6 + - - +
381A TRP* 2.9 22.3 + - - +
394A PRO* 3.8 5.6 - - + +
395A GLY* 3.4 11.6 + - - -
396A SER* 2.8 43.0 + - - +
402A GLU 4.3 0.7 - - - +
403A PRO* 3.0 13.7 - - - +
404A GLY 2.9 28.8 + - - +
405A TRP 4.2 2.7 + - - -
406A PHE* 4.1 15.5 - - + -
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Residues in contact with MET 378 (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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18A SER* 4.1 18.8 - - - +
374A PHE* 2.7 21.2 + - + +
375A GLU* 3.4 15.0 - - - +
377A GLU* 1.3 72.4 - - - +
379A GLU* 1.3 57.9 + - - +
381A TRP* 3.0 19.9 + - + +
382A LYS* 2.9 47.2 + - + +
394A PRO* 6.2 2.7 - - - -
396A SER* 5.3 10.5 - - - +
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Residues in contact with GLU 379 (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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370A ARG* 2.9 46.5 + - - +
375A GLU 3.1 10.2 + - - +
376A ALA* 3.5 10.8 - - - +
377A GLU 3.2 0.2 - - - -
378A MET* 1.3 80.2 - - - +
380A LEU* 1.3 63.3 + - - +
382A LYS* 3.4 12.9 + - - +
383A LYS* 3.2 49.5 + - + +
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Residues in contact with LEU 380 (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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365A MET* 4.1 23.6 - - + +
368A LEU* 3.8 32.3 - - + +
369A LEU* 4.2 12.8 - - + -
376A ALA 3.0 14.1 + - - +
377A GLU 3.6 7.6 - - - +
379A GLU* 1.3 78.4 - - - +
381A TRP* 1.3 60.2 + - - +
383A LYS* 3.5 5.9 + - + +
384A ILE* 3.0 49.0 + - + +
406A PHE* 4.2 11.7 - - + -
428A PHE* 4.1 24.0 - - + -
433A TYR* 4.4 10.1 - - - +
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Residues in contact with TRP 381 (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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18A SER* 3.4 50.0 - - - -
21A LEU* 4.4 11.7 - - + -
22A GLY* 4.0 20.9 - - - -
25A GLU* 6.1 0.9 - - + -
377A GLU 2.9 12.4 + - - +
378A MET* 3.2 21.8 - - + +
380A LEU* 1.3 75.2 - - - +
382A LYS* 1.3 91.7 + - + +
384A ILE* 3.2 4.8 + - - +
385A VAL* 3.0 45.0 + - + +
386A TYR* 5.2 12.6 - + - -
391A ASN* 4.8 0.4 - - - -
392A ILE* 3.0 26.3 + - + -
394A PRO* 3.4 26.8 - - + +
406A PHE* 4.0 19.5 - + + -
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Residues in contact with LYS 382 (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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378A MET* 2.9 37.5 + - + +
379A GLU* 3.7 13.7 - - - +
381A TRP* 1.3 89.1 - - + +
383A LYS* 1.3 55.7 + - + +
385A VAL* 3.2 1.5 + - - -
386A TYR* 2.7 65.3 + - + +
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Residues in contact with LYS 383 (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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370A ARG* 4.4 12.7 - - - +
379A GLU* 3.2 44.1 + - + +
380A LEU* 3.7 7.6 - - + +
382A LYS* 1.3 78.4 - - + +
384A ILE* 1.3 55.2 + - - +
386A TYR* 5.1 0.4 - - - -
387A GLU* 2.6 67.3 + - - +
388A VAL* 3.2 2.3 + - - -
428A PHE* 4.4 19.3 - - + -
432A TYR* 4.5 18.6 - - + -
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Residues in contact with ILE 384 (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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365A MET* 4.2 15.0 - - + -
380A LEU* 3.0 42.4 + - + +
381A TRP* 3.5 6.3 - - - +
383A LYS* 1.3 74.8 - - - +
385A VAL* 1.3 58.6 + - + +
388A VAL* 3.1 21.7 - - + +
389A HIS 2.8 24.6 + - - -
390A LEU* 3.0 37.9 + - + +
392A ILE* 3.8 32.1 - - + -
406A PHE* 4.2 8.3 - - + -
425A LEU* 5.7 5.6 - - + -
428A PHE* 4.7 5.8 - - + -
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Residues in contact with VAL 385 (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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22A GLY* 5.0 7.9 - - - +
25A GLU* 4.7 10.5 - - + -
40A ILE* 4.5 24.0 - - + +
381A TRP* 3.0 48.9 + - + +
382A LYS 3.8 2.2 - - - +
384A ILE* 1.3 78.7 - - + +
386A TYR* 1.3 78.2 + - + +
389A HIS* 3.2 22.7 + - - -
390A LEU 3.3 22.2 - - - +
391A ASN* 4.5 7.6 - - - +
392A ILE 4.9 0.2 - - - +
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Residues in contact with TYR 386 (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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25A GLU* 3.7 38.7 + - + +
40A ILE* 6.2 2.0 - - + -
381A TRP* 5.2 10.9 - + - -
382A LYS* 2.7 61.1 + - + +
385A VAL* 1.3 84.5 - - + +
387A GLU* 1.3 62.1 + - + +
389A HIS* 3.6 15.5 + - - -
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Residues in contact with GLU 387 (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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383A LYS* 2.6 56.1 + - - +
386A TYR* 1.3 80.9 - - + +
388A VAL* 1.3 61.6 + - + +
389A HIS* 2.9 23.9 + - - -
428A PHE* 3.9 11.4 - - + -
432A TYR* 3.7 23.3 + - - -
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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