Contacts of the helix formed by residues 373 - 392 (chain A) in PDB entry 2Y4U
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 373 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340A VAL* 5.0 2.6 - - - +
344A LYS* 4.0 9.0 + - - +
370A ASN* 3.7 34.5 + - + +
371A GLU 3.8 1.2 - - - -
372A ASN* 1.3 74.1 - - - +
374A GLN* 1.3 59.4 + - - +
375A GLN* 2.6 35.6 + - - +
376A ILE* 3.1 26.4 + - + +
377A ARG* 3.0 26.2 + - - +
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Residues in contact with GLN 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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372A ASN 3.0 2.8 + - - +
373A ASP* 1.3 71.9 + - - +
375A GLN* 1.3 65.4 + - - +
377A ARG* 3.2 26.9 - - - +
378A GLU* 2.7 58.1 + - - +
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Residues in contact with GLN 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LYS* 3.0 37.2 - - - +
363A TYR* 4.8 3.1 - - - -
373A ASP* 2.6 24.8 + - - +
374A GLN* 1.3 84.3 + - - +
376A ILE* 1.3 56.7 + - - +
378A GLU* 3.9 6.0 - - - +
379A GLY* 3.1 23.6 + - - -
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Residues in contact with ILE 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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340A VAL* 4.1 9.9 - - + -
344A LYS* 4.4 12.6 - - + -
363A TYR* 3.6 38.0 - - + +
366A ALA* 3.6 27.8 - - + +
367A GLN* 4.0 11.2 - - - +
370A ASN* 3.4 37.2 - - + +
373A ASP* 3.1 23.5 + - + +
375A GLN* 1.3 72.6 - - - +
377A ARG* 1.3 68.5 + - + +
379A GLY* 3.1 10.6 + - - -
380A LEU* 3.4 16.9 + - + +
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Residues in contact with ARG 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A GLN* 4.5 14.1 - - - +
371A GLU 4.2 7.4 - - - +
372A ASN* 2.9 42.4 + - - +
373A ASP 3.0 10.5 + - - +
374A GLN* 3.2 31.8 - - - +
376A ILE* 1.3 77.2 - - + +
378A GLU* 1.3 67.5 + - + +
379A GLY 3.2 0.7 + - - -
380A LEU* 3.3 16.4 + - - +
381A GLU* 3.4 21.2 + - - +
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Residues in contact with GLU 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A GLN* 2.7 44.1 + - - +
375A GLN* 4.1 5.3 - - - +
377A ARG* 1.3 75.6 + - + +
379A GLY* 1.3 64.8 + - - +
381A GLU* 4.0 14.4 - - - +
382A LYS* 3.1 26.3 + - - +
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Residues in contact with GLY 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LEU* 6.0 1.2 - - - +
363A TYR* 3.8 29.4 + - - -
375A GLN 3.1 15.1 + - - -
376A ILE 3.1 6.4 + - - -
378A GLU* 1.3 78.5 - - - +
380A LEU* 1.3 57.6 + - - +
382A LYS* 3.7 4.0 - - - +
383A ALA* 2.9 28.8 + - - +
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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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360A ILE* 3.9 32.8 - - + +
363A TYR* 3.2 43.3 - - + +
364A GLU* 4.3 12.3 - - + +
367A GLN* 4.6 11.0 - - + +
376A ILE* 3.4 19.5 - - + +
377A ARG* 3.3 8.3 + - - +
379A GLY* 1.3 72.1 - - - +
381A GLU* 1.3 56.7 + - + +
383A ALA* 2.9 4.7 + - - -
384A GLN* 2.6 57.5 + - - +
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Residues in contact with GLU 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ARG* 3.4 19.5 + - - +
378A GLU* 4.1 14.4 - - - +
379A GLY 3.4 0.4 - - - -
380A LEU* 1.3 80.3 - - + +
382A LYS* 1.3 61.7 + - - +
384A GLN* 4.5 7.9 - - - +
385A ARG* 3.1 25.3 + - - +
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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
----------------------------------------------------------
351A LEU* 4.7 20.9 - - + -
378A GLU 3.1 18.4 + - - +
379A GLY* 3.7 4.5 - - - +
381A GLU* 1.3 78.0 - - - +
383A ALA* 1.3 61.6 + - - +
385A ARG* 3.4 30.8 - - - +
386A LEU* 3.1 40.9 + - + +
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Residues in contact with ALA 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LEU* 4.3 25.5 - - + +
356A TYR* 4.0 8.5 - - + -
359A ALA* 5.0 2.9 - - + -
360A ILE* 4.2 19.7 - - + -
363A TYR* 4.6 7.6 - - + -
379A GLY 2.9 17.9 + - - +
380A LEU* 2.9 6.4 + - - +
382A LYS* 1.3 75.0 - - - +
384A GLN* 1.3 59.8 + - - +
386A LEU* 3.0 9.2 + - - +
387A LEU* 2.8 26.0 + - - +
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Residues in contact with GLN 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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360A ILE* 4.0 20.3 - - + +
364A GLU* 4.9 6.8 - - - +
380A LEU* 2.6 49.6 + - - +
381A GLU* 4.1 7.1 - - - +
383A ALA* 1.3 69.5 - - - +
385A ARG* 1.3 65.9 + - - +
387A LEU* 3.1 26.7 + - + +
388A LYS* 3.3 12.8 + - - +
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Residues in contact with ARG 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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381A GLU 3.1 18.5 + - - +
382A LYS* 3.4 44.9 + - - +
383A ALA 3.2 0.2 - - - -
384A GLN* 1.3 80.5 - - - +
386A LEU* 1.3 74.9 + - + +
387A LEU 3.3 0.2 + - - -
388A LYS* 3.4 11.3 + - - +
389A GLN* 3.5 22.0 + - + +
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Residues in contact with LEU 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LEU* 6.0 3.4 - - + -
356A TYR* 3.7 31.7 + - + +
382A LYS* 3.1 32.5 + - + +
383A ALA* 3.0 9.5 + - - +
385A ARG* 1.3 103.6 - - + +
387A LEU* 1.3 64.7 + - - +
388A LYS 3.3 0.2 - - - -
389A GLN* 3.9 11.2 - - + +
390A SER* 3.1 25.3 + - - -
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Residues in contact with LEU 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A TYR* 3.8 29.1 - - + -
357A ASP* 5.0 7.2 - - + +
360A ILE* 5.8 7.6 - - + -
383A ALA 2.8 13.9 + - - +
384A GLN* 3.1 21.7 + - + +
386A LEU* 1.3 77.4 - - - +
388A LYS* 1.3 65.9 + - + +
390A SER* 2.4 28.2 + - - +
391A GLN* 3.1 46.4 + - + +
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Residues in contact with LYS 388 (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 GLN 3.3 9.1 + - - +
385A ARG* 3.9 8.1 - - - +
386A LEU 3.3 0.2 - - - -
387A LEU* 1.3 79.0 - - + +
389A GLN* 1.3 60.2 + - + +
390A SER 2.9 3.8 - - - -
391A GLN* 2.8 34.5 + - - +
392A LYS* 3.1 16.3 + - - +
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Residues in contact with GLN 389 (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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385A ARG* 3.5 20.1 + - + +
386A LEU* 3.6 14.0 + - + +
388A LYS* 1.3 78.1 - - + +
390A SER* 1.3 56.1 + - - +
392A LYS* 3.3 42.8 - - - +
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Residues in contact with SER 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A TYR* 4.1 22.6 - - - -
386A LEU 3.1 13.9 + - - -
387A LEU* 2.4 34.7 + - - +
388A LYS 2.9 0.6 - - - -
389A GLN* 1.3 78.6 - - - +
391A GLN* 1.3 64.7 + - - +
392A LYS 3.8 4.3 - - - +
393A ARG* 4.5 2.3 + - - -
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Residues in contact with GLN 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A LEU* 3.1 40.8 - - + +
388A LYS* 2.8 16.4 + - - +
390A SER* 1.3 84.7 + - - +
392A LYS* 1.3 61.8 + - - +
393A ARG* 3.2 6.4 + - - +
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Residues in contact with LYS 392 (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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388A LYS 3.1 14.0 + - - +
389A GLN* 3.3 47.0 - - - +
390A SER 3.8 1.8 - - - +
391A GLN* 1.3 76.2 - - - +
393A ARG* 1.3 70.5 + - - +
394A ASP* 3.7 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