Contacts of the helix formed by residues 362 - 381 (chain A) in PDB entry 2Y0P
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 SER 362 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361A ASP* 1.3 79.7 - - - +
363A ILE* 1.4 56.2 + - - +
364A GLU* 3.3 8.5 - - - -
365A ASP* 3.3 13.3 + - - +
366A LYS* 2.8 35.3 + - - +
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Residues in contact with ILE 363 (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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362A SER* 1.4 73.2 - - - +
364A GLU* 1.4 57.8 + - - +
366A LYS* 3.6 6.2 + - - +
367A ASN* 3.2 28.1 + - - +
419A PHE* 4.6 3.8 - - - -
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Residues in contact with GLU 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A SER* 3.3 5.5 - - - -
363A ILE* 1.4 76.2 - - - +
365A ASP* 1.4 62.5 + - - +
367A ASN* 3.6 7.8 + - - +
368A ALA 3.6 13.3 + - - -
365B ASP* 4.4 14.3 - - + +
366B LYS* 4.5 9.5 + - - +
367B ASN* 3.4 50.8 + - + +
418B GLU 5.6 0.7 - - - +
419B PHE* 4.4 7.3 - - - -
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Residues in contact with ASP 365 (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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361A ASP* 2.7 27.3 + - + +
362A SER* 3.3 21.7 + - - +
364A GLU* 1.4 76.2 - - - +
366A LYS* 1.4 63.0 + - - +
368A ALA* 3.5 11.7 + - - +
369A ARG* 2.8 50.2 + - - +
367B ASN* 4.8 9.2 + - - +
420B LYS* 4.1 12.0 - - + +
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Residues in contact with LYS 366 (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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361A ASP 4.9 4.7 - - - +
362A SER 2.8 21.7 + - - +
363A ILE* 4.0 6.3 - - - +
364A GLU 3.4 0.2 - - - -
365A ASP* 1.4 70.5 - - - +
367A ASN* 1.4 65.4 + - - +
369A ARG* 3.1 19.6 + - - +
370A VAL* 3.3 14.7 + - - +
410A LEU* 3.9 20.6 - - + +
414A ASP* 5.0 7.9 - - - +
419A PHE* 3.9 12.3 - - + -
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Residues in contact with ASN 367 (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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363A ILE 3.2 17.5 + - - +
364A GLU 3.7 7.0 - - - +
365A ASP 3.4 0.4 - - - -
366A LYS* 1.4 75.3 - - - +
368A ALA* 1.4 58.7 + - - +
370A VAL* 3.4 2.7 + - - +
371A ILE* 3.4 29.5 + - - +
418A GLU 5.2 0.2 - - - +
419A PHE* 3.6 28.5 - - + +
420A LYS* 3.7 39.1 + - - +
365B ASP* 4.0 23.6 - - + +
368B ALA* 4.3 5.4 - - + +
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Residues in contact with ALA 368 (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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364A GLU 3.6 8.5 + - - +
365A ASP* 3.5 7.3 + - - +
366A LYS 3.2 0.6 - - - -
367A ASN* 1.4 74.3 - - - +
369A ARG* 1.4 83.3 + - - +
371A ILE* 3.5 4.8 + - - +
372A GLU* 3.3 25.6 + - - +
367B ASN* 4.1 18.4 - - + +
368B ALA* 4.1 11.6 - - - +
371B ILE* 3.8 20.3 - - + +
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Residues in contact with ARG 369 (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 ASP* 2.8 39.1 + - - +
366A LYS* 3.1 11.8 + - - +
368A ALA* 1.4 101.1 - - - +
370A VAL* 1.4 56.6 + - - +
372A GLU* 3.6 29.3 + - - +
373A LEU* 3.2 27.2 + - - +
410A LEU* 4.0 27.7 - - + +
367B ASN* 5.7 0.2 + - - -
371B ILE* 4.8 7.1 - - - +
420B LYS* 4.0 20.8 + - - +
421B VAL 5.7 2.0 + - - -
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Residues in contact with VAL 370 (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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366A LYS 3.3 15.7 - - - +
367A ASN* 3.4 8.1 - - - +
368A ALA 3.2 0.8 - - - -
369A ARG* 1.4 74.1 - - - +
371A ILE* 1.4 57.1 + - + +
373A LEU* 3.1 8.8 + - + +
374A ILE* 2.8 50.4 + - + +
410A LEU* 4.0 8.1 - - + -
419A PHE* 3.7 34.1 - - + -
421A VAL* 5.2 0.4 - - + -
432A LEU* 3.7 30.3 - - + -
435A ILE* 4.3 16.2 - - + -
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Residues in contact with ILE 371 (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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367A ASN* 3.4 36.5 + - - +
368A ALA 3.5 6.3 + - - +
370A VAL* 1.4 76.5 - - + +
372A GLU* 1.4 64.1 - - - +
374A ILE* 3.5 18.8 + - + +
375A ALA* 3.1 24.6 + - + +
420A LYS 3.8 14.4 - - - +
421A VAL* 5.4 0.7 - - + -
422A ASP* 5.2 6.1 - - - +
368B ALA* 3.9 20.6 - - + +
371B ILE* 3.9 20.6 - - + -
372B GLU* 3.8 36.6 - - + +
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Residues in contact with GLU 372 (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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368A ALA 3.3 15.5 + - - +
369A ARG* 3.6 38.0 + - - +
370A VAL 3.3 0.4 - - - -
371A ILE* 1.4 75.8 - - - +
373A LEU* 1.4 56.8 + - - +
375A ALA* 3.5 6.4 + - - +
376A ALA* 2.9 28.5 + - - +
371B ILE* 3.6 29.8 - - + +
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Residues in contact with LEU 373 (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 ARG 3.2 10.4 + - - +
370A VAL* 3.1 9.8 + - + +
372A GLU* 1.4 77.0 - - - +
374A ILE* 1.4 65.1 + - + +
376A ALA* 3.3 9.1 + - + +
377A TYR* 3.1 45.7 + - + -
410A LEU* 4.5 19.1 - - + -
432A LEU* 5.0 2.9 - - + -
436A LEU* 3.7 33.4 - - + -
439A LEU* 4.6 1.8 - - + -
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Residues in contact with ILE 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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370A VAL* 2.8 41.0 + - + +
371A ILE* 3.7 17.5 - - + +
372A GLU 3.4 0.2 - - - -
373A LEU* 1.4 74.1 - - + +
375A ALA* 1.3 60.6 + - - +
377A TYR* 3.5 3.1 + - - +
378A ARG* 3.2 62.5 + - - +
421A VAL* 4.0 22.9 - - + -
435A ILE* 3.7 26.7 - - + -
439A LEU* 3.8 16.2 - - + +
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Residues in contact with ALA 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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371A ILE* 3.1 18.5 + - + +
372A GLU* 3.6 6.7 - - - +
374A ILE* 1.3 74.9 - - - +
376A ALA* 1.4 54.6 + - - +
378A ARG* 3.1 8.7 + - - +
379A ASN* 2.7 53.7 + - - +
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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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372A GLU 2.9 19.1 + - - +
373A LEU* 3.5 14.8 - - + +
375A ALA* 1.4 73.9 - - - +
377A TYR* 1.3 56.5 + - + +
379A ASN* 4.2 5.1 - - - +
380A ARG* 2.8 43.7 + - + +
381A GLY 3.4 1.2 + - - -
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Residues in contact with TYR 377 (chain A).
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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373A LEU* 3.1 43.9 + - + -
374A ILE 3.8 6.7 - - - +
376A ALA* 1.3 74.2 - - + +
378A ARG* 1.3 62.6 + - - +
381A GLY* 2.9 27.4 + - - +
382A HIS* 5.6 0.2 - - - -
436A LEU* 3.6 26.5 - - + +
439A LEU* 3.8 37.9 - - + -
440A ARG* 3.9 23.2 - - + +
443A TYR* 3.6 16.0 - - + +
444A CYS* 3.6 31.9 - - - -
449A VAL 5.7 0.2 - - - +
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Residues in contact with ARG 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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374A ILE* 3.2 38.3 + - - +
375A ALA* 3.1 11.6 + - - +
377A TYR* 1.3 77.6 - - - +
379A ASN* 1.3 59.7 + - - +
382A HIS* 5.0 0.2 - - - -
439A LEU* 4.5 1.5 - - + +
443A TYR* 3.9 11.5 - - + +
449A VAL 4.3 9.7 - - - +
450A GLU* 5.7 0.3 - - - -
451A TYR* 3.3 32.6 + - - +
452A THR* 3.4 20.1 + - + +
464A GLN* 3.2 32.5 + - - +
468A GLU* 2.8 40.3 + - - +
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Residues in contact with ASN 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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375A ALA* 2.7 39.2 + - - +
376A ALA* 4.2 3.7 - - - +
378A ARG* 1.3 76.4 - - - +
380A ARG* 1.3 69.7 + - + +
381A GLY 3.8 0.4 - - - -
382A HIS* 2.9 21.4 + - - -
452A THR* 3.3 34.2 + - - +
379B ASN* 5.6 6.3 + - - +
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Residues in contact with ARG 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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376A ALA* 2.8 24.4 + - + +
379A ASN* 1.3 84.9 - - + +
381A GLY* 1.3 62.1 + - - +
382A HIS* 3.2 8.3 - - - +
383A LEU* 3.1 47.0 + - + +
384A MET* 4.1 4.9 + - - +
454B ILE 3.3 13.1 + - - -
455B LEU* 2.7 40.1 + - - -
457B PRO* 4.2 20.4 - - - +
460B GLN* 3.7 13.1 - - - +
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Residues in contact with GLY 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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376A ALA 3.4 2.6 + - - -
377A TYR* 2.9 26.8 + - - -
379A ASN 3.8 0.6 - - - -
380A ARG* 1.3 76.7 - - - +
382A HIS* 1.4 54.9 + - - +
384A MET* 3.0 21.2 + - - +
385A ALA 3.2 4.5 + - - -
443A TYR* 3.1 18.4 - - - +
444A CYS* 3.5 20.0 - - - -
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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