Contacts of the helix formed by residues 372 - 386 (chain A) in PDB entry 4Y05
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 GLY 372 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321A ASN* 3.0 15.3 - - - +
357A THR 3.7 3.6 - - - -
358A MET 3.4 11.7 - - - -
359A GLY 3.6 17.7 - - - -
360A GLY* 3.9 0.8 - - - -
371A LYS* 1.3 70.3 + - - +
373A ILE* 1.4 66.1 + - - -
374A TYR 3.3 2.2 - - - -
375A ALA* 3.4 4.8 + - - -
376A MET* 3.2 27.9 + - - +
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Residues in contact with ILE 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ASN* 4.9 4.5 - - + +
324A VAL* 4.4 6.1 - - + -
325A TYR* 4.1 19.3 - - + +
328A THR* 4.0 12.1 - - - +
329A ALA* 3.6 17.7 - - + -
344A CYS* 4.7 2.2 - - - -
357A THR* 3.0 29.5 + - + +
358A MET* 2.9 19.5 + - + +
372A GLY* 1.4 69.0 - - - -
374A TYR* 1.3 65.9 + - - +
376A MET* 4.0 5.1 - - - +
377A ALA* 2.9 22.7 + - - +
490A LEU* 3.4 25.1 - - + -
562A ILE* 3.6 31.0 - - + -
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Residues in contact with TYR 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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358A MET* 3.0 41.5 + - + +
359A GLY* 4.0 8.3 - - - +
373A ILE* 1.3 75.9 - - - +
375A ALA* 1.4 53.7 + - - +
377A ALA* 3.9 1.7 - - - +
378A SER* 2.7 37.2 + - - -
401A PHE* 4.1 22.8 - + - -
449A ILE* 3.3 37.2 - - + -
453A SER* 5.5 1.1 - - - -
472A ALA* 3.9 8.3 + - - +
474A PHE* 3.6 33.6 - + + -
490A LEU* 3.6 34.8 - - + -
492A ASP* 3.5 29.6 + - - +
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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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359A GLY 5.8 1.6 - - - +
371A LYS* 3.8 17.7 - - + -
372A GLY* 3.4 10.4 + - - +
373A ILE 3.3 0.4 - - - -
374A TYR* 1.4 76.2 - - - +
376A MET* 1.3 60.7 + - - +
378A SER* 3.4 7.0 + - - -
379A ALA* 2.9 30.2 + - - +
442A ALA* 5.1 1.6 - - - +
446A ILE* 4.1 30.8 - - + +
449A ILE* 4.6 6.7 - - + -
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Residues in contact with MET 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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321A ASN* 4.2 7.6 - - + +
322A GLU* 3.4 39.5 - - + +
325A TYR* 3.2 51.5 + - + -
371A LYS* 4.0 17.9 - - + +
372A GLY 3.2 21.8 + - - +
373A ILE* 4.0 2.0 - - - +
375A ALA* 1.3 74.7 - - - +
377A ALA* 1.4 64.6 + - - +
379A ALA* 3.6 7.2 + - - +
380A ASP* 3.1 20.3 + - - +
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Residues in contact with ALA 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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325A TYR* 3.4 18.3 + - + +
333A VAL* 4.3 12.1 - - + +
373A ILE 2.9 17.5 + - - +
374A TYR 3.9 3.6 - - - +
376A MET* 1.4 72.1 - - - +
378A SER* 1.3 59.5 + - - +
380A ASP* 3.2 3.5 + - - +
381A VAL* 2.9 34.9 + - - +
476A ILE* 4.0 14.1 - - + -
488A PHE* 4.7 5.2 - - + -
490A LEU* 4.3 15.7 - - + -
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Residues in contact with SER 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A TYR 2.7 22.8 + - - -
375A ALA* 3.6 7.6 - - - -
377A ALA* 1.3 75.2 - - - +
379A ALA* 1.4 61.8 + - - +
381A VAL* 3.1 13.2 + - - +
382A PHE* 3.1 23.3 + - - -
442A ALA* 4.2 6.1 - - - -
445A VAL* 3.2 41.4 - - - +
446A ILE* 6.1 0.2 - - - -
474A PHE* 3.6 9.7 - - - -
476A ILE* 4.0 9.2 - - - +
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Residues in contact with ALA 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ALA 2.9 18.7 + - - +
376A MET* 3.6 8.1 - - - +
378A SER* 1.4 73.9 - - - +
380A ASP* 1.4 64.3 + - - +
382A PHE* 3.2 5.5 + - - +
383A LEU* 3.1 32.6 + - + +
442A ALA* 3.8 18.5 - - + +
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Residues in contact with ASP 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A TYR* 2.6 40.8 + - - +
330A ALA* 4.6 4.0 - - - +
333A VAL* 4.2 12.7 - - + +
376A MET 3.1 8.0 + - - +
377A ALA 3.2 2.0 + - - +
379A ALA* 1.4 77.5 - - - +
381A VAL* 1.3 60.3 + - - +
383A LEU* 3.3 21.8 + - - +
384A LEU* 2.9 35.5 + - + +
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Residues in contact with VAL 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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333A VAL* 3.9 16.6 - - + -
336A ILE* 4.3 8.7 - - + -
337A PHE* 3.4 23.4 - - + -
377A ALA 2.9 20.6 + - - +
378A SER* 3.1 8.9 + - - +
380A ASP* 1.3 74.8 - - - +
382A PHE* 1.3 59.8 + - + +
384A LEU 3.2 1.7 + - - -
385A LYS* 3.0 26.4 + - - +
397A VAL* 4.0 28.3 - - + -
476A ILE* 3.9 31.6 - - + -
478A LEU* 4.0 8.1 - - + -
488A PHE* 5.8 0.4 - - + -
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Residues in contact with PHE 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 SER* 3.1 24.6 + - - -
379A ALA* 3.2 7.2 + - - +
381A VAL* 1.3 77.8 - - + +
383A LEU* 1.3 64.0 + - + +
385A LYS* 3.9 22.9 - - + +
386A ASN* 3.5 21.5 + - - +
397A VAL* 3.8 23.3 - - + -
439A VAL* 3.7 28.9 - - + -
440A ASN* 3.5 25.1 - - - -
441A SER* 3.3 26.0 - - - -
442A ALA* 3.4 19.5 - - + +
445A VAL* 3.9 14.4 - - + -
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Residues in contact with LEU 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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379A ALA* 3.1 23.0 + - + +
380A ASP* 3.7 26.9 - - - +
381A VAL 3.3 0.4 - - - -
382A PHE* 1.3 78.1 - - + +
384A LEU* 1.3 69.9 + - + +
386A ASN* 3.4 13.4 + - - +
387A GLN* 3.6 16.9 + - - +
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Residues in contact with LEU 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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333A VAL* 3.7 28.5 - - + -
334A GLN* 4.1 17.9 - - + +
337A PHE* 3.6 27.4 - - + -
380A ASP* 2.9 15.8 + - + +
383A LEU* 1.3 79.5 - - + +
385A LYS* 1.3 57.6 + - - +
387A GLN* 3.2 48.8 + - - +
390A TYR* 3.4 26.0 - - + +
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Residues in contact with LYS 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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337A PHE* 3.7 21.8 - - + -
381A VAL 3.0 14.2 + - - +
382A PHE* 3.9 24.7 - - + +
384A LEU* 1.3 76.3 - - - +
386A ASN* 1.3 58.3 + - + +
387A GLN 3.3 2.2 - - - -
390A TYR* 4.0 5.7 - - + +
391A ARG* 3.4 24.3 - - - +
395A LEU* 3.0 40.7 + - + -
396A GLU* 4.6 2.3 - - - +
397A VAL* 3.5 30.2 - - + +
440A ASN* 6.3 0.4 - - - +
478A LEU* 5.3 0.2 - - + -
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Residues in contact with ASN 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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382A PHE 3.5 17.2 + - - +
383A LEU* 3.4 7.8 + - - +
384A LEU 3.3 1.2 - - - -
385A LYS* 1.3 76.2 - - + +
387A GLN* 1.4 62.0 + - - +
388A PRO* 4.0 2.1 - - - +
391A ARG* 4.3 6.7 - - - +
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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