Contacts of the helix formed by residues 444 - 457 (chain A) in PDB entry 1YOK
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 444 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392A TYR* 4.0 6.0 - - - -
442A GLN 3.2 3.7 + - - +
443A PHE* 1.3 76.1 - - - +
445A GLN* 1.3 60.6 + - - +
446A ARG* 3.1 23.3 + - - +
447A GLU* 2.7 52.3 + - - +
448A PHE* 2.8 26.3 + - - +
484A TYR* 2.6 26.2 + - - -
489A TYR* 3.0 21.1 + - - +
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Residues in contact with GLN 445 (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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309A LEU* 3.6 25.0 + - + +
312A GLU* 3.9 32.4 + - - +
392A TYR* 3.0 30.2 + - + +
444A ASP* 1.3 72.3 - - - +
446A ARG* 1.3 82.0 + - - +
448A PHE* 3.0 5.2 + - + +
449A VAL* 3.0 24.3 + - - +
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Residues in contact with ARG 446 (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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301A ILE* 3.9 24.6 - - + +
305A ILE* 3.6 21.9 - - + +
309A LEU* 4.0 15.1 - - + +
444A ASP* 3.1 30.3 + - - +
445A GLN* 1.3 94.0 + - - +
447A GLU* 1.3 61.6 + - - +
449A VAL* 3.1 23.6 - - - +
450A CYS* 3.4 14.0 + - - -
484A TYR* 3.0 43.1 + - + +
489A TYR* 5.3 0.8 + - - -
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Residues in contact with GLU 447 (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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442A GLN 3.5 1.7 - - - +
443A PHE* 3.2 25.4 - - + -
444A ASP* 2.7 50.6 + - - +
446A ARG* 1.3 70.8 - - - +
448A PHE* 1.3 61.4 + - - +
450A CYS* 3.4 3.3 + - - +
451A LEU* 3.0 27.2 + - - +
481A LEU* 4.3 13.2 - - + +
484A TYR* 4.0 13.6 - - + -
485A THR* 4.9 1.3 - - + +
489A TYR* 3.7 10.6 - - - -
495A LYS* 2.9 32.9 + - - +
499A LEU* 3.7 24.5 - - + +
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Residues in contact with PHE 448 (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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312A GLU* 3.2 27.8 - - - -
388A LEU* 3.7 26.7 - - + -
389A ASP* 4.6 12.8 - - - -
392A TYR* 3.3 63.0 - + + -
443A PHE* 3.5 17.2 - + + -
444A ASP 2.8 15.2 + - - +
445A GLN* 3.0 11.6 + - + +
447A GLU* 1.3 75.6 - - - +
449A VAL* 1.3 58.7 + - - +
451A LEU* 3.1 6.6 + - - +
452A LYS* 2.9 54.7 + - + +
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Residues in contact with VAL 449 (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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305A ILE* 4.5 8.3 - - + -
308A LEU* 4.4 19.7 - - + +
309A LEU* 3.6 24.0 - - + +
312A GLU* 3.1 48.0 - - + +
445A GLN* 3.0 13.5 + - + +
446A ARG* 3.1 20.2 - - - +
448A PHE* 1.3 74.1 - - + +
450A CYS* 1.3 60.9 + - - +
452A LYS* 3.2 8.8 + - - +
453A PHE* 3.0 33.0 + - + -
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Residues in contact with CYS 450 (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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305A ILE* 3.8 31.9 - - - -
308A LEU* 4.7 5.8 - - - -
446A ARG 3.4 15.2 + - - +
447A GLU 3.5 9.2 - - - +
448A PHE 3.2 0.4 - - - -
449A VAL* 1.3 78.2 - - - +
451A LEU* 1.3 64.2 + - - +
453A PHE 3.2 1.9 + - - -
454A LEU* 2.9 28.6 + - - +
477A VAL* 3.7 27.4 - - + +
480A ALA* 5.0 0.2 - - - -
481A LEU* 4.1 32.5 - - + -
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Residues in contact with LEU 451 (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 LEU* 4.1 12.6 - - + -
438A LEU* 5.5 1.6 - - + -
443A PHE* 3.8 25.8 - - + -
447A GLU 3.0 17.4 + - - +
448A PHE 3.4 7.4 - - - +
450A CYS* 1.3 77.3 - - - +
452A LYS* 1.3 64.5 + - - +
454A LEU* 3.3 18.4 + - + +
455A VAL* 2.9 28.1 + - - +
481A LEU* 4.3 14.6 - - + -
499A LEU* 3.9 33.0 - - + +
500A LEU* 5.1 0.2 - - + -
502A ARG* 4.8 10.5 - - + -
503A LEU* 4.3 19.0 - - + +
506A ILE* 4.9 8.1 - - + -
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Residues in contact with LYS 452 (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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312A GLU* 3.4 27.0 + - - -
313A PRO* 5.2 2.8 - - - +
356A ILE* 6.0 2.0 - - - +
359A TRP* 3.4 41.7 - - + +
385A LEU* 4.2 19.6 - - + +
388A LEU* 3.6 20.6 - - + -
389A ASP* 4.6 12.4 + - - +
448A PHE* 2.9 48.3 + - + +
449A VAL* 3.5 9.9 - - - +
450A CYS 3.2 0.4 - - - -
451A LEU* 1.3 75.3 - - - +
453A PHE* 1.3 58.5 + - - +
455A VAL* 3.1 5.6 + - - +
456A LEU* 2.7 30.6 + - - +
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Residues in contact with PHE 453 (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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308A LEU* 3.8 45.3 - - + -
311A CYS* 5.1 0.7 - - + -
359A TRP* 3.6 23.8 - + - -
363A SER* 3.1 25.6 - - - -
364A ILE* 3.6 19.5 - - + -
365A PHE* 4.6 0.7 - + - -
366A PHE 5.4 0.2 - - - -
449A VAL* 3.0 31.0 + - + +
450A CYS 3.9 2.9 - - - +
452A LYS* 1.3 73.3 - - - +
454A LEU* 1.3 61.3 + - - +
456A LEU* 4.2 7.6 - - + +
457A PHE* 2.8 68.2 + + + +
473A VAL* 4.3 7.0 - - + -
474A GLN* 6.4 0.2 - - - -
477A VAL* 4.1 18.4 - - + -
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Residues in contact with LEU 454 (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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450A CYS 2.9 19.6 + - - +
451A LEU* 3.7 13.5 - - + +
453A PHE* 1.3 77.1 - - - +
455A VAL* 1.3 61.2 + - - +
457A PHE 4.0 5.9 - - - +
458A SER* 4.1 4.9 + - - -
474A GLN* 3.4 57.6 + - - +
477A VAL* 4.1 9.6 - - + -
478A ASN* 4.0 18.4 - - + +
481A LEU* 4.4 9.6 - - + -
500A LEU* 3.9 28.5 - - + -
503A LEU* 4.2 19.2 - - + +
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Residues in contact with VAL 455 (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 CYS* 3.6 16.3 - - + +
384A GLU* 3.4 39.1 - - + +
385A LEU* 4.1 16.2 - - + +
388A LEU* 4.3 11.2 - - + -
451A LEU 2.9 17.1 + - - +
452A LYS* 3.2 10.5 - - - +
454A LEU* 1.3 78.7 - - - +
456A LEU* 1.3 66.0 + - - +
458A SER* 3.9 11.6 + - - -
503A LEU* 3.3 26.5 - - + -
506A ILE* 5.2 6.3 - - + -
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Residues in contact with LEU 456 (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 TRP* 4.1 27.6 - - + -
360A ALA* 4.3 4.3 - - + -
363A SER* 5.9 0.2 - - - +
366A PHE* 3.8 33.9 - - + -
377A LEU* 3.8 21.7 - - + +
378A LEU* 3.8 20.2 - - + -
381A CYS* 3.7 25.3 - - - +
385A LEU* 4.7 3.6 - - + -
452A LYS 2.7 19.9 + - - +
453A PHE* 3.8 5.6 - - + +
455A VAL* 1.3 75.8 - - - +
457A PHE* 1.3 82.0 + - + +
458A SER* 3.0 8.9 + - - -
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Residues in contact with PHE 457 (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 PHE* 3.9 11.2 - - + -
366A PHE* 3.7 35.9 - + + -
369A LEU* 4.1 21.3 - - + -
377A LEU* 4.0 11.9 - - + -
453A PHE* 2.8 56.7 + + - +
454A LEU 4.0 4.0 - - - -
456A LEU* 1.3 80.8 - - + +
458A SER* 1.3 63.7 + - - +
469A LEU* 5.4 3.4 - - + -
470A VAL* 3.7 37.0 - - + +
473A VAL* 3.9 21.8 - - + -
474A GLN* 3.1 24.3 + - - +
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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