Contacts of the helix formed by residues 441 - 456 (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 SER 441 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382A PHE* 3.3 20.2 - - - -
440A ASN* 1.3 81.1 - - - +
442A ALA* 1.3 61.3 + - - +
443A ASP* 3.3 12.8 + - - +
444A ASP* 3.1 38.4 + - - +
445A VAL* 3.4 9.4 + - - +
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Residues in contact with ALA 442 (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 5.1 1.3 - - - +
378A SER* 4.2 2.5 - - - -
379A ALA* 3.8 36.3 - - + +
382A PHE* 3.4 17.3 - - + +
441A SER* 1.3 73.3 - - - +
443A ASP* 1.3 60.6 + - - +
444A ASP 3.4 0.2 - - - -
445A VAL* 3.4 7.0 + - - +
446A ILE* 3.0 36.6 + - + +
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Residues in contact with ASP 443 (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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441A SER* 3.1 10.3 + - - +
442A ALA* 1.3 77.0 - - - +
444A ASP* 1.3 63.9 + - - +
446A ILE* 3.5 14.4 + - - +
447A LYS* 3.1 22.3 + - - +
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Residues in contact with ASP 444 (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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439A VAL* 4.1 16.6 - - + -
440A ASN* 3.3 31.9 + - - +
441A SER* 3.1 23.6 + - - +
443A ASP* 1.3 77.0 - - - +
445A VAL* 1.4 59.6 + - - +
447A LYS* 3.2 10.3 + - - +
448A MET* 3.0 27.7 + - + +
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Residues in contact with VAL 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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378A SER* 3.2 28.9 - - - +
382A PHE* 3.9 11.0 - - + -
397A VAL* 5.6 0.4 - - + -
399A VAL* 4.1 9.6 - - + -
439A VAL* 3.7 25.4 - - + -
441A SER 3.4 14.0 + - - +
442A ALA 3.6 7.0 - - - +
443A ASP 3.3 0.6 - - - -
444A ASP* 1.4 73.4 - - - +
446A ILE* 1.3 54.1 + - + +
448A MET* 2.9 11.9 + - - +
449A ILE* 2.8 39.4 + - + +
474A PHE* 3.5 26.0 - - + -
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Residues in contact with ILE 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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375A ALA* 4.1 32.1 - - + +
378A SER* 6.1 0.4 - - - -
442A ALA* 3.0 24.5 + - + +
443A ASP* 3.9 16.8 - - - +
444A ASP 3.4 0.4 - - - -
445A VAL* 1.3 75.1 - - + +
447A LYS* 1.3 57.1 + - - +
449A ILE* 3.5 8.3 + - + +
450A ASP* 3.0 45.6 + - - +
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Residues in contact with LYS 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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443A ASP 3.1 13.6 + - - +
444A ASP* 3.4 11.7 - - - +
445A VAL 3.2 0.2 - - - -
446A ILE* 1.3 75.9 - - - +
448A MET* 1.4 51.3 + - - +
450A ASP* 3.8 6.3 - - - +
451A MET* 2.8 34.8 + - - +
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Residues in contact with MET 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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399A VAL* 4.7 12.1 - - + -
401A PHE* 5.0 0.4 - - + -
413A LEU* 3.5 28.5 - - + +
437A HIS* 3.3 45.5 - - + -
438A LEU 4.3 4.3 - - - +
439A VAL* 3.6 21.3 - - + -
444A ASP* 3.0 16.9 + - + +
445A VAL* 2.9 14.6 + - - +
447A LYS* 1.4 73.1 - - - +
449A ILE* 1.3 52.7 + - + +
451A MET* 3.1 13.9 + - - +
452A GLY* 2.7 31.9 + - - -
474A PHE* 5.7 0.2 - - + -
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Residues in contact with ILE 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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359A GLY* 5.3 9.4 - - - +
374A TYR* 3.3 52.5 - - + -
375A ALA* 4.2 8.7 - - + +
401A PHE* 3.7 10.8 - - + -
445A VAL* 2.8 40.3 + - + +
446A ILE* 3.8 8.5 - - + +
448A MET* 1.3 71.2 - - - +
450A ASP* 1.4 59.5 + - - +
452A GLY* 3.2 0.9 + - - -
453A SER* 2.6 50.4 + - - +
474A PHE* 4.1 14.6 - - + -
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Residues in contact with ASP 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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362A LEU* 5.2 10.3 - - - +
446A ILE* 3.0 35.8 + - - +
447A LYS* 3.8 5.9 - - - +
449A ILE* 1.4 77.1 - - - +
451A MET* 1.4 65.5 + - - +
453A SER* 4.1 5.6 + - - +
454A ALA* 3.2 23.7 + - - +
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Residues in contact with MET 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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412A LEU 4.6 2.9 - - - +
413A LEU* 4.0 36.3 - - - +
415A LYS 6.1 1.3 - - - +
447A LYS 2.8 19.3 + - - +
448A MET* 3.1 13.7 + - - +
450A ASP* 1.4 75.5 - - - +
452A GLY* 1.3 62.9 + - - +
454A ALA* 3.6 14.0 - - - +
455A CYS* 3.7 11.8 + - - -
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Residues in contact with GLY 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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401A PHE* 3.7 20.4 - - - -
412A LEU* 3.8 22.9 - - - +
413A LEU* 4.4 1.9 - - - +
448A MET 2.7 17.9 + - - -
449A ILE 3.5 2.7 - - - -
451A MET* 1.3 71.6 - - - +
453A SER* 1.4 63.8 + - - +
455A CYS* 3.0 21.1 + - - +
456A ARG 3.4 4.7 + - - -
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Residues in contact with SER 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A GLY* 5.7 2.9 - - - -
374A TYR* 5.5 1.7 - - - -
401A PHE* 3.7 10.8 - - - -
449A ILE* 2.6 37.7 + - - +
450A ASP* 4.1 6.5 - - - -
452A GLY* 1.4 72.1 - - - +
454A ALA* 1.4 61.4 + - - +
455A CYS 3.4 0.5 + - - -
456A ARG* 3.6 22.3 + - - +
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Residues in contact with ALA 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 ASP 3.2 17.8 + - - +
451A MET* 3.6 8.5 - - - +
452A GLY 3.2 0.2 - - - -
453A SER* 1.4 75.8 - - - +
455A CYS* 1.4 63.7 + - - +
456A ARG 4.5 1.6 - - - +
457A THR* 5.0 3.5 - - - +
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Residues in contact with CYS 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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412A LEU* 3.4 37.7 - - + -
415A LYS* 5.1 6.5 - - - -
416A LYS* 3.8 23.4 + - + +
451A MET* 3.7 10.1 + - - -
452A GLY 3.0 9.2 + - - +
454A ALA* 1.4 82.3 - - - +
456A ARG* 1.4 64.1 + - - +
457A THR* 3.2 16.6 + - - +
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Residues in contact with ARG 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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401A PHE* 6.2 0.9 - - + -
403A GLU* 3.5 20.4 - - + +
412A LEU* 3.8 18.8 - - + +
416A LYS* 4.2 2.7 - - - +
452A GLY 3.4 4.5 + - - +
453A SER* 3.6 19.2 + - - +
454A ALA 4.5 0.9 - - - +
455A CYS* 1.4 76.4 - - - +
457A THR* 1.4 61.4 - - - +
467A SER* 4.2 14.9 - - - -
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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