Contacts of the helix formed by residues 501 - 509 (chain D) in PDB entry 1Y9D
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 501 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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508B GLY* 2.8 17.8 + - - +
510B HIS* 4.0 14.7 - - + -
499D ASP* 3.7 0.8 + - - -
500D ILE* 1.3 70.1 - - - +
502D PHE* 1.3 58.1 + - - +
503D SER* 2.4 32.2 + - - -
504D LYS* 3.1 46.7 + - + +
505D ILE* 3.1 13.2 + - - +
515D ARG* 3.3 33.9 + - - +
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Residues in contact with PHE 502 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426D ILE* 6.0 0.2 - - + -
447D ASP* 4.1 11.2 - - + -
450D ALA* 3.7 15.3 - - + -
451D SER* 3.6 24.7 - - - -
454D MET* 3.6 41.5 - - + -
457D LEU* 4.6 3.4 - - + -
471D VAL* 3.8 29.4 - - + -
473D THR* 4.5 2.5 - - - -
500D ILE* 3.3 26.6 + - + -
501D ASP* 1.3 70.3 - - - +
503D SER* 1.4 57.8 + - - +
505D ILE* 3.7 15.1 - - + +
506D ALA* 2.9 28.2 + - - +
539D LEU* 3.8 22.1 - - + +
541D ASP* 2.8 23.1 + - - +
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Residues in contact with SER 503 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501D ASP* 2.4 29.8 + - - -
502D PHE* 1.4 77.5 - - - +
504D LYS* 1.3 58.4 + - - +
506D ALA* 3.5 1.9 + - - +
507D ASP* 2.9 27.2 + - - +
513D ALA* 3.6 27.1 - - - +
514D PHE* 3.9 24.0 - - - -
515D ARG* 3.6 10.4 - - - +
539D LEU* 4.6 0.7 - - - -
541D ASP* 3.9 4.2 + - - +
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Residues in contact with LYS 504 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504B LYS* 3.8 15.5 - - + +
507B ASP* 3.4 43.8 + - - +
508B GLY* 3.7 13.0 - - - +
510B HIS* 5.1 7.7 + - - -
501D ASP* 3.1 35.7 + - + +
503D SER* 1.3 77.1 + - - +
505D ILE* 1.3 54.6 + - - +
506D ALA 3.2 1.1 - - - -
507D ASP* 3.3 9.4 + - + +
508D GLY* 2.6 33.6 + - - -
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Residues in contact with ILE 505 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454B MET* 5.3 0.4 - - - -
505B ILE* 3.6 47.6 - - + +
508B GLY* 4.2 3.6 - - - -
509B VAL* 4.3 5.2 - - + -
454D MET* 3.9 36.8 - - + +
457D LEU* 4.2 19.5 - - + -
500D ILE* 3.7 22.9 - - + -
501D ASP 3.1 14.7 + - - +
502D PHE* 3.7 15.3 - - + +
504D LYS* 1.3 73.9 - - - +
506D ALA* 1.3 64.8 + - - +
508D GLY* 3.0 12.0 + - - -
509D VAL* 3.1 14.2 + - + +
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Residues in contact with ALA 506 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457D LEU* 4.8 2.7 - - + -
502D PHE 2.9 18.8 + - - +
503D SER 3.7 0.2 - - - +
505D ILE* 1.3 75.1 - - - +
507D ASP* 1.3 67.3 + - - +
509D VAL* 3.0 19.1 + - - +
511D MET* 2.9 34.7 + - + +
513D ALA* 3.6 24.5 - - + -
539D LEU* 4.1 17.9 - - + -
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Residues in contact with ASP 507 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504B LYS* 3.3 35.6 + - + +
503D SER 2.9 18.2 + - - +
504D LYS* 3.3 11.1 + - + +
506D ALA* 1.3 76.1 - - - +
508D GLY* 1.3 53.5 + - - +
510D HIS* 2.7 31.4 + - - +
511D MET 3.6 9.5 + - - +
513D ALA* 6.2 0.2 - - + -
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Residues in contact with GLY 508 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500B ILE* 3.5 4.9 - - - -
501B ASP* 2.8 35.6 + - - +
504B LYS* 3.6 21.9 - - - +
505B ILE* 4.0 4.9 - - - -
504D LYS 2.6 18.5 + - - -
505D ILE 3.0 6.7 + - - -
507D ASP* 1.3 71.3 - - - +
509D VAL* 1.3 60.6 + - - +
510D HIS* 3.7 3.5 + - - -
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Residues in contact with VAL 509 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454B MET* 5.6 1.3 - - + -
498B ASN* 5.4 0.3 + - - -
499B ASP 4.6 1.7 - - - +
500B ILE* 3.8 30.7 - - + -
505B ILE* 4.5 5.4 - - + -
454D MET 5.3 2.0 - - - +
455D GLN* 4.7 4.5 - - - +
457D LEU* 3.9 28.3 - - + +
458D ALA* 3.9 25.3 - - + +
461D VAL* 3.5 15.9 - - + +
505D ILE* 3.1 9.7 + - + +
506D ALA* 3.0 22.4 + - - +
508D GLY* 1.3 77.3 - - - +
510D HIS* 1.3 73.7 + - - +
511D MET* 4.1 10.8 - - + -
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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