Contacts of the helix formed by residues 471 - 475 (chain D) in PDB entry 1XSK
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 471 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83D PRO* 4.0 3.8 - - - -
258D THR 3.5 22.4 - - - -
442D TYR* 3.4 12.8 - - - -
469D SER 3.0 0.6 + - - -
470D VAL* 1.3 77.0 - - - +
472D ALA* 1.3 62.6 + - - +
473D GLN* 3.1 18.3 + - - +
474D LYS* 3.1 30.1 + - - +
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Residues in contact with ALA 472 (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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441D ALA 5.5 1.1 - - - +
442D TYR* 3.7 13.5 - - + -
445D ASN* 5.6 3.4 - - + +
467D SER 5.3 0.2 - - - +
468D ALA* 3.8 16.8 - - + -
469D SER 2.8 30.4 + - - +
470D VAL 3.4 0.2 - - - -
471D GLY* 1.3 74.4 - - - +
473D GLN* 1.3 57.6 + - - +
474D LYS 2.8 13.3 + - - -
475D PHE* 2.9 30.4 + - + -
478D HIS* 3.4 13.5 - - - +
505D PHE* 3.8 2.0 - - + -
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Residues in contact with GLN 473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D ILE* 5.3 0.3 - - - +
254D TYR* 4.4 10.7 + - - -
255D THR* 4.9 0.2 - - - +
258D THR* 3.0 38.6 + - - -
259D GLY* 3.1 25.7 + - - +
261D PRO* 3.2 24.1 - - + +
262D ALA 3.9 1.0 + - - -
470D VAL* 4.7 0.3 - - - -
471D GLY* 3.2 19.4 + - - +
472D ALA* 1.3 77.8 + - - +
474D LYS* 1.3 58.6 + - - +
475D PHE 3.2 2.3 + - - -
476D PRO* 4.0 8.3 - - - +
478D HIS* 4.3 1.3 - - - -
504D GLY 3.2 29.8 - - - +
505D PHE* 3.4 39.2 - - + -
506D GLY 5.5 0.5 + - - -
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Residues in contact with LYS 474 (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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83D PRO* 4.4 10.9 + - - +
258D THR 4.4 4.5 + - - -
259D GLY* 3.6 25.8 - - - -
260D ARG 3.4 23.8 - - - +
262D ALA* 3.5 10.3 - - - +
442D TYR* 2.8 28.8 + - - -
446D GLU* 5.5 0.2 + - - -
449D TRP* 3.9 6.2 + - - -
471D GLY 3.1 20.6 - - - +
472D ALA 2.8 1.6 + - - -
473D GLN* 1.3 75.1 - - - +
475D PHE* 1.3 75.1 + - + +
476D PRO* 2.9 16.2 - - - +
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Residues in contact with PHE 475 (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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442D TYR* 3.6 40.4 - + - -
445D ASN* 4.0 18.8 - - + -
446D GLU* 3.6 32.1 - - + -
449D TRP* 3.3 52.0 - + + -
450D ASN* 5.7 0.7 - - - -
463D LEU* 4.1 16.7 - - + +
465D ALA* 5.0 1.9 - - - +
471D GLY 4.1 0.7 - - - -
472D ALA* 2.9 23.6 + - + +
474D LYS* 1.3 95.3 - - + +
476D PRO* 1.3 70.0 - - - +
477D VAL 4.4 0.9 - - - +
478D HIS* 3.2 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