Contacts of the helix formed by residues 471 - 475 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83C PRO* 4.2 4.3 - - - -
254C TYR* 5.0 0.2 + - - -
258C THR 3.6 21.5 - - - -
442C TYR* 3.4 13.3 - - - -
470C VAL* 1.3 75.8 - - - +
472C ALA* 1.3 59.9 + - - +
473C GLN* 3.1 21.9 + - - +
474C LYS* 3.2 30.2 + - - +
475C PHE* 4.3 0.2 - - - -
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Residues in contact with ALA 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C ALA 5.4 1.6 - - - +
442C TYR* 3.6 19.4 - - + -
445C ASN* 5.6 3.8 - - + -
467C SER 5.2 0.4 - - - +
468C ALA* 3.7 17.5 - - + -
469C SER 2.8 36.2 + - - +
470C VAL 3.3 0.8 + - - -
471C GLY* 1.3 67.1 - - - +
473C GLN* 1.3 57.1 + - - +
474C LYS 2.9 12.4 + - - -
475C PHE* 3.0 24.6 + - + +
478C HIS* 3.5 13.0 - - - +
505C PHE* 3.8 2.5 - - + -
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Residues in contact with GLN 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C ILE* 5.4 0.2 - - - +
254C TYR* 4.3 10.5 + - - -
255C THR* 4.5 1.4 - - - +
258C THR* 2.9 30.5 + - - -
259C GLY* 2.9 33.2 + - - +
261C PRO* 3.0 24.3 - - + +
262C ALA 3.9 0.7 + - - -
470C VAL* 4.7 0.7 - - - -
471C GLY* 3.1 21.9 + - - -
472C ALA* 1.3 76.0 + - - +
474C LYS* 1.3 58.8 + - - +
475C PHE 3.2 2.4 + - - -
476C PRO* 4.1 7.5 - - - +
478C HIS* 4.4 1.8 - - - -
503C SER 5.0 0.2 - - - +
504C GLY* 3.1 30.2 + - - +
505C PHE* 3.3 37.5 - - + -
506C GLY 5.4 0.3 + - - -
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Residues in contact with LYS 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C PRO* 4.8 8.5 + - - +
258C THR 4.5 4.8 + - - +
259C GLY* 3.7 25.4 - - - -
260C ARG 3.6 23.1 - - - +
262C ALA* 3.5 12.3 - - + +
442C TYR* 2.9 27.6 + - - -
446C GLU* 5.1 1.0 + - - -
449C TRP* 3.7 5.0 - - - -
471C GLY 3.2 19.3 - - - +
472C ALA 2.9 1.0 - - - -
473C GLN* 1.3 75.3 - - - +
475C PHE* 1.3 80.4 + - + +
476C PRO* 3.0 14.6 - - - +
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Residues in contact with PHE 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C TYR* 3.6 29.2 - + - -
445C ASN* 4.1 10.3 - - + -
446C GLU* 3.6 44.6 - - + -
449C TRP* 3.3 48.9 - + + -
450C ASN* 5.1 0.9 - - - -
463C LEU* 4.0 20.5 - - + +
465C ALA* 5.1 1.2 - - - +
471C GLY 4.3 2.0 - - - -
472C ALA* 3.0 19.1 + - + +
474C LYS* 1.3 107.3 - - + +
476C PRO* 1.3 67.9 - - - +
477C VAL 4.4 1.7 - - - +
478C HIS* 3.6 14.2 + - + +
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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
------------------------------------------------------------
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