Contacts of the helix formed by residues 479 - 492 (chain A) in PDB entry 2XNF
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 479 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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427A LEU* 5.0 5.0 - - + +
477A ASN* 4.4 0.2 - - - +
478A LYS* 1.3 117.9 + - + +
480A LEU* 1.3 65.2 + - - +
481A GLU* 3.1 6.2 - - - +
482A SER* 3.1 25.1 + - - +
483A LEU* 3.1 28.3 + - - +
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Residues in contact with LEU 480 (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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477A ASN* 3.5 38.4 - - + +
478A LYS 3.9 1.6 + - - -
479A ASP* 1.3 73.4 - - - +
481A GLU* 1.3 55.6 + - + +
483A LEU* 3.6 11.9 - - + +
484A LYS* 2.7 36.3 + - - +
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Residues in contact with GLU 481 (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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479A ASP* 3.1 6.2 - - + +
480A LEU* 1.3 80.2 - - + +
482A SER* 1.3 58.3 + - - +
484A LYS* 2.8 41.0 + - - +
485A GLY* 3.0 25.8 + - - -
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Residues in contact with SER 482 (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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408A TRP* 5.0 15.2 - - - -
425A ARG* 6.6 0.2 - - - -
426A SER 5.7 1.6 - - - -
427A LEU* 4.1 18.4 - - - -
479A ASP* 3.1 27.3 + - - +
481A GLU* 1.3 75.8 - - - +
483A LEU* 1.3 65.2 + - - +
485A GLY* 3.4 1.4 + - - -
486A LEU* 3.0 26.0 + - - +
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Residues in contact with LEU 483 (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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427A LEU* 3.7 31.4 - - + -
475A PHE* 3.7 36.6 - - + -
476A THR 4.8 0.2 - - - +
477A ASN* 4.3 19.3 - - + -
479A ASP 3.1 31.5 + - - +
480A LEU* 3.6 19.3 - - + +
482A SER* 1.3 77.4 - - - +
484A LYS* 1.3 51.8 + - - +
486A LEU* 3.1 5.8 + - + +
487A TYR* 2.7 67.1 + - + +
522A PHE* 4.8 1.3 - - + -
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Residues in contact with LYS 484 (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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480A LEU 2.7 22.2 + - - +
481A GLU* 2.8 44.3 + - - +
483A LEU* 1.3 73.3 - - - +
485A GLY* 1.3 62.1 + - - +
487A TYR* 3.3 11.8 + - - +
488A ARG* 3.1 57.3 + - - +
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Residues in contact with GLY 485 (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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408A TRP* 6.1 1.3 - - - -
481A GLU 3.0 16.6 + - - -
482A SER* 3.9 1.6 - - - -
484A LYS* 1.3 78.0 - - - +
486A LEU* 1.3 61.8 + - - +
488A ARG* 3.3 12.5 + - - +
489A ILE* 3.3 27.7 + - - +
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Residues in contact with LEU 486 (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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408A TRP* 4.2 32.8 - - + +
427A LEU* 4.0 23.8 - - + -
450A MET* 5.0 6.7 - - + -
452A LEU* 5.6 3.8 - - + -
475A PHE* 4.8 9.0 - - + -
482A SER 3.0 17.8 + - - +
483A LEU* 3.5 6.5 - - + +
485A GLY* 1.3 73.9 - - - +
487A TYR* 1.3 54.7 + - + +
489A ILE* 3.1 11.6 + - + +
490A MET* 2.7 64.1 + - + +
522A PHE* 3.5 26.5 - - + -
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Residues in contact with TYR 487 (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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483A LEU* 2.7 51.2 + - + +
484A LYS* 3.3 13.7 + - - +
486A LEU* 1.3 71.6 - - + +
488A ARG* 1.3 67.2 + - - +
490A MET* 4.6 0.7 - - - +
491A GLY* 2.8 30.6 + - - +
515A TYR* 3.7 34.2 - + + -
520A LYS* 4.3 27.4 + - - +
522A PHE* 3.7 35.3 - + - -
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Residues in contact with ARG 488 (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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484A LYS* 3.1 47.1 + - + +
485A GLY* 3.3 11.2 - - - +
486A LEU 3.2 0.2 - - - -
487A TYR* 1.3 84.4 - - - +
489A ILE* 1.3 64.5 + - + +
491A GLY 3.9 0.7 - - - -
492A ASN* 3.1 25.6 + - - +
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Residues in contact with ILE 489 (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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408A TRP* 4.7 20.9 - - + -
410A GLU* 5.6 10.5 - - + +
452A LEU* 3.9 23.8 - - + -
485A GLY 3.4 18.2 - - - +
486A LEU* 3.1 11.8 + - + +
488A ARG* 1.3 78.0 - - + +
490A MET* 1.3 63.8 + - + +
492A ASN* 3.1 10.6 + - - +
494A PHE* 3.1 52.3 + - + +
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Residues in contact with MET 490 (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 MET* 4.4 7.9 - - - -
452A LEU* 3.6 27.4 - - + -
455A GLN* 4.5 4.2 - - - +
486A LEU* 2.7 44.3 + - + +
487A TYR 4.8 0.2 - - - +
489A ILE* 1.3 73.6 - - + +
491A GLY* 1.3 60.5 + - - +
492A ASN 3.4 0.3 + - - -
493A GLY* 3.5 6.8 + - - -
494A PHE 3.3 20.2 + - - +
496A GLY* 3.7 11.7 - - - +
513A LEU* 3.3 52.3 - - + +
514A LEU 4.1 1.3 - - - +
515A TYR* 3.8 28.0 + - + +
522A PHE* 3.7 10.1 - - + -
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Residues in contact with GLY 491 (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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487A TYR 2.8 19.2 + - - -
488A ARG 3.9 1.8 - - - -
490A MET* 1.3 75.5 - - - +
492A ASN* 1.3 57.8 + - - +
493A GLY 3.2 3.9 + - - -
515A TYR* 4.0 17.4 - - - -
517A SER* 4.9 5.6 + - - -
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Residues in contact with ASN 492 (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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456A GLN* 6.0 0.3 + - - -
488A ARG 3.1 18.0 + - - +
489A ILE* 3.1 9.8 + - - +
491A GLY* 1.3 76.8 - - - +
493A GLY* 1.3 59.3 + - - +
494A PHE* 4.2 17.6 - - + -
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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