Contacts of the helix formed by residues 421 - 433 (chain A) in PDB entry 2XJF
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 ARG 421 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422A ARG* 1.3 65.9 + - - +
423A ILE* 3.3 3.8 - - - +
424A LYS* 3.1 36.1 + - - +
425A LYS* 3.4 20.4 + - - +
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Residues in contact with ARG 422 (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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391A GLU* 2.8 31.4 + - - -
395A LEU* 4.0 27.8 - - + -
421A ARG* 1.3 75.4 - - - +
423A ILE* 1.3 60.1 + - + +
425A LYS* 3.3 32.8 + - - +
426A VAL* 2.9 44.7 + - - +
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Residues in contact with ILE 423 (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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392A LEU* 4.0 16.8 - - + +
395A LEU* 3.8 41.7 - - + +
396A ASP* 3.8 22.4 - - + +
421A ARG 3.3 1.9 - - - +
422A ARG* 1.3 78.4 - - + +
424A LYS* 1.3 78.3 + - - +
426A VAL* 4.2 0.9 - - - +
427A THR* 2.7 38.2 + - - +
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Residues in contact with LYS 424 (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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421A ARG* 3.1 38.7 + - - +
422A ARG 3.3 0.4 - - - -
423A ILE* 1.3 101.5 - - - +
425A LYS* 1.3 58.0 + - - +
427A THR* 3.4 9.1 - - + +
428A HIS* 2.9 28.6 + - - +
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Residues in contact with LYS 425 (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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421A ARG 3.4 11.4 + - - +
422A ARG* 3.3 42.0 + - - +
424A LYS* 1.3 76.7 - - - +
426A VAL* 1.3 61.8 + - - +
428A HIS* 3.3 7.2 + - + +
429A ASP* 3.0 60.9 + - - +
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Residues in contact with VAL 426 (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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388A LEU* 3.4 26.0 - - + +
391A GLU* 3.4 31.0 - - + +
392A LEU* 3.6 38.4 - - + +
395A LEU* 4.4 3.8 - - + -
422A ARG* 2.9 37.7 + - + +
423A ILE 4.2 1.8 - - - +
425A LYS* 1.3 74.5 - - + +
427A THR* 1.3 55.7 + - - +
429A ASP* 3.3 3.7 + - - +
430A MET* 2.8 34.8 + - + +
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Residues in contact with THR 427 (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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392A LEU* 3.9 20.5 - - - +
423A ILE* 2.7 28.0 + - - +
424A LYS* 3.4 9.8 - - + +
426A VAL* 1.3 76.6 - - - +
428A HIS* 1.3 65.6 + - - +
430A MET* 3.4 4.7 + - - +
431A ASP* 3.0 42.9 + - - +
443A SER* 3.9 13.5 - - - +
444A GLY* 4.2 12.0 - - - +
445A SER 5.2 0.7 + - - -
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Residues in contact with HIS 428 (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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424A LYS 2.9 18.6 + - - +
425A LYS* 3.3 8.7 + - + +
427A THR* 1.3 77.3 - - - +
429A ASP* 1.3 66.4 + - - +
431A ASP* 3.3 6.1 + - + +
432A MET* 3.0 66.1 + - + +
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Residues in contact with ASP 429 (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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388A LEU* 4.3 15.7 - - + +
425A LYS* 3.0 51.3 + - - +
426A VAL* 3.3 4.3 + - - +
428A HIS* 1.3 82.5 + - - +
430A MET* 1.3 67.9 + - - +
432A MET* 3.7 9.9 + - - +
433A CYS* 3.5 19.4 + - - -
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Residues in contact with MET 430 (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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382A TRP* 4.5 6.7 - - + -
385A LYS* 5.3 7.9 - - + +
388A LEU* 3.7 22.1 - - + +
389A PHE* 3.7 35.7 - - + +
392A LEU* 3.9 17.7 - - - -
426A VAL 2.8 18.6 + - - +
427A THR 3.6 4.9 - - - +
429A ASP* 1.3 79.9 - - - +
431A ASP* 1.3 67.8 + - - +
433A CYS* 3.3 18.0 + - - +
434A TYR* 3.4 27.0 - - + +
439A SER* 5.8 0.4 - - - -
442A ARG* 3.7 32.3 - - + -
444A GLY* 3.8 16.8 - - - +
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Residues in contact with ASP 431 (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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111A LYS* 5.1 0.6 + - - -
120A VAL* 5.4 3.8 - - - +
427A THR* 3.0 26.1 + - - +
428A HIS* 3.3 6.5 + - + +
430A MET* 1.3 83.9 - - - +
432A MET* 1.3 74.1 + - + +
434A TYR* 3.1 18.3 + - - +
435A GLY 3.2 10.6 - - - +
438A GLY* 3.5 19.4 - - - -
439A SER* 5.1 1.2 + - - -
442A ARG 4.4 2.1 - - - +
443A SER* 3.0 31.5 + - - -
444A GLY* 3.2 20.7 + - - -
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Residues in contact with MET 432 (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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127A PHE* 6.3 0.4 - - + -
428A HIS* 3.0 54.1 + - + +
429A ASP* 4.3 8.1 - - - +
430A MET 3.3 0.6 - - - -
431A ASP* 1.3 88.6 - - + +
433A CYS* 1.3 62.0 + - - +
434A TYR 3.1 1.0 + - - -
435A GLY* 3.2 35.6 + - - +
436A MET* 3.6 38.1 - - - +
438A GLY 4.9 0.7 - - - +
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Residues in contact with CYS 433 (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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381A VAL* 3.7 30.8 - - + +
385A LYS* 3.5 38.4 - - + -
388A LEU* 4.9 5.2 - - - -
429A ASP 3.5 16.1 + - - -
430A MET 3.3 9.4 + - - +
431A ASP 3.2 0.8 - - - -
432A MET* 1.3 77.2 - - - +
434A TYR* 1.3 60.1 + - - +
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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