Contacts of the helix formed by residues 490 - 504 (chain A) in PDB entry 1JXO
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 SER 490 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468A GLU 2.6 29.2 + - - -
469A GLU 2.9 15.4 + - - -
471A TRP* 3.4 36.1 - - - -
488A ILE 3.4 1.8 + - - -
489A PRO* 1.3 76.4 - - - +
491A LYS* 1.3 64.3 + - - +
492A ARG* 3.4 4.2 + - - -
493A ARG* 3.1 16.3 + - - +
494A VAL* 2.9 20.8 + - - +
523A TYR* 4.0 0.4 - - - -
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Residues in contact with LYS 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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471A TRP* 3.7 28.6 - - + -
490A SER* 1.3 73.0 - - - +
492A ARG* 1.3 63.6 + - - +
494A VAL* 3.8 0.2 - - - -
495A GLU* 3.0 51.5 + - - +
522A SER* 3.4 17.3 + - - +
523A TYR* 3.2 43.3 + - + +
524A GLU* 5.3 0.4 - - - +
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Residues in contact with ARG 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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468A GLU* 3.3 42.9 - - - +
469A GLU* 4.7 0.7 - - - -
471A TRP* 5.3 0.6 - - - -
490A SER* 3.4 9.3 + - - +
491A LYS* 1.3 80.6 - - - +
493A ARG* 1.3 58.0 + - - +
495A GLU* 4.4 2.6 - - - +
496A ARG* 3.0 60.6 + - + +
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Residues in contact with ARG 493 (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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469A GLU* 2.6 63.2 + - - +
470A TRP* 3.4 35.0 - - - +
489A PRO* 3.8 15.8 - - + +
490A SER* 3.1 21.4 + - - +
492A ARG* 1.3 76.9 - - - +
494A VAL* 1.3 62.6 + - - +
496A ARG* 3.8 16.9 + - - +
497A ARG* 3.3 22.0 + - - +
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Residues in contact with VAL 494 (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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437A PHE* 3.8 24.5 - - + -
489A PRO* 3.6 32.8 - - + +
490A SER 2.9 19.0 + - - +
491A LYS 3.8 2.5 - - - +
493A ARG* 1.3 75.9 - - - +
495A GLU* 1.3 63.5 + - - +
497A ARG* 3.3 8.6 - - - +
498A GLU* 2.9 35.6 + - - +
521A LEU 4.1 2.9 - - - +
522A SER* 3.6 28.3 - - - -
523A TYR* 4.0 4.3 - - + +
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Residues in contact with GLU 495 (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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491A LYS* 3.0 42.3 + - - +
492A ARG* 4.4 2.3 - - - +
494A VAL* 1.3 71.2 - - - +
496A ARG* 1.3 60.5 + - - +
497A ARG 2.9 1.8 - - - -
498A GLU* 2.6 29.4 + - - +
499A TRP* 2.7 28.0 + - + +
520A VAL* 3.9 27.3 - - + +
521A LEU* 4.9 0.2 - - - -
522A SER* 2.8 33.4 + - - +
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Residues in contact with ARG 496 (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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469A GLU* 2.6 44.5 + - - -
492A ARG* 3.0 49.5 + - + +
493A ARG* 3.8 21.4 + - - +
495A GLU* 1.3 75.6 - - - +
497A ARG* 1.3 58.4 + - - +
499A TRP* 3.5 9.3 + - - +
500A SER* 3.0 32.2 + - - -
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Residues in contact with ARG 497 (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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493A ARG 3.3 10.3 + - - +
494A VAL* 3.3 12.3 - - - +
495A GLU 2.9 0.2 - - - -
496A ARG* 1.3 82.5 - - - +
498A GLU* 1.3 77.6 + - - +
500A SER* 3.6 7.0 + - - -
501A ARG* 3.2 29.1 + - - +
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Residues in contact with GLU 498 (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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494A VAL* 2.9 38.1 + - - +
495A GLU 2.6 13.6 + - - +
497A ARG* 1.3 92.8 + - - +
499A TRP* 1.3 65.1 + - - +
500A SER 3.1 0.2 - - - -
501A ARG* 3.1 17.3 + - + +
502A LEU* 3.1 17.0 + - + +
520A VAL* 3.8 36.8 - - + -
521A LEU 4.2 10.0 - - - +
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Residues in contact with TRP 499 (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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495A GLU* 2.7 41.6 + - + +
496A ARG* 4.0 7.9 - - - +
498A GLU* 1.3 73.7 - - - +
500A SER* 1.3 52.4 + - - +
502A LEU* 3.2 20.9 + - + +
503A LYS* 2.7 36.9 + - - +
520A VAL* 3.5 43.4 - - + +
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Residues in contact with SER 500 (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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496A ARG* 3.0 21.2 + - - -
497A ARG* 3.6 9.6 - - - -
499A TRP* 1.3 77.0 - - - +
501A ARG* 1.3 63.0 + - - +
503A LYS* 3.4 7.5 + - - +
504A ALA* 3.1 21.3 + - - +
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Residues in contact with ARG 501 (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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497A ARG* 3.2 24.4 + - - +
498A GLU* 3.1 13.9 + - + +
500A SER* 1.3 78.9 - - - +
502A LEU* 1.3 65.3 + - + +
504A ALA* 3.0 22.5 + - - +
505A LYS* 3.8 10.1 + - - +
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Residues in contact with LEU 502 (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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498A GLU* 3.1 10.1 + - + +
499A TRP* 3.7 35.9 - - + +
501A ARG* 1.3 81.0 - - + +
503A LYS* 1.3 58.1 + - - +
505A LYS* 2.9 47.1 + - + +
506A ASP* 3.6 7.8 + - - +
520A VAL* 3.9 17.3 - - + +
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Residues in contact with LYS 503 (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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499A TRP 2.7 21.4 + - - +
500A SER* 3.8 9.2 - - - +
501A ARG 3.2 0.2 - - - -
502A LEU* 1.3 73.5 - - - +
504A ALA* 1.3 61.2 + - - +
505A LYS 3.0 1.1 + - - -
506A ASP* 3.2 35.6 + - - +
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Residues in contact with ALA 504 (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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500A SER 3.1 11.4 + - - +
501A ARG* 3.0 17.3 + - - +
503A LYS* 1.3 77.6 - - - +
505A LYS* 1.3 61.2 + - + +
506A ASP 4.8 1.6 - - - +
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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