Contacts of the helix formed by residues 490 - 504 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468B GLU 2.7 28.5 + - - -
469B GLU 2.9 16.9 + - - -
471B TRP* 3.5 36.1 - - - -
488B ILE 3.4 1.4 + - - -
489B PRO* 1.3 76.8 - - - +
491B LYS* 1.3 64.9 + - - +
492B ARG* 3.4 3.8 + - - -
493B ARG* 2.9 19.0 + - - +
494B VAL* 3.0 21.7 + - - +
523B TYR* 4.0 0.4 - - - -
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Residues in contact with LYS 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471B TRP* 3.6 30.7 - - + -
490B SER* 1.3 73.0 - - - +
492B ARG* 1.3 64.8 + - - +
494B VAL* 3.4 0.5 + - - +
495B GLU* 2.5 67.7 + - - +
522B SER* 3.6 15.7 - - - +
523B TYR* 3.9 25.3 - - + +
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Residues in contact with ARG 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468B GLU* 4.1 9.0 - - + +
469B GLU* 5.2 3.8 - - - +
471B TRP* 5.3 0.6 - - - -
490B SER* 3.4 8.4 + - - +
491B LYS* 1.3 79.6 - - - +
493B ARG* 1.3 57.8 + - - +
495B GLU* 4.0 3.5 - - - +
496B ARG* 2.9 35.2 + - - +
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Residues in contact with ARG 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468B GLU 4.8 0.2 + - - -
469B GLU* 2.4 67.6 + - - +
470B TRP* 3.4 35.1 - - - +
489B PRO* 3.8 16.5 - - + +
490B SER* 2.9 21.2 + - - +
492B ARG* 1.3 78.1 - - - +
494B VAL* 1.3 62.5 + - - +
496B ARG* 3.6 4.8 + - - +
497B ARG* 3.3 21.5 + - - +
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Residues in contact with VAL 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B PHE* 3.7 23.3 - - + -
489B PRO* 3.6 31.6 - - + +
490B SER 3.0 18.8 + - - +
491B LYS 3.8 0.2 - - - +
493B ARG* 1.3 76.8 - - - +
495B GLU* 1.3 62.5 + - - +
497B ARG* 3.2 10.1 + - - +
498B GLU* 3.1 23.6 + - + +
521B LEU 3.9 11.4 - - - +
522B SER* 3.5 26.9 - - - -
523B TYR* 4.0 4.7 - - + -
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Residues in contact with GLU 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491B LYS* 2.5 52.4 + - - +
492B ARG* 4.1 3.2 - - - +
494B VAL* 1.3 72.4 - - - +
496B ARG* 1.3 57.9 + - - +
498B GLU* 2.9 9.5 + - - +
499B TRP* 2.7 50.3 + - + -
520B VAL* 4.1 25.1 - - + +
521B LEU* 4.8 0.2 - - - -
522B SER* 2.9 30.2 + - - +
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Residues in contact with ARG 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492B ARG 2.9 20.3 + - - +
493B ARG* 3.9 5.6 - - - +
495B GLU* 1.3 76.4 - - - +
497B ARG* 1.3 58.3 + - - +
499B TRP* 4.1 8.0 - - - +
500B SER* 3.0 29.8 + - - -
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Residues in contact with ARG 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493B ARG 3.3 10.1 + - - +
494B VAL* 3.2 11.5 + - - +
495B GLU 3.0 0.6 - - - -
496B ARG* 1.3 80.5 - - - +
498B GLU* 1.3 65.0 + - - +
500B SER* 3.4 7.8 - - - -
501B ARG* 3.2 20.4 + - - +
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Residues in contact with GLU 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494B VAL* 3.1 20.1 + - + +
495B GLU 2.9 7.5 + - - +
497B ARG* 1.3 78.4 - - - +
499B TRP* 1.3 65.8 + - - +
500B SER 3.1 1.3 - - - -
501B ARG* 3.2 19.2 + - - +
502B LEU* 3.2 17.8 + - - +
520B VAL* 3.7 28.9 - - + +
521B LEU 4.2 19.6 + - - +
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Residues in contact with TRP 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696A SER* 4.4 4.0 + - - -
698A GLU* 3.5 39.0 - - + +
699A GLU* 3.4 31.9 - - + -
702A HIS* 3.7 29.2 - + + -
495B GLU* 2.7 43.7 + - + +
496B ARG* 4.1 6.7 - - - +
498B GLU* 1.3 72.5 - - - +
500B SER* 1.3 52.0 + - - +
502B LEU* 3.2 17.4 + - + +
503B LYS* 2.8 36.7 + - - +
520B VAL* 3.5 43.0 - - + +
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Residues in contact with SER 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496B ARG 3.0 19.8 + - - -
497B ARG* 3.4 10.5 - - - -
498B GLU 3.1 0.2 - - - -
499B TRP* 1.3 77.9 - - - +
501B ARG* 1.3 60.8 + - - +
503B LYS* 3.4 6.9 + - - +
504B ALA* 3.2 20.8 + - - +
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Residues in contact with ARG 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497B ARG 3.2 9.6 + - - +
498B GLU* 3.2 16.2 + - - +
500B SER* 1.3 79.4 - - - +
502B LEU* 1.3 64.1 + - + +
504B ALA* 3.1 22.4 + - - +
505B LYS* 3.7 10.5 + - - +
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Residues in contact with LEU 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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702A HIS* 4.0 29.6 - - + +
706A ARG* 2.8 25.4 + - - +
498B GLU* 3.2 9.7 + - - +
499B TRP* 3.2 23.7 + - + +
501B ARG* 1.3 81.5 - - + +
503B LYS* 1.3 58.2 + - - +
505B LYS* 3.0 34.0 + - - +
506B ASP* 3.5 0.8 - - - +
520B VAL* 3.7 31.2 - - + +
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Residues in contact with LYS 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554A GLU* 5.4 2.7 - - - +
555A PHE* 6.1 0.2 - - - -
705A LYS* 4.3 9.0 - - - +
499B TRP 2.8 21.7 + - - +
500B SER* 3.8 7.6 - - - +
502B LEU* 1.3 71.1 - - - +
504B ALA* 1.3 64.8 + - - +
505B LYS 3.2 0.5 + - - -
506B ASP* 3.2 34.8 + - - +
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Residues in contact with ALA 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500B SER 3.2 12.2 + - - +
501B ARG* 3.1 17.6 + - - +
502B LEU 3.1 0.6 - - - -
503B LYS* 1.3 78.1 - - - +
505B LYS* 1.3 60.9 + - + +
506B ASP 4.7 2.1 - - - +
508B GLY* 5.9 0.2 - - - -
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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
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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