Contacts of the helix formed by residues 490 - 503 (chain N) in PDB entry 5GJQ
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 490 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459N ASP* 5.1 9.6 - - - +
485N ALA* 5.5 1.1 - - + -
488N THR* 3.3 7.3 + - - +
489N ALA* 1.3 73.7 - - - +
491N GLN* 1.3 69.9 + - + +
492N ASP* 3.8 14.6 - - + +
493N VAL* 3.0 40.0 + - + +
494N TYR 3.0 2.6 + - - -
519N VAL* 2.8 24.3 - - + +
520N MET* 5.4 0.4 - - - -
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Residues in contact with GLN 491 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489N ALA 4.1 1.0 - - - -
490N ARG* 1.3 71.6 - - + +
492N ASP* 1.3 69.9 + - - +
494N TYR* 2.9 14.2 + - + +
495N ASP* 2.2 45.0 + - + +
520N MET* 5.5 3.7 - - - -
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Residues in contact with ASP 492 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462N LEU* 5.2 8.5 - - + -
490N ARG* 3.2 13.4 - - + +
491N GLN* 1.3 91.1 - - - +
493N VAL* 1.3 60.0 + - - +
495N ASP* 3.7 10.1 - - - -
496N LEU* 2.3 43.8 + - + +
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Residues in contact with VAL 493 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459N ASP* 4.5 11.0 - - - +
462N LEU* 5.4 4.2 - - + +
481N LEU* 4.1 23.3 - - + -
482N GLY* 4.3 1.6 - - - -
485N ALA* 3.6 29.2 - - + -
490N ARG* 3.0 32.6 + - + +
492N ASP* 1.3 78.3 - - + +
494N TYR* 1.3 67.2 + - - +
496N LEU* 5.0 2.0 - - - -
497N LEU* 3.1 29.9 + - + +
515N ALA 4.0 10.3 - - - +
519N VAL* 3.5 20.6 - - + -
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Residues in contact with TYR 494 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490N ARG 3.0 5.5 + - - +
491N GLN* 2.9 16.2 + - + +
493N VAL* 1.3 81.2 - - - +
495N ASP* 1.3 64.9 + - + +
498N LYS* 2.6 67.8 + - + +
516N LEU* 3.3 37.3 - - + +
519N VAL* 4.3 1.0 - - + +
520N MET* 4.8 16.6 - - + -
525N ASN* 6.2 0.7 - - - -
528N ALA* 3.4 27.8 - - + -
531N ASP* 2.5 38.4 + - - +
532N MET* 3.4 20.5 - - + +
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Residues in contact with ASP 495 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491N GLN* 2.2 35.5 + - + +
492N ASP* 3.0 10.1 + - - +
494N TYR* 1.3 73.2 - - + +
496N LEU* 1.3 58.6 + - - +
498N LYS* 2.4 41.2 + - + +
499N THR* 3.1 8.6 + - - -
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Residues in contact with LEU 496 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462N LEU* 4.0 22.9 - - + -
465N LEU* 5.6 3.6 - - + -
466N LYS* 4.9 19.1 - - + +
469N SER* 4.6 4.9 + - - -
492N ASP* 2.3 35.0 + - + +
493N VAL* 4.5 0.9 - - - +
495N ASP* 1.3 71.5 - - - +
497N LEU* 1.3 61.9 + - + +
499N THR* 3.5 7.0 + - - -
500N ASN* 3.1 19.3 + - - +
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Residues in contact with LEU 497 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465N LEU* 6.1 3.6 - - + -
478N SER* 3.8 34.3 - - - +
481N LEU* 5.0 8.5 - - + -
493N VAL* 3.1 27.6 + - + +
496N LEU* 1.3 76.6 - - + +
498N LYS* 1.3 55.8 + - - +
500N ASN* 2.7 10.8 + - + -
501N LEU* 2.1 38.7 + - - -
512N ALA* 3.4 20.9 - - + -
515N ALA* 2.8 37.2 - - + -
516N LEU* 3.3 22.9 - - + +
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Residues in contact with LYS 498 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494N TYR* 2.6 52.9 + - + +
495N ASP* 2.4 31.4 + - + +
497N LEU* 1.3 67.0 - - - +
499N THR* 1.3 49.9 + - - +
501N LEU* 3.2 12.4 - - + +
502N TYR* 2.7 33.0 + - - +
516N LEU* 4.9 2.2 - - - -
531N ASP* 2.8 25.3 + - - -
535N TYR* 3.4 30.5 - - + +
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Residues in contact with THR 499 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469N SER* 5.1 4.3 - - - -
495N ASP* 3.1 9.1 + - - -
496N LEU* 3.8 7.8 - - - -
497N LEU 2.8 1.0 + - - -
498N LYS* 1.3 73.3 - - - +
500N ASN* 1.3 54.4 + - - +
501N LEU 3.0 0.7 - - - -
502N TYR* 2.6 11.0 + - - +
503N GLN* 2.2 48.5 + - - +
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Residues in contact with ASN 500 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465N LEU* 6.4 0.7 - - + -
469N SER* 3.4 16.7 - - - -
474N ARG* 2.9 33.7 - - - -
478N SER* 3.3 15.5 - - - -
496N LEU 3.1 9.5 + - - +
497N LEU* 2.7 18.1 + - + +
499N THR* 1.3 73.9 - - - +
501N LEU* 1.3 65.4 + - - +
503N GLN* 3.3 21.8 - - - +
504N ASP 3.7 1.0 + - - -
505N ASP 4.5 0.3 + - - -
508N THR* 3.9 14.2 - - - -
509N GLY* 3.4 11.0 + - - -
512N ALA* 4.7 0.4 - - - -
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Residues in contact with LEU 501 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497N LEU 2.1 29.0 + - - +
498N LYS* 3.2 11.9 - - - +
500N ASN* 1.3 66.9 - - - +
502N TYR* 1.3 53.0 + - - +
504N ASP* 2.8 31.5 + - - +
509N GLY* 3.4 24.3 - - - +
512N ALA* 3.5 18.5 - - + +
513N GLY* 4.2 3.6 - - - +
516N LEU* 5.7 1.1 - - + -
532N MET* 4.0 15.3 - - + -
535N TYR* 3.5 47.8 - - + -
539N THR* 5.5 0.9 - - + -
544N ILE* 4.1 17.2 - - + +
548N LEU* 3.9 22.0 - - + -
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Residues in contact with TYR 502 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498N LYS 2.7 20.0 + - - +
499N THR* 2.6 13.6 + - - +
501N LEU* 1.3 75.2 - - - +
503N GLN* 1.3 56.3 + - + +
504N ASP* 2.8 32.9 - - - +
535N TYR* 3.4 32.1 - + + +
538N GLU* 4.1 16.2 - - - -
539N THR* 5.0 2.0 - - + -
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Residues in contact with GLN 503 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469N SER* 3.8 23.8 - - - +
470N ASN* 5.5 2.5 - - + -
499N THR* 2.2 47.7 + - - +
500N ASN* 3.3 15.9 - - - +
501N LEU 2.9 0.4 + - - -
502N TYR* 1.3 65.6 - - + +
504N ASP* 1.3 69.8 + - - +
505N ASP* 3.3 7.0 + - + +
508N THR* 6.2 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