Contacts of the helix formed by residues 507 - 520 (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 VAL 507 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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399N TRP* 3.6 29.2 - - + -
437N TYR* 5.2 2.5 - - + +
471N ASP* 3.7 3.6 - - - -
472N ILE* 3.7 18.6 - - - +
475N HIS* 2.3 55.7 + - + -
505N ASP* 3.2 11.8 - - - -
506N ALA* 1.3 82.4 - - - +
508N THR* 1.3 55.1 + - - +
510N GLU* 3.8 0.2 - - - +
772N TRP* 5.7 3.1 - - - -
63V ASP* 5.0 2.2 + - - -
65V TYR* 5.9 7.1 - - + -
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Residues in contact with THR 508 (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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470N ASN* 3.1 2.8 - - - -
471N ASP 2.6 43.5 + - - -
474N ARG* 3.7 21.1 - - - -
475N HIS* 3.3 12.8 + - - +
478N SER* 4.3 1.2 - - - -
500N ASN* 3.9 7.6 - - - -
503N GLN* 6.2 0.2 - - - -
505N ASP* 2.8 21.9 + - - -
507N VAL* 1.3 70.1 - - - +
509N GLY* 1.3 54.3 + - - -
510N GLU 2.7 17.6 + - - -
511N ALA* 2.8 19.2 + - - +
512N ALA 3.7 1.9 + - - -
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Residues in contact with GLY 509 (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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500N ASN 3.4 23.1 + - - -
501N LEU* 3.4 21.7 - - - +
505N ASP* 2.4 22.0 + - - +
508N THR* 1.3 71.2 - - - +
510N GLU* 1.3 62.8 + - - +
511N ALA 3.4 0.2 - - - -
512N ALA* 3.2 16.5 - - - +
513N GLY* 3.2 3.8 + - - -
544N ILE* 4.1 10.6 - - - +
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Residues in contact with GLU 510 (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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475N HIS* 4.0 6.7 - - + -
505N ASP 3.7 3.4 + - - -
506N ALA 3.4 19.1 - - - +
507N VAL 3.8 5.6 - - - +
508N THR 2.7 4.6 + - - -
509N GLY* 1.3 71.6 - - - +
511N ALA* 1.3 55.2 + - - +
513N GLY* 2.7 29.7 + - - -
514N LEU* 3.3 17.9 + - + +
543N LYS* 2.6 43.6 - - + +
544N ILE* 3.2 7.0 + - + +
546N ARG* 4.9 4.5 - - - +
547N GLY* 3.3 24.1 + - - -
768N GLN* 5.2 2.4 - - - +
772N TRP* 5.6 14.2 - - + +
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Residues in contact with ALA 511 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475N HIS* 3.6 8.8 - - - +
478N SER* 3.1 40.3 - - - +
479N LEU* 3.4 27.1 - - + -
508N THR 2.8 6.0 + - - +
510N GLU* 1.3 75.1 - - - +
512N ALA* 1.3 52.8 + - - +
514N LEU* 2.8 13.6 + - - +
515N ALA* 2.7 34.3 + - - +
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Residues in contact with ALA 512 (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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478N SER* 4.5 0.2 - - - -
497N LEU* 3.4 38.3 - - + +
500N ASN* 4.4 1.6 - - - -
501N LEU* 3.5 30.5 - - + +
508N THR 3.7 2.2 + - - -
509N GLY* 3.2 12.8 + - - +
510N GLU 3.0 0.4 + - - -
511N ALA* 1.3 77.8 - - - +
513N GLY* 1.3 58.5 + - - +
514N LEU 2.9 5.9 + - - -
516N LEU* 2.9 31.1 + - + +
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Residues in contact with GLY 513 (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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501N LEU* 4.2 1.9 - - - +
509N GLY 3.2 5.1 + - - -
510N GLU* 2.7 17.4 + - - -
512N ALA* 1.3 72.4 - - - +
514N LEU* 1.3 56.4 + - - -
516N LEU* 5.1 2.0 - - - -
517N GLY 4.3 2.0 + - - -
532N MET* 5.2 2.9 - - - +
544N ILE 5.5 0.9 - - - -
547N GLY* 3.0 28.9 - - - +
548N LEU* 4.2 22.7 - - - +
551N GLY* 3.2 18.0 - - - -
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Residues in contact with LEU 514 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479N LEU* 4.9 11.0 - - + -
510N GLU* 3.9 18.8 - - + +
511N ALA* 2.8 18.5 + - + +
513N GLY* 1.3 82.4 - - - +
515N ALA* 1.3 53.0 + - - +
516N LEU 3.2 1.3 - - - -
517N GLY* 2.7 9.4 + - - -
518N LEU* 2.7 45.4 + - + +
547N GLY* 4.2 7.4 - - - +
550N VAL* 3.6 34.3 - - + -
554N LEU* 3.3 5.6 - - + +
765N VAL* 6.4 1.6 - - + -
772N TRP* 6.4 0.2 - - + -
775N LEU* 5.0 17.0 - - + -
778N PHE* 5.4 7.9 - - + -
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Residues in contact with ALA 515 (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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478N SER 3.8 8.7 - - - +
479N LEU 4.7 1.1 - - - +
482N GLY* 3.2 27.8 - - - +
493N VAL* 4.0 2.3 - - - +
497N LEU* 2.8 28.3 - - + -
511N ALA 2.7 13.3 + - - +
514N LEU* 1.3 74.5 - - - +
516N LEU* 1.3 49.4 - - - +
518N LEU* 2.7 16.0 + - + +
519N VAL* 2.6 36.6 + - - +
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Residues in contact with LEU 516 (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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494N TYR* 3.3 59.9 - - + +
497N LEU* 3.4 17.0 - - + -
498N LYS* 4.3 3.8 - - - +
501N LEU* 5.7 0.9 - - + -
512N ALA* 2.9 22.3 + - + +
513N GLY 5.1 0.2 - - - -
515N ALA* 1.3 77.1 - - - +
517N GLY* 1.3 63.4 + - - +
519N VAL* 3.5 2.7 + - - +
520N MET* 3.2 24.4 + - - +
532N MET* 4.8 12.3 - - + -
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Residues in contact with GLY 517 (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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513N GLY 4.3 0.6 + - - -
514N LEU 2.7 14.2 + - - -
516N LEU* 1.3 74.9 - - - +
518N LEU* 1.3 51.5 + - - -
520N MET 3.4 1.0 - - - -
521N LEU* 2.6 37.4 + - - +
532N MET* 6.0 0.8 - - - -
551N GLY* 3.7 18.2 - - - -
554N LEU* 3.4 24.9 - - - +
555N VAL* 4.1 5.2 + - - -
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Residues in contact with LEU 518 (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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479N LEU 5.2 2.5 - - - +
482N GLY 3.4 28.9 - - - +
483N LEU* 3.9 6.5 - - - +
486N MET* 3.6 28.0 - - + +
487N GLY 2.6 27.0 + - - -
514N LEU* 2.7 24.1 + - + +
515N ALA* 2.7 27.2 + - + +
517N GLY* 1.3 67.3 - - - -
519N VAL* 1.3 60.5 + - - +
521N LEU* 3.0 12.7 - - + +
554N LEU* 3.5 24.0 - - + -
761N VAL* 4.5 10.8 - - + -
765N VAL* 5.9 1.6 - - + -
778N PHE* 5.3 11.2 - - + -
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Residues in contact with VAL 519 (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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485N ALA 3.5 7.7 + - - -
487N GLY 3.5 7.1 - - - +
488N THR 2.7 29.1 - - - +
489N ALA* 3.6 3.9 + - - +
490N ARG* 2.8 51.4 - - - +
493N VAL* 3.5 22.9 - - + +
494N TYR 4.3 4.3 - - - +
515N ALA 2.6 12.9 + - - +
516N LEU 3.6 5.6 - - - +
518N LEU* 1.3 76.4 - - - +
520N MET* 1.3 67.4 + - + +
521N LEU 3.2 2.1 + - - -
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Residues in contact with MET 520 (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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489N ALA* 3.7 31.6 - - + +
490N ARG 4.8 2.7 - - - -
491N GLN* 5.5 2.2 - - - -
494N TYR* 4.8 14.1 - - + -
516N LEU 3.2 13.9 + - - +
517N GLY 3.4 1.8 - - - -
519N VAL* 1.3 85.6 - - + +
521N LEU* 1.3 66.1 + - - +
522N GLY* 3.0 4.2 + - - -
524N LYS* 3.1 60.0 + - + +
525N ASN* 3.9 18.6 - - + +
528N ALA* 5.7 2.9 - - + -
555N VAL* 3.9 4.7 - - + -
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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