Contacts of the helix formed by residues 471 - 486 (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 ASP 471 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470N ASN* 1.3 82.8 - - - +
472N ILE* 1.3 56.3 + - + +
473N VAL* 4.5 3.3 - - + +
474N ARG 2.6 23.4 + - - -
475N HIS 2.6 6.0 + - - -
505N ASP* 3.8 13.2 - - - +
507N VAL* 3.7 12.1 - - - -
508N THR* 2.6 26.3 + - - -
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Residues in contact with ILE 472 (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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399N TRP* 4.4 2.5 - - + -
402N PHE* 3.6 20.4 - - + -
436N ALA* 4.0 15.9 - - + +
437N TYR* 2.9 56.8 - - + -
440N GLY* 4.1 5.4 - - - -
443N LEU* 4.3 1.6 - - - +
471N ASP* 1.3 75.4 - - + +
473N VAL* 1.3 54.4 + - - +
474N ARG 2.6 12.3 + - - -
475N HIS* 2.7 18.3 + - - -
476N GLY* 2.9 13.7 + - - +
477N GLY 4.0 0.3 + - - -
507N VAL* 3.7 6.5 - - - +
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Residues in contact with VAL 473 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436N ALA* 4.9 13.4 + - + +
439N GLU* 5.5 9.9 - - + -
440N GLY* 5.2 2.0 - - - +
443N LEU* 4.0 21.4 - - + +
464N GLN* 5.3 2.9 - - - +
465N LEU* 5.0 6.8 + - - +
468N ALA* 4.6 9.0 - - + +
470N ASN 4.0 7.6 - - - +
471N ASP* 3.2 3.4 + - + +
472N ILE* 1.3 76.8 - - - +
474N ARG* 1.3 57.8 + - - +
477N GLY* 4.5 3.1 + - - -
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Residues in contact with ARG 474 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465N LEU* 4.6 7.5 - - + +
468N ALA 4.0 2.5 - - - +
469N SER* 3.1 13.7 - - - -
470N ASN* 2.4 43.4 + - - +
471N ASP 2.6 6.2 + - - +
472N ILE 2.6 3.8 + - - -
473N VAL* 1.3 73.3 - - - +
475N HIS* 1.3 50.1 + - - +
478N SER* 1.6 50.0 + - - +
500N ASN* 2.9 35.7 - - - -
508N THR* 3.7 4.5 - - - +
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Residues in contact with HIS 475 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399N TRP* 3.4 29.6 - + - -
402N PHE* 4.2 0.2 - + - -
471N ASP 2.6 11.2 + - - +
472N ILE* 2.7 7.5 + - - +
474N ARG* 1.3 67.2 - - - +
476N GLY* 1.3 54.7 + - - +
477N GLY 3.1 0.7 - - - -
478N SER* 2.6 6.4 + - - -
479N LEU* 2.3 65.1 + - + +
507N VAL* 2.3 46.6 + - + -
508N THR* 3.3 11.3 + - - +
510N GLU* 4.0 9.6 - - + -
511N ALA* 3.6 25.7 - - + +
772N TRP* 3.7 21.8 - + - -
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Residues in contact with GLY 476 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402N PHE* 3.8 8.3 - - - -
440N GLY 3.4 18.4 - - - -
443N LEU* 3.3 7.6 - - - -
444N TYR* 2.8 22.3 + - - +
472N ILE 2.9 12.5 + - - -
475N HIS* 1.3 74.4 - - - +
477N GLY* 1.3 56.2 + - - +
479N LEU* 3.2 15.4 - - - +
480N GLY 3.0 15.1 + - - -
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Residues in contact with GLY 477 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443N LEU* 3.3 30.7 - - - +
461N LEU* 5.6 7.0 - - - +
465N LEU* 4.2 16.8 - - - -
472N ILE 4.0 1.0 + - - -
473N VAL 4.7 1.1 - - - -
474N ARG 3.9 2.8 + - - -
475N HIS 3.1 0.4 - - - -
476N GLY* 1.3 72.4 - - - +
478N SER* 1.3 58.2 + - - +
479N LEU 2.9 4.6 + - - -
480N GLY* 3.1 0.7 + - - -
481N LEU* 2.8 32.7 + - - +
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Residues in contact with SER 478 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465N LEU* 4.2 6.0 - - - +
474N ARG* 1.6 61.0 + - - +
475N HIS* 2.6 9.3 + - - -
477N GLY* 1.3 70.1 - - - -
479N LEU* 1.3 59.5 + - - +
481N LEU* 4.3 3.8 + - - +
497N LEU* 3.8 21.7 - - - +
500N ASN* 3.3 9.3 - - - -
508N THR 4.3 1.8 - - - -
511N ALA* 3.1 31.0 - - - +
515N ALA* 3.8 11.4 - - - +
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Residues in contact with LEU 479 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402N PHE* 3.1 36.3 - - + -
444N TYR* 3.4 18.4 - - + -
475N HIS* 2.3 48.8 + - + +
476N GLY* 3.2 17.7 - - - +
477N GLY 2.9 0.8 - - - -
478N SER* 1.3 70.1 - - - +
480N GLY* 1.3 66.8 + - - +
481N LEU 3.0 3.3 + - - -
482N GLY* 3.6 1.9 + - - -
483N LEU* 3.4 16.6 + - - +
510N GLU* 6.3 0.2 - - + -
511N ALA* 3.4 20.6 - - + -
514N LEU* 4.9 11.0 - - + -
515N ALA* 4.7 1.7 - - - +
518N LEU* 5.2 2.3 - - - +
772N TRP* 5.3 0.9 - - - +
774N PRO 5.2 2.9 - - - +
775N LEU* 5.0 13.0 - - + -
778N PHE* 5.3 14.1 - - + -
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Residues in contact with GLY 480 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443N LEU 3.9 8.1 - - - -
444N TYR* 3.6 19.2 - - - +
447N GLY* 4.6 3.8 - - - -
458N ILE* 4.5 2.6 - - - +
461N LEU* 6.3 2.5 - - - -
476N GLY 3.0 8.1 + - - -
477N GLY* 3.8 1.1 - - - -
479N LEU* 1.3 79.5 - - - +
481N LEU* 1.3 65.9 + - - +
483N LEU* 3.0 28.1 - - - +
484N ALA* 3.3 8.7 + - - +
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Residues in contact with LEU 481 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458N ILE* 3.4 28.2 - - + +
461N LEU* 6.4 1.8 - - + -
462N LEU* 4.5 18.2 - - + +
465N LEU* 5.4 4.7 - - + -
477N GLY 2.8 17.7 + - - +
478N SER* 4.4 8.1 - - - +
479N LEU 3.0 1.6 + - - -
480N GLY* 1.3 80.1 - - - +
482N GLY* 1.3 60.5 + - - +
484N ALA 3.1 0.5 + - - -
485N ALA* 2.8 25.3 + - - +
493N VAL* 4.1 28.7 - - + -
497N LEU* 5.0 8.3 - - + -
515N ALA* 5.0 0.7 - - + -
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Residues in contact with GLY 482 (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 3.6 1.0 + - - -
481N LEU* 1.3 81.1 - - - +
483N LEU* 1.3 55.4 + - - +
485N ALA* 3.7 11.2 - - - -
486N MET* 2.5 36.2 + - - +
493N VAL* 4.3 1.6 - - - -
515N ALA* 3.2 36.9 - - - +
518N LEU* 3.4 8.2 - - - +
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Residues in contact with LEU 483 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444N TYR* 3.2 29.2 - - + +
447N GLY* 3.4 14.1 - - - +
448N LEU* 3.3 33.4 - - + +
451N ALA* 3.8 19.6 - - + +
452N ASN 4.5 0.3 + - - -
479N LEU 3.4 8.5 + - - +
480N GLY* 3.0 20.4 - - - +
482N GLY* 1.3 78.5 - - - +
484N ALA* 1.3 60.7 + - - +
486N MET* 3.3 19.5 - - + +
518N LEU* 3.9 8.1 - - - +
778N PHE* 4.4 26.7 - - + -
781N LEU* 5.8 8.3 - - + -
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Residues in contact with ALA 484 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447N GLY* 4.8 5.6 - - - -
450N HIS 3.7 13.5 - - - +
451N ALA* 3.6 4.0 - - - +
452N ASN* 3.0 40.9 + - - +
454N GLY* 4.1 20.4 - - - +
455N GLY* 4.3 4.6 - - - +
458N ILE* 4.4 6.5 - - + -
480N GLY 3.3 5.1 + - - +
481N LEU 3.1 6.4 + - - +
483N LEU* 1.3 76.5 - - - +
485N ALA* 1.3 59.1 + - - +
486N MET 3.0 12.4 + - - +
488N THR* 5.1 2.4 - - - -
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Residues in contact with ALA 485 (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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455N GLY* 6.1 2.0 - - - -
458N ILE* 4.5 6.4 - - + +
459N ASP* 5.6 0.7 - - - +
481N LEU 2.8 17.2 + - - +
482N GLY* 3.3 9.6 - - - -
484N ALA* 1.3 75.2 - - - +
486N MET* 1.3 62.7 + - - +
487N GLY 3.3 0.2 + - - -
488N THR* 2.9 36.4 + - - +
490N ARG* 5.5 0.7 - - + -
493N VAL* 3.6 34.1 - - + -
519N VAL* 3.5 3.8 - - - -
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Residues in contact with MET 486 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258N GLN* 5.0 9.7 - - - +
451N ALA* 5.3 6.5 - - + -
452N ASN* 5.4 2.4 - - - +
482N GLY 2.5 20.6 + - - +
483N LEU* 3.3 17.3 - - + +
484N ALA 3.0 7.2 - - - +
485N ALA* 1.3 71.9 - - - +
487N GLY* 1.3 62.8 + - - +
488N THR* 3.0 6.2 + - - -
518N LEU* 3.3 24.5 - - + +
521N LEU* 3.8 16.4 - - + -
757N MET* 5.8 0.2 - - - -
758N PRO* 3.5 31.4 - - + -
761N VAL* 3.5 37.9 - - + -
781N LEU* 4.8 12.1 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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