Contacts of the helix formed by residues 455 - 472 (chain R) in PDB entry 6CNB
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 GLU 455 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393R LEU* 5.1 0.7 - - - +
396R ILE* 5.0 6.7 - - + +
454R SER* 1.3 85.0 + - - +
456R ASP* 1.3 65.8 + - - +
458R SER* 3.1 19.2 + - - -
459R LYS* 3.3 7.4 + - - +
483R ILE* 4.0 16.2 - - + -
486R ILE* 4.6 11.8 - - - +
546R ARG* 2.6 38.0 + - - -
588R THR* 3.5 39.9 + - + +
591R TYR* 3.6 21.6 - - + +
592R LEU* 3.9 17.5 - - + +
595R VAL* 4.3 3.1 - - - +
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Residues in contact with ASP 456 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454R SER* 3.4 6.5 + - - +
455R GLU* 1.3 78.6 - - - +
457R ASP* 1.3 64.8 + - - +
458R SER 2.9 5.9 + - - -
460R LEU* 3.1 28.7 + - + +
591R TYR* 2.8 50.5 - - - +
594R LYS* 3.2 28.4 - - - +
595R VAL* 3.2 12.6 - - + +
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Residues in contact with ASP 457 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435R PRO* 3.4 40.0 - - + +
437R THR* 4.0 13.4 - - + +
452R ALA* 5.2 0.4 - - - -
453R LYS* 5.4 6.6 + - - +
454R SER* 4.0 16.3 + - - +
455R GLU 3.5 0.2 - - - -
456R ASP* 1.3 82.8 - - - +
458R SER* 1.3 62.7 + - - +
460R LEU* 4.3 10.3 - - - +
461R ALA* 3.3 23.9 - - - +
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Residues in contact with SER 458 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396R ILE* 5.2 5.1 - - - +
398R ALA* 4.6 2.8 - - - +
437R THR* 5.6 0.4 - - - -
449R VAL* 3.5 18.9 - - - +
452R ALA* 3.8 15.5 - - - +
454R SER 3.4 15.1 + - - -
455R GLU* 3.2 15.7 - - - -
456R ASP 2.9 2.4 + - - -
457R ASP* 1.3 76.2 - - - +
459R LYS* 1.3 57.3 + - - -
461R ALA* 4.2 0.5 - - - +
462R SER* 2.4 37.7 + - - -
481R PHE* 3.3 19.3 - - - -
483R ILE* 5.4 1.2 - - - +
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Residues in contact with LYS 459 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455R GLU 3.3 5.9 + - - +
458R SER* 1.3 79.7 + - - +
460R LEU* 1.3 64.7 + - - +
462R SER* 3.3 7.1 - - - -
463R ARG* 2.9 25.4 + - + +
478R PHE* 3.1 33.2 - - + -
481R PHE* 3.0 44.5 - - + +
592R LEU* 4.4 12.8 - - + -
595R VAL* 3.6 17.2 - - + +
596R SER 3.5 16.8 - - - +
597R ASP* 3.1 36.7 + - - +
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Residues in contact with LEU 460 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435R PRO* 4.8 13.7 - - + -
456R ASP* 3.1 25.5 + - + +
457R ASP* 4.3 6.1 - - - +
459R LYS* 1.3 79.9 - - - +
461R ALA* 1.3 68.9 + - + +
463R ARG* 3.3 11.4 + - - +
464R LYS* 3.3 39.5 + - - +
594R LYS 5.9 1.3 - - - +
595R VAL* 3.4 21.7 - - + +
605R VAL* 4.5 17.5 - - + +
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Residues in contact with ALA 461 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432R ILE* 5.0 2.2 - - + -
435R PRO* 3.9 16.2 - - + -
437R THR* 3.6 23.3 - - - +
457R ASP 3.3 18.8 + - - +
458R SER 4.2 0.2 - - - +
460R LEU* 1.3 77.1 - - - +
462R SER* 1.3 59.1 + - - +
464R LYS* 2.7 35.4 + - + +
465R TYR* 2.9 24.8 + - + -
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Residues in contact with SER 462 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400R VAL* 4.4 8.0 - - - +
447R MET* 4.8 8.2 - - - +
449R VAL* 3.7 24.1 - - - +
458R SER 2.4 31.1 + - - -
459R LYS* 3.3 10.8 - - - -
461R ALA* 1.3 75.8 - - - +
463R ARG* 1.3 63.2 + - - +
465R TYR* 3.3 28.5 + - - +
466R ALA* 3.6 5.2 + - - +
478R PHE* 4.0 20.8 - - - -
481R PHE* 3.9 1.6 - - - -
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Residues in contact with ARG 463 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459R LYS* 2.9 14.3 + - + +
460R LEU* 3.6 9.6 - - - +
461R ALA 3.2 0.2 - - - -
462R SER* 1.3 72.2 - - - +
464R LYS* 1.3 61.1 + - - +
466R ALA* 2.9 28.3 + - - +
470R GLN* 5.1 1.1 - - - -
478R PHE* 3.1 45.4 - - - +
595R VAL* 6.2 0.7 - - + -
596R SER 3.9 10.0 + - - +
597R ASP 3.7 6.3 + - - -
598R ASP 2.3 34.9 + - - -
599R PRO* 3.4 14.2 - - - -
601R ASN* 2.2 54.5 + - - +
602R LEU* 3.2 35.2 - - + +
605R VAL* 3.7 13.0 - - + -
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Residues in contact with LYS 464 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432R ILE* 6.3 2.7 - - + -
434R GLU 5.3 4.0 - - - +
435R PRO* 5.3 6.3 - - + -
460R LEU* 3.3 34.9 + - + +
461R ALA* 2.7 27.7 + - + +
463R ARG* 1.3 73.8 - - - +
465R TYR* 1.3 59.1 + - + -
467R ARG* 3.0 16.0 + - - +
602R LEU* 4.8 1.3 - - - -
605R VAL* 2.3 38.3 + - - +
606R ASP* 4.9 1.8 - - - +
607R ASP* 3.0 43.4 - - - +
610R LEU* 3.1 27.3 - - + +
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Residues in contact with TYR 465 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430R MET* 4.3 23.5 - - + +
431R ARG* 4.0 18.7 - - - -
432R ILE* 3.9 8.4 - - + +
437R THR* 3.2 21.5 + - - -
438R THR* 2.8 39.8 + - - -
439R ALA* 3.5 19.7 - - + -
440R LEU 5.6 2.5 - - - +
447R MET* 4.6 15.3 - - - -
449R VAL* 6.4 0.2 - - + -
461R ALA* 2.9 42.7 + - + -
462R SER* 3.5 18.2 - - - +
463R ARG 3.1 0.4 - - - -
464R LYS* 1.3 77.7 - - + +
466R ALA* 1.3 60.4 + - - +
467R ARG 3.1 1.1 + - - -
468R ILE* 3.5 22.9 + - + +
469R ILE* 4.1 9.6 + - - +
610R LEU* 5.3 0.9 - - - -
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Residues in contact with ALA 466 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402R LEU* 4.5 12.6 - - + -
447R MET* 5.6 2.6 - - + +
462R SER 3.6 4.5 + - - +
463R ARG* 2.9 24.2 + - - +
465R TYR* 1.3 76.1 - - - +
467R ARG* 1.3 58.8 + - - +
468R ILE 3.3 0.2 - - - -
469R ILE* 4.0 9.4 - - - +
470R GLN* 2.9 39.0 + - + +
476R ALA* 4.0 19.7 - - + +
477R LYS 5.2 2.0 - - - +
478R PHE* 5.9 3.1 - - + -
602R LEU* 4.0 1.6 - - - -
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Residues in contact with ARG 467 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463R ARG 3.3 2.8 + - - -
464R LYS* 3.0 19.7 + - - +
466R ALA* 1.3 76.2 - - - +
468R ILE* 1.3 52.8 + - - +
470R GLN 5.3 1.0 + - - -
471R LYS* 2.5 78.4 + - - +
602R LEU* 3.4 30.8 - - + +
603R GLU* 2.7 45.1 + - - +
606R ASP* 3.1 38.6 + - + +
610R LEU* 3.5 15.0 - - + -
611R ASN* 4.5 2.4 + - - +
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Residues in contact with ILE 468 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411R VAL* 5.2 8.5 - - + +
414R HIS 3.8 10.1 - - - +
415R ALA* 4.3 21.8 - - + -
416R ARG 5.6 0.4 - - - +
417R ASN 5.7 0.4 - - - +
430R MET* 4.7 20.2 - - + -
464R LYS 5.4 0.2 - - - +
465R TYR* 3.5 14.7 + - + +
466R ALA 3.3 0.6 - - - -
467R ARG* 1.3 77.2 - - - +
469R ILE* 1.3 58.5 + - + +
471R LYS* 3.1 2.9 + - - +
472R ILE* 2.4 62.0 + - + +
610R LEU* 3.5 33.4 - - + +
613R HIS* 5.4 7.6 - - + +
614R LEU* 6.5 1.1 - - + -
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Residues in contact with ILE 469 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402R LEU* 3.7 27.6 - - + -
404R CYS* 5.8 0.4 - - - -
406R LEU* 3.7 21.1 - - + -
411R VAL* 4.5 22.4 - - + -
430R MET* 5.8 4.3 - - + -
441R ILE* 4.6 9.2 - - + -
447R MET* 5.7 1.6 - - + -
465R TYR 4.4 11.4 - - - +
466R ALA* 3.6 5.4 + - - +
467R ARG 3.5 0.2 - - - -
468R ILE* 1.3 76.4 - - + +
470R GLN* 1.3 56.1 + - - +
472R ILE 2.6 10.0 + - - -
473R GLY* 2.4 39.2 + - - +
474R PHE* 3.3 33.0 - - + +
476R ALA* 3.4 14.1 - - + -
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Residues in contact with GLN 470 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463R ARG* 5.1 0.5 - - - -
466R ALA* 2.9 23.0 + - - +
467R ARG* 5.3 2.4 + - - +
469R ILE* 1.3 73.5 - - - +
471R LYS* 1.3 57.0 + - - +
473R GLY 4.4 2.4 - - - +
474R PHE 3.8 6.3 - - - -
475R ALA 2.7 24.9 + - - +
476R ALA* 2.4 34.6 + - + +
477R LYS* 3.8 11.5 - - - +
599R PRO 4.3 12.8 + - - +
600R ASP* 5.6 1.6 + - - +
602R LEU* 3.0 38.4 - - + +
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Residues in contact with LYS 471 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467R ARG* 2.5 67.7 + - - +
468R ILE 3.3 2.7 - - - +
469R ILE 3.4 0.2 - - - -
470R GLN* 1.3 77.6 - - - +
472R ILE* 1.3 64.6 + - + +
610R LEU* 3.6 25.8 - - + -
611R ASN* 2.7 27.7 + - - +
614R LEU* 3.9 24.0 - - + -
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Residues in contact with ILE 472 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410R THR* 5.1 15.0 - - + +
411R VAL* 6.0 3.1 - - - -
413R LEU* 6.1 1.3 - - + -
414R HIS* 3.6 49.8 - - + +
468R ILE* 2.4 40.5 + - + +
469R ILE 2.6 3.9 + - - -
471R LYS* 1.3 82.0 - - + +
473R GLY* 1.3 65.7 + - - +
610R LEU* 6.0 0.7 - - + -
614R LEU* 4.5 16.6 - - + -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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