Contacts of the helix formed by residues 456 - 469 (chain O) in PDB entry 6NRB
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 456 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A LYS* 4.2 8.8 - - - +
433A ARG* 3.0 30.4 + - - +
471D LEU* 4.4 12.8 - - - +
472D ASN* 5.4 8.8 + - - +
451O ASP* 4.3 2.6 - - - +
454O GLY 3.7 11.7 - - - +
455O PHE* 1.3 67.8 - - - +
457O ALA* 1.3 66.3 + - - +
458O THR 3.6 0.2 - - - -
459O ASN* 3.0 26.3 + - + +
460O ILE* 3.0 28.0 + - - +
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Residues in contact with ALA 457 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LYS* 3.7 12.2 - - - +
447O ARG* 3.4 50.5 - - + +
450O CYS* 3.9 8.3 - - - -
451O ASP* 3.5 12.8 + - + -
455O PHE 3.1 5.5 + - - -
456O ASP* 1.3 69.1 - - - +
458O THR* 1.3 59.2 + - - +
459O ASN 3.2 0.2 + - - -
460O ILE* 3.2 2.1 + - - +
461O LEU* 2.7 40.0 + - - +
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Residues in contact with THR 458 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A GLN* 5.4 1.8 - - - +
111A LYS* 3.5 18.9 + - - +
432A SER 4.1 0.7 - - - -
433A ARG* 4.0 9.9 + - - +
436A LEU* 3.5 31.4 - - + +
447O ARG* 3.2 29.8 - - - +
457O ALA* 1.3 74.4 - - - +
459O ASN* 1.3 72.6 + - - +
461O LEU* 4.2 7.6 - - - -
462O ASN* 2.4 55.3 + - - +
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Residues in contact with ASN 459 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A SER* 2.0 41.2 + - - +
433A ARG* 2.8 53.4 + - - +
471D LEU* 5.6 1.2 - - - +
456O ASP* 3.0 19.7 - - + +
457O ALA 3.2 0.2 - - - -
458O THR* 1.3 83.7 + - - +
460O ILE* 1.3 57.9 + - + +
463O LYS* 2.4 48.1 + - - +
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Residues in contact with ILE 460 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414O MET* 3.4 4.2 - - + +
450O CYS* 3.9 9.6 - - - -
455O PHE* 3.5 24.9 - - + +
456O ASP 3.0 19.1 + - - +
457O ALA 3.8 1.8 - - - +
459O ASN* 1.3 79.0 - - + +
461O LEU* 1.3 66.3 + - - +
463O LYS* 4.1 11.0 - - - +
464O LEU 3.4 3.5 + - - -
477O VAL* 3.6 27.1 - - + -
482O GLU 3.0 27.4 - - - +
483O ASP* 3.8 10.3 - - + -
484O ILE* 3.1 48.7 - - + +
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Residues in contact with LEU 461 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414O MET* 3.4 34.6 - - + +
443O GLU* 3.2 38.4 - - + +
446O PRO* 3.6 30.1 - - + -
447O ARG* 3.5 38.1 - - + +
450O CYS* 5.6 0.4 - - - -
457O ALA* 2.7 30.0 + - - +
458O THR* 3.5 2.7 - - - +
460O ILE* 1.3 75.9 - - + +
462O ASN* 1.3 64.9 + - - +
464O LEU 3.0 1.4 + - - -
465O ARG* 3.0 23.9 + - - +
477O VAL* 5.0 0.9 - - + -
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Residues in contact with ASN 462 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432A SER 3.0 25.8 - - - +
435A GLN* 2.8 44.1 - - - +
436A LEU* 4.0 10.9 - - - +
421O ARG* 5.6 0.2 - - - +
443O GLU* 5.0 3.0 + - - -
447O ARG* 5.7 2.0 + - - +
458O THR* 2.4 44.7 + - - +
461O LEU* 1.3 75.1 - - - +
463O LYS* 1.3 53.7 + - - +
465O ARG* 3.0 23.9 - - - +
466O ALA* 2.7 31.2 + - - +
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Residues in contact with LYS 463 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A GLY* 4.7 1.6 - - - -
432A SER* 3.8 14.5 - - - +
459O ASN* 2.4 44.4 + - - +
460O ILE* 3.5 17.6 - - - +
461O LEU 3.0 0.2 + - - -
462O ASN* 1.3 70.9 - - - +
464O LEU* 1.3 61.7 + - + +
466O ALA* 3.7 6.1 - - - +
467O ARG* 3.6 16.7 + - - +
483O ASP* 5.5 3.2 - - - +
484O ILE* 3.5 37.3 - - + +
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Residues in contact with LEU 464 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414O MET* 3.4 29.6 - - + -
460O ILE 3.4 0.2 + - - -
461O LEU 3.0 3.0 + - - -
463O LYS* 1.3 77.0 - - - +
465O ARG* 1.3 53.0 - - - +
466O ALA 3.2 0.7 - - - -
467O ARG* 2.7 43.5 + - - +
468O HIS* 2.2 48.6 + - - +
475O TYR* 3.4 13.9 - - + -
476O GLY* 3.4 29.2 - - - +
484O ILE* 3.5 37.0 - - + -
485O ALA 3.8 3.6 - - - +
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Residues in contact with ARG 465 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428A THR* 3.9 13.1 - - + +
435A GLN* 2.8 43.3 - - - +
414O MET* 2.9 24.6 + - + +
415O GLU* 5.5 1.1 - - - +
417O SER* 3.5 0.2 - - - -
418O LYS* 2.9 38.7 - - + +
421O ARG* 3.1 38.2 - - - +
443O GLU* 2.8 30.7 + - - -
461O LEU 3.0 16.5 + - - +
462O ASN* 3.0 22.6 + - - +
464O LEU* 1.3 73.1 - - - +
466O ALA* 1.3 61.1 + - - +
468O HIS* 3.5 9.1 - - + +
469O ALA* 2.8 29.3 + - - +
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Residues in contact with ALA 466 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A THR 3.4 13.9 + - - +
429A SER* 3.3 24.8 - - - +
430A MET 4.3 1.6 - - - +
431A GLY* 3.9 12.3 - - - -
462O ASN 2.7 16.2 + - - +
463O LYS 3.7 7.0 - - - +
465O ARG* 1.3 76.8 - - - +
467O ARG* 1.3 59.4 + - - +
469O ALA* 3.7 7.6 - - - +
470O GLN* 3.4 21.9 + - - +
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Residues in contact with ARG 467 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463O LYS* 3.6 8.0 + - - +
464O LEU* 2.7 41.1 + - - +
466O ALA* 1.3 72.6 - - - +
468O HIS* 1.3 57.2 + - - -
469O ALA 3.1 1.8 - - - -
470O GLN* 3.0 38.3 + - + +
471O GLY 3.5 6.1 + - - -
475O TYR* 3.4 45.4 - - + +
484O ILE* 3.9 22.4 - - - +
485O ALA* 5.5 3.4 + - - +
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Residues in contact with HIS 468 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411O ALA 3.9 2.0 - - - -
414O MET* 3.5 23.8 - - + +
415O GLU* 3.0 37.4 - - + +
418O LYS* 4.4 0.9 + - - -
464O LEU* 2.2 47.7 + - + +
465O ARG* 3.2 11.2 + - - -
467O ARG* 1.3 64.2 - - - +
469O ALA* 1.3 61.6 + - - +
470O GLN 2.9 6.9 + - - -
471O GLY* 4.2 5.7 + - - -
472O GLY 3.0 24.1 + - - +
473O THR* 3.1 32.8 - - - -
475O TYR* 3.2 40.1 + + + +
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Residues in contact with ALA 469 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A THR* 4.6 6.7 - - + +
429A SER* 5.2 10.1 - - - +
418O LYS* 3.5 32.3 + - + +
465O ARG 2.8 16.3 + - - +
466O ALA* 3.7 11.9 - - - +
467O ARG 3.1 0.6 - - - -
468O HIS* 1.3 75.7 - - - +
470O GLN* 1.3 62.3 + - + +
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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