Contacts of the helix formed by residues 448 - 466 (chain B) in PDB entry 3BYH
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 MET 448 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446B ILE* 3.2 20.0 - - - +
447B LYS* 1.3 94.3 - - + +
449B PRO* 1.3 75.4 - - + +
450B PHE* 4.5 8.1 - - + +
451B ARG* 3.3 33.9 + - + +
452B LYS* 3.7 0.6 + - - -
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Residues in contact with PRO 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447B LYS 3.2 9.4 - - - +
448B MET* 1.3 87.1 - - + +
450B PHE* 1.3 66.6 + - + +
452B LYS* 3.0 25.2 + - + +
453B VAL* 3.1 20.7 + - + +
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Residues in contact with PHE 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448B MET* 3.2 7.5 - - + -
449B PRO* 1.3 82.2 - - + +
451B ARG* 1.3 75.8 + - + +
452B LYS 3.3 0.2 + - - -
453B VAL* 3.3 8.5 + - + +
454B GLU* 3.0 63.3 + - + +
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Residues in contact with ARG 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B SER* 3.1 36.4 + - - +
446B ILE* 3.8 12.8 - - + -
448B MET* 3.3 33.2 + - + +
449B PRO 3.2 1.0 - - - -
450B PHE* 1.3 97.7 - - + +
452B LYS* 1.3 60.6 + - - +
454B GLU* 3.9 5.6 - - - +
455B ASN* 3.3 31.1 + - - +
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Residues in contact with LYS 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B ARG 4.9 0.9 - - - +
420B ASN* 4.0 32.8 - - + +
446B ILE* 3.5 42.8 + - + -
447B LYS* 4.9 5.9 + - - +
448B MET 4.0 3.4 - - - +
449B PRO* 3.0 16.6 + - + +
451B ARG* 1.3 76.0 - - - +
453B VAL* 1.3 65.1 + - - +
455B ASN* 3.3 4.3 + - - +
456B CYS* 3.2 27.5 + - - -
479B VAL* 4.1 26.7 - - + -
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Residues in contact with VAL 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B PRO* 3.1 14.9 + - + +
450B PHE* 3.8 11.4 - - + +
452B LYS* 1.3 77.0 - - + +
454B GLU* 1.3 57.5 + - - +
456B CYS* 3.5 2.2 + - - +
457B ASN* 3.0 43.3 + - - +
476B ASN* 4.6 22.4 - - + +
479B VAL* 4.2 20.9 - - + -
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Residues in contact with GLU 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B HIS* 3.5 38.5 + - + +
442B SER* 4.5 10.7 + - - -
450B PHE* 3.0 49.7 + - + +
451B ARG* 3.9 5.8 - - - +
453B VAL* 1.3 75.4 - - - +
455B ASN* 1.3 65.9 + - - +
457B ASN* 3.3 7.6 + - + +
458B GLN* 3.2 20.8 + - - +
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Residues in contact with ASN 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420B ASN 3.2 26.9 + - - +
421B GLY* 4.0 8.3 - - - -
422B TRP* 4.2 6.7 - - - +
425B LEU* 4.1 14.5 - - + +
440B HIS 4.3 1.7 - - - +
441B ALA* 3.3 11.4 - - - +
442B SER* 3.0 45.2 + - - -
446B ILE* 3.6 4.9 - - - +
451B ARG 3.3 15.1 + - - +
452B LYS 3.3 2.2 + - - +
454B GLU* 1.3 78.4 - - - +
456B CYS* 1.3 62.2 + - - +
458B GLN* 3.1 8.7 + - - +
459B VAL* 3.1 25.1 + - - +
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Residues in contact with CYS 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419B ARG 3.7 1.1 - - - -
421B GLY* 3.6 26.7 - - - -
452B LYS 3.2 17.4 + - - +
453B VAL 4.0 1.3 - - - +
455B ASN* 1.3 80.0 - - - +
457B ASN* 1.3 58.4 + - - +
459B VAL* 3.2 10.8 + - - +
460B ILE* 3.0 30.3 + - - +
475B GLY* 3.1 25.1 - - - +
478B ILE* 3.6 23.9 - - + +
479B VAL* 3.6 18.6 - - + -
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Residues in contact with ASN 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A VAL 5.3 3.5 - - - +
46A GLY* 4.7 10.0 - - - -
453B VAL* 3.0 35.0 + - - +
454B GLU* 3.8 7.2 - - - +
455B ASN 3.2 0.4 - - - -
456B CYS* 1.3 73.4 - - - +
458B GLN* 1.3 60.0 + - - +
460B ILE* 3.4 5.4 + - - +
461B LYS* 2.9 27.7 + - - +
474B ALA* 3.9 8.5 - - - +
475B GLY* 2.7 34.6 - - - +
476B ASN* 4.6 0.6 + - - +
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Residues in contact with GLN 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425B LEU* 4.2 6.7 - - + +
435B SER 4.3 1.4 + - - -
436B VAL* 3.5 18.5 - - - +
437B ASN* 2.8 54.2 - - - +
440B HIS* 4.2 16.6 - - + +
441B ALA* 4.5 4.7 - - - +
454B GLU 3.2 10.8 + - - +
455B ASN* 3.1 11.8 + - - +
457B ASN* 1.3 73.6 - - - +
459B VAL* 1.3 65.7 + - - +
461B LYS* 4.2 17.7 - - + +
462B ILE* 2.9 43.2 + - + +
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Residues in contact with VAL 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B GLY* 3.8 17.5 - - - +
424B LEU* 3.8 18.4 - - + -
425B LEU* 3.7 18.2 - - + +
428B LEU* 3.9 19.1 - - + +
455B ASN 3.1 15.3 + - - +
456B CYS* 3.3 13.7 - - - +
457B ASN 3.2 0.2 - - - -
458B GLN* 1.3 78.1 - - - +
460B ILE* 1.3 61.9 + - - +
462B ILE 4.0 0.3 - - - -
463B GLY* 3.0 19.2 + - - -
478B ILE* 3.9 9.4 - - + -
489B LEU* 3.7 32.7 - - + +
493B LEU* 6.4 0.2 - - + -
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Residues in contact with ILE 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLY 6.3 1.3 - - - -
47A MET* 6.4 0.7 - - - -
456B CYS 3.0 18.3 + - - +
457B ASN* 3.7 9.6 - - - +
459B VAL* 1.3 76.0 - - + +
461B LYS* 1.3 66.2 + - - +
463B GLY* 3.1 2.6 + - - -
464B LYS* 2.9 47.9 + - + +
470B LEU* 4.7 14.2 - - + +
473B VAL* 4.7 6.1 - - + +
474B ALA* 3.7 35.4 - - - +
475B GLY* 4.1 0.9 - - - +
478B ILE* 4.0 19.7 - - + -
485B LEU* 4.7 18.2 - - + -
489B LEU* 5.0 5.8 - - + -
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Residues in contact with LYS 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457B ASN 2.9 18.0 + - - +
458B GLN* 3.2 18.1 + - + +
460B ILE* 1.3 76.9 - - - +
462B ILE* 1.3 66.9 + - + +
464B LYS* 3.1 8.9 + - - +
465B GLN* 2.9 48.9 + - + +
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Residues in contact with ILE 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425B LEU* 4.6 1.1 - - + -
428B LEU* 4.0 25.6 - - + -
435B SER* 3.4 44.0 - - - +
436B VAL* 3.7 19.7 - - + -
458B GLN* 2.9 40.3 + - + +
461B LYS* 1.3 77.3 - - + +
463B GLY* 1.3 61.5 + - - +
465B GLN* 3.3 20.3 + - - +
466B LEU* 3.0 33.2 + - + +
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Residues in contact with GLY 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428B LEU* 5.1 3.1 - - - +
459B VAL 3.0 16.1 + - - -
460B ILE* 3.1 4.6 + - - -
462B ILE* 1.3 78.2 - - - +
464B LYS* 1.3 57.9 + - - +
466B LEU* 3.2 8.1 + - - +
468B PHE* 3.1 50.0 + - - +
470B LEU* 4.4 4.5 - - - -
489B LEU* 5.0 5.6 - - - -
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Residues in contact with LYS 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A MET* 3.9 13.5 - - - +
48A GLY* 3.4 29.9 - - - +
50A LYS* 4.5 10.1 - - - +
460B ILE* 2.9 35.4 + - + +
461B LYS* 3.7 8.5 - - - +
463B GLY* 1.3 73.5 - - - +
465B GLN* 1.3 61.0 - - + +
467B LYS* 3.0 22.3 + - - +
468B PHE 4.4 10.2 - - - +
470B LEU* 3.4 37.3 + - + +
472B ASN 5.9 0.8 - - - +
473B VAL 4.7 5.4 + - - -
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Residues in contact with GLN 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435B SER 5.4 3.0 + - - -
461B LYS* 2.9 34.4 + - + +
462B ILE* 3.5 33.9 - - + +
463B GLY 3.2 0.2 - - - -
464B LYS* 1.3 73.2 - - + +
466B LEU* 1.3 60.7 + - + +
467B LYS* 3.0 30.2 + - - +
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Residues in contact with LEU 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428B LEU* 4.2 19.7 - - + -
431B VAL* 6.3 0.4 - - + -
432B SER* 4.0 20.0 - - - +
435B SER* 5.9 0.2 - - - -
462B ILE* 3.0 30.2 + - + +
463B GLY 3.6 5.8 - - - +
464B LYS 3.2 0.6 - - - -
465B GLN* 1.3 76.4 - - + +
467B LYS* 1.3 73.9 + - - +
468B PHE* 3.2 38.4 + - + -
493B LEU* 5.2 1.1 - - + -
496B PHE* 3.8 37.2 - - + -
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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
------------------------------------------------------------
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