Contacts of the helix formed by residues 445 - 460 (chain B) in PDB entry 2WO6
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 THR 445 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441B GLU 5.6 2.0 - - - +
442B SER* 6.3 0.4 - - - -
443B GLY* 5.3 3.8 - - - +
444B HIS* 1.3 82.2 - - - +
446B VAL* 1.3 59.9 + - - +
447B ALA* 3.5 11.3 + - - +
448B ASP* 2.6 36.5 + - - +
449B TYR* 2.9 30.0 + - - -
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Residues in contact with VAL 446 (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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429B VAL* 3.8 33.1 + - + +
430B GLU* 4.3 23.1 - - + +
444B HIS 4.0 0.6 + - - -
445B THR* 1.3 72.4 - - - +
447B ALA* 1.3 57.8 + - - +
449B TYR* 3.5 2.1 + - - +
450B LEU* 2.8 51.1 + - + +
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Residues in contact with ALA 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B THR* 3.0 11.3 + - - +
446B VAL* 1.3 74.7 - - - +
448B ASP* 1.3 68.2 + - - +
450B LEU* 3.1 14.6 + - - +
451B LYS* 2.9 35.0 + - - +
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Residues in contact with ASP 448 (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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259B LEU* 4.2 9.2 - - + -
263B ARG* 4.6 13.7 + - - +
443B GLY* 3.0 34.8 - - - +
445B THR* 2.6 31.0 + - - +
447B ALA* 1.3 76.6 - - - +
449B TYR* 1.3 56.2 + - - +
451B LYS* 2.7 42.9 + - - +
452B PHE* 2.9 11.8 + - - +
478B PHE* 4.6 2.9 - - + -
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Residues in contact with TYR 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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259B LEU* 4.1 11.6 - - + +
355B HIS* 2.7 40.2 + + - -
427B LEU* 3.8 26.2 - - + +
429B VAL* 3.9 34.3 - - + +
432B GLY* 4.7 1.1 - - - -
433B GLY* 3.3 18.6 - - - -
434B PRO* 3.3 3.8 - - - +
438B ARG* 3.2 11.9 - - + +
444B HIS* 3.2 44.1 - + + -
445B THR 2.9 23.9 + - - +
446B VAL 3.9 4.0 - - - +
448B ASP* 1.3 72.1 - - - +
450B LEU* 1.3 56.9 + - - +
452B PHE* 3.8 10.7 - + - +
453B LYS* 2.9 31.5 + - - +
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Residues in contact with LEU 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B HIS* 4.2 6.3 - - + -
429B VAL* 3.8 19.1 - - + -
446B VAL* 2.8 38.3 + - + +
447B ALA* 3.2 12.3 - - - +
449B TYR* 1.3 75.6 - - - +
451B LYS* 1.3 64.2 + - + +
453B LYS* 4.0 28.2 - - - +
454B ASP* 3.1 23.0 + - - +
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Residues in contact with LYS 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B ALA* 2.9 26.7 + - - +
448B ASP* 2.7 26.6 + - - +
450B LEU* 1.3 71.2 - - + +
452B PHE* 1.3 63.6 + - - +
454B ASP* 3.3 4.7 + - - -
455B LEU* 3.0 19.8 + - - +
476B HIS* 3.2 12.0 - - - -
477B SER* 3.5 44.0 + - - +
478B PHE* 3.9 20.6 - - + +
480B LYS* 4.8 9.3 + - - +
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Residues in contact with PHE 452 (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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259B LEU* 3.7 21.1 - - + -
262B THR* 3.8 19.3 - - + -
351B LEU* 3.6 36.1 - - + -
352B VAL* 4.3 1.1 - - - -
355B HIS* 4.4 6.5 - + + -
427B LEU* 3.7 39.7 - - + -
448B ASP 2.9 9.2 + - - +
449B TYR* 3.8 13.7 - + - +
451B LYS* 1.3 75.5 - - - +
453B LYS* 1.3 65.1 + - - +
455B LEU* 3.2 4.0 + - + +
456B ILE* 3.0 50.8 + - + +
478B PHE* 3.6 40.9 - + + -
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Residues in contact with LYS 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B LEU* 4.1 15.7 - - + +
424B HIS* 2.9 56.7 + - - +
427B LEU* 4.0 15.2 - - + +
429B VAL* 4.4 2.9 - - + -
449B TYR 2.9 19.0 + - - +
450B LEU* 4.0 20.0 - - - +
451B LYS 3.3 0.2 - - - -
452B PHE* 1.3 77.3 - - - +
454B ASP* 1.3 60.0 + - - +
456B ILE* 3.3 1.7 + - - +
457B LEU* 2.9 48.4 + - + +
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Residues in contact with ASP 454 (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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450B LEU 3.1 16.8 + - - +
451B LYS* 3.4 6.3 - - - +
452B PHE 3.2 0.2 - - - -
453B LYS* 1.3 80.0 - - - +
455B LEU* 1.3 66.8 + - - +
457B LEU* 3.1 11.0 + - - +
458B ARG* 3.0 32.7 + - - +
476B HIS* 2.6 27.5 + - + +
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Residues in contact with LEU 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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266B ALA* 5.1 2.5 - - + -
351B LEU* 5.4 2.0 - - + -
451B LYS 3.0 13.3 + - - +
452B PHE* 3.2 9.6 + - + +
454B ASP* 1.3 74.5 - - - +
456B ILE* 1.3 65.8 + - + +
458B ARG* 3.1 6.7 + - - +
459B MET* 2.9 48.3 + - + +
468B ILE* 4.1 17.9 - - + -
473B ALA* 4.3 7.2 - - + -
476B HIS* 3.5 35.8 + - + +
478B PHE* 3.7 30.1 - - + -
479B PHE* 3.8 22.2 - - + -
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Residues in contact with ILE 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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348B GLY* 3.6 25.6 - - - +
351B LEU* 3.9 16.6 - - + -
352B VAL* 3.7 16.2 - - + -
423B LEU* 3.6 24.0 - - + -
427B LEU* 5.4 0.2 - - + -
452B PHE* 3.0 51.3 + - + +
453B LYS* 3.7 4.3 - - - +
455B LEU* 1.3 77.1 - - + +
457B LEU* 1.3 57.1 + - - +
459B MET* 3.0 9.2 + - + +
460B LEU* 2.8 47.2 + - + +
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Residues in contact with LEU 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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376B VAL* 5.7 0.4 - - + -
377B LEU* 3.9 27.8 - - + +
423B LEU* 4.2 22.9 - - + -
453B LYS* 2.9 43.4 + - + +
454B ASP* 3.7 8.1 - - - +
456B ILE* 1.3 75.4 - - - +
458B ARG* 1.3 63.8 + - + +
460B LEU* 3.2 14.5 + - + +
461B ASP* 3.2 13.0 + - - +
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Residues in contact with ARG 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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454B ASP* 3.0 31.7 + - - +
455B LEU* 3.5 8.5 - - - +
457B LEU* 1.3 77.3 - - + +
459B MET* 1.3 61.2 + - - +
460B LEU 3.4 0.2 + - - -
461B ASP* 3.4 28.9 + - - +
466B THR* 2.9 29.7 + - - -
467B ARG* 3.5 0.3 - - - +
468B ILE* 3.2 60.0 + - + +
476B HIS* 5.2 2.0 - - + +
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Residues in contact with MET 459 (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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270B CYS* 4.0 23.8 - - - -
344B MET* 3.7 28.7 - - - +
345B TRP* 3.7 13.3 - - - -
347B LEU* 4.1 2.7 - - + -
348B GLY* 3.7 30.1 - - - -
351B LEU* 4.0 19.1 - - + -
455B LEU* 2.9 47.6 + - + +
456B ILE* 3.0 13.2 + - - +
458B ARG* 1.3 74.8 - - - +
460B LEU* 1.3 57.8 + - - +
461B ASP 3.4 1.6 - - - -
467B ARG* 3.3 21.4 + - - -
468B ILE* 3.7 15.5 - - + -
473B ALA* 4.7 1.3 - - + -
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Residues in contact with LEU 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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345B TRP* 3.5 57.5 - - + +
348B GLY* 4.4 2.5 - - - -
349B CYS* 4.1 11.9 - - - +
360B LEU* 3.6 25.4 - - + -
361B PHE* 4.4 7.2 - - + -
376B VAL* 5.9 0.9 - - + -
377B LEU* 3.5 33.1 - - + +
423B LEU* 5.1 4.9 - - + -
456B ILE* 2.8 41.2 + - + +
457B LEU* 3.2 8.0 + - - +
459B MET* 1.3 73.9 - - - +
461B ASP* 1.3 63.9 + - - +
462B TYR* 3.5 3.5 + - - -
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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