Contacts of the helix formed by residues 451 - 464 (chain B) in PDB entry 2QFZ
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 HIS 451 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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446B PRO 5.1 1.1 - - - +
447B ASP* 2.8 27.6 + - + +
450B SER* 1.3 74.7 - - - +
452B PHE* 1.3 66.1 + - - +
453B HIS 3.2 2.9 + - - -
454B LEU* 3.2 21.7 + - - +
455B TYR* 3.6 13.8 - - + -
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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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220B TRP* 4.2 10.3 - + - -
441B THR* 4.1 10.8 - - + -
442B TYR* 4.1 17.3 - + - -
445B GLU* 3.9 28.9 - - + -
446B PRO 5.1 1.1 + - - +
447B ASP 3.1 6.8 + - - +
448B GLY* 3.4 11.4 - - - +
451B HIS* 1.3 76.9 - - - +
453B HIS* 1.3 56.7 + - - +
455B TYR* 3.0 25.0 + + + -
456B VAL* 3.3 11.2 + - + +
498B LEU* 3.8 30.5 - - + -
501B ALA* 3.9 23.8 - - + -
502B TYR* 3.9 35.2 - + - -
505B LYS* 4.0 19.3 - - + +
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Residues in contact with HIS 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B LYS* 5.8 3.4 - - + -
421B TRP 2.9 27.9 + - - -
422B MET* 3.6 21.7 - - - -
425B LEU* 3.6 38.3 - - + +
426B LEU* 3.7 9.2 - - + +
442B TYR* 2.7 40.1 + - + +
448B GLY 3.0 6.9 + - - +
449B PHE 3.5 20.0 - - - +
450B SER 5.2 1.3 - - - +
451B HIS 3.2 1.0 - - - -
452B PHE* 1.3 75.3 - - - +
454B LEU* 1.3 61.9 + - - +
456B VAL* 3.3 1.1 + - - +
457B CYS* 3.1 40.2 + - - -
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Residues in contact with LEU 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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388B LYS* 5.7 10.3 - - + +
391B MET* 5.6 14.8 - - + -
392B LEU* 3.9 7.2 - - - +
395B LEU* 3.9 13.1 - - + +
422B MET* 4.8 11.4 - - + -
450B SER 5.1 3.7 + - - +
451B HIS* 3.2 15.5 + - - +
453B HIS* 1.3 79.7 - - - +
455B TYR* 1.3 62.9 + - + +
457B CYS* 3.5 6.9 + - - +
458B ALA* 3.2 24.8 + - - +
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Residues in contact with TYR 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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395B LEU* 3.6 31.9 - - + +
451B HIS* 3.6 23.1 - - + -
452B PHE* 3.0 16.6 + + + +
454B LEU* 1.3 77.1 - - + +
456B VAL* 1.3 64.8 + - - +
458B ALA* 3.4 4.0 + - - +
459B ALA* 3.1 19.4 + - - +
501B ALA* 3.5 31.0 - - + +
504B LEU* 3.9 15.1 - - + +
505B LYS* 3.7 48.4 + - + +
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Residues in contact with VAL 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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426B LEU* 3.7 18.4 - - + -
438B LEU* 4.2 8.7 - - + -
442B TYR* 3.5 37.7 - - + +
452B PHE* 3.3 13.4 + - + +
453B HIS 3.3 2.4 + - - +
455B TYR* 1.3 77.3 - - - +
457B CYS* 1.3 51.5 + - - +
459B ALA* 3.3 3.5 + - - +
460B PHE* 2.8 32.7 + - - +
497B LEU* 3.9 20.7 - - + +
498B LEU* 3.8 16.4 - - + -
501B ALA* 3.6 20.2 - - + -
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Residues in contact with CYS 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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392B LEU* 3.9 8.7 - - + +
421B TRP* 3.6 31.5 - - + -
422B MET* 3.5 26.7 - - + -
426B LEU* 4.1 7.6 - - - -
453B HIS* 3.1 47.2 + - - +
454B LEU 3.7 5.6 - - - +
455B TYR 3.3 0.2 - - - -
456B VAL* 1.3 73.5 - - - +
458B ALA* 1.3 65.1 + - - +
460B PHE* 3.3 7.7 + - - +
461B LEU* 3.0 19.6 + - - +
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Residues in contact with ALA 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B LEU* 3.6 14.5 - - + +
395B LEU* 4.1 12.8 - - + -
396B VAL* 4.2 8.4 - - + +
399B ILE* 3.9 23.8 - - + -
454B LEU 3.2 13.6 + - - +
455B TYR 3.6 8.7 - - - +
457B CYS* 1.3 76.1 - - - +
459B ALA* 1.3 57.0 + - - +
461B LEU* 3.5 2.4 + - - +
462B VAL* 3.1 33.3 + - - +
504B LEU* 4.1 5.8 - - + -
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Residues in contact with ALA 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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455B TYR 3.1 17.0 + - - +
456B VAL 3.7 3.8 - - - +
458B ALA* 1.3 73.6 - - - +
460B PHE* 1.3 59.1 + - - +
462B VAL* 3.8 6.6 - - - +
463B ARG* 2.9 30.7 + - - +
497B LEU* 3.5 18.8 - - + +
500B GLU* 3.9 11.3 - - + +
501B ALA* 3.9 22.4 - - + +
504B LEU* 3.9 12.1 - - + +
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Residues in contact with PHE 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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421B TRP* 3.8 23.3 - + - -
426B LEU* 3.9 21.1 - - + -
429B GLU* 3.8 34.8 - - + -
430B VAL* 4.1 7.9 - - + -
456B VAL 2.8 18.2 + - - +
457B CYS* 3.5 7.4 - - - +
459B ALA* 1.3 74.4 - - - +
461B LEU* 1.3 61.0 + - - +
463B ARG* 3.2 7.6 - - - +
464B TRP* 2.8 35.1 + - - -
484B LEU* 3.1 31.9 - - + -
486B THR* 4.0 6.3 - - + -
489B TRP* 3.8 27.8 - + - -
497B LEU* 3.3 22.4 - - + +
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Residues in contact with LEU 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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392B LEU* 5.6 2.2 - - + -
396B VAL* 4.1 21.5 - - + -
403B VAL* 4.3 13.0 - - + +
407B LEU* 4.4 3.6 - - + -
414B TYR* 4.0 27.4 - - + -
417B PHE* 4.1 16.8 - - + -
421B TRP* 4.0 18.8 - - + -
457B CYS 3.0 16.7 + - - +
458B ALA* 3.8 4.9 - - - +
460B PHE* 1.3 74.6 - - - +
462B VAL* 1.3 64.5 + - - +
464B TRP* 3.1 15.4 + - + -
465B ARG* 3.8 0.9 + - - -
468B ILE* 3.5 44.2 - - + +
481B LEU* 3.8 19.1 - - + -
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Residues in contact with VAL 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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396B VAL* 5.2 6.1 - - + -
399B ILE* 4.4 15.3 - - + -
400B ASP* 3.8 36.3 - - + +
403B VAL* 5.5 2.9 - - + -
458B ALA 3.1 21.6 + - - +
459B ALA* 3.8 8.7 - - - +
461B LEU* 1.3 77.7 - - + +
463B ARG* 1.3 59.0 + - - +
465B ARG* 3.0 34.7 + - - +
504B LEU* 5.5 3.6 - - + -
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Residues in contact with ARG 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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459B ALA 2.9 14.5 + - - +
460B PHE* 3.2 14.8 - - - +
462B VAL* 1.3 77.8 - - - +
464B TRP* 1.3 95.1 + - + +
465B ARG* 3.4 3.2 + - - +
466B LYS 5.2 0.7 + - - -
467B GLU* 4.3 8.1 + - - +
489B TRP* 3.8 34.1 - - + +
493B ASP* 4.9 6.7 + - - -
497B LEU* 4.9 4.3 - - + -
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Residues in contact with TRP 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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421B TRP* 5.8 0.4 - + - -
460B PHE* 2.8 37.1 + + - -
461B LEU* 3.1 13.0 + - + +
463B ARG* 1.3 96.3 - - + +
465B ARG* 1.3 65.6 + - - +
466B LYS 3.1 3.9 + - - -
467B GLU* 3.1 31.0 + - - +
468B ILE* 3.0 24.7 + - + +
480B PHE* 4.0 14.4 - + + -
481B LEU* 5.7 0.2 - - + -
484B LEU* 3.5 36.2 - - + +
485B PRO* 3.6 36.6 - - + -
486B THR* 3.5 29.6 - - + -
489B TRP* 3.6 27.8 - + - -
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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