Contacts of the helix formed by residues 451 - 464 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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446A PRO 4.8 6.1 + - - -
447A ASP* 2.7 27.9 + - + +
450A SER* 1.3 73.3 - - - +
452A PHE* 1.3 68.7 + - - +
453A HIS 3.2 1.1 - - - -
454A LEU* 3.0 32.2 + - + +
455A TYR* 3.6 37.0 + + - -
505A LYS* 4.2 22.1 + - + +
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Residues in contact with PHE 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A TRP* 4.2 1.8 - + - -
441A THR* 4.1 11.7 - - + -
442A TYR* 4.1 12.8 - + - -
445A GLU* 3.9 26.0 - - + +
446A PRO 5.1 1.1 - - - +
447A ASP 3.3 4.4 + - - -
448A GLY* 3.5 17.9 - - - +
451A HIS* 1.3 81.7 + - - +
453A HIS* 1.3 62.8 + - - +
455A TYR* 3.0 21.2 + + + +
456A VAL* 3.2 18.2 + - + +
498A LEU* 3.9 28.5 - - + -
501A ALA* 3.8 33.7 - - + -
502A TYR* 3.9 20.9 - + - -
505A LYS* 4.0 29.4 - - + -
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Residues in contact with HIS 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A LYS* 5.9 2.5 - - + -
421A TRP 3.0 24.6 + - - -
422A MET* 3.6 23.3 - - - -
425A LEU* 3.7 30.5 - - + +
426A LEU* 3.6 31.0 - - + -
442A TYR* 2.8 33.8 + - + +
448A GLY 3.0 10.7 + - - +
449A PHE 3.2 22.4 - - - +
450A SER 4.6 2.7 - - - +
451A HIS 3.1 0.4 + - - -
452A PHE* 1.3 75.7 - - - +
454A LEU* 1.3 63.8 + - + +
456A VAL* 3.2 2.1 + - - +
457A CYS* 2.9 29.6 + - - -
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Residues in contact with LEU 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A LYS* 3.7 35.4 - - + +
391A MET* 3.9 45.5 - - + -
392A LEU* 4.1 7.4 - - - +
395A LEU* 4.1 10.5 - - + +
422A MET* 4.0 15.5 - - + -
450A SER 4.1 11.7 - - - +
451A HIS* 3.0 24.0 + - + +
453A HIS* 1.3 79.9 - - + +
455A TYR* 1.3 63.2 + - + +
457A CYS* 3.2 9.4 + - - +
458A ALA* 3.1 25.1 + - - +
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Residues in contact with TYR 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A LEU* 3.8 28.5 - - + -
451A HIS* 3.6 51.3 + + - -
452A PHE* 3.0 21.2 + + + +
454A LEU* 1.3 76.7 - - + +
456A VAL* 1.3 60.0 + - - +
458A ALA* 3.4 6.5 + - - +
459A ALA* 3.1 27.0 + - - +
501A ALA* 3.6 25.2 - - + +
504A LEU* 3.9 12.2 - - + +
505A LYS* 3.6 40.3 + - + +
508A PHE* 4.3 8.4 - - + +
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Residues in contact with VAL 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A LEU* 3.9 15.7 - - + -
438A LEU* 4.1 9.4 - - + -
442A TYR* 3.4 40.4 - - + +
452A PHE* 3.2 12.4 + - + +
453A HIS 3.2 4.6 + - - +
455A TYR* 1.3 74.7 - - - +
457A CYS* 1.3 58.8 + - - +
459A ALA* 3.4 2.6 + - - +
460A PHE* 2.8 28.6 + - - +
497A LEU* 3.9 23.7 - - + +
498A LEU* 3.9 14.4 - - + -
501A ALA* 3.7 20.9 - - + -
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Residues in contact with CYS 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A LEU* 4.0 13.6 - - + +
421A TRP* 3.5 33.7 - - + -
422A MET* 3.9 20.0 - - + -
426A LEU* 3.9 9.4 - - - -
453A HIS* 2.9 44.3 + - - +
454A LEU 3.2 10.3 + - - +
456A VAL* 1.3 77.6 - - - +
458A ALA* 1.3 56.0 + - - +
460A PHE* 3.3 5.3 + - - -
461A LEU* 3.0 25.1 + - - +
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Residues in contact with ALA 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A LEU* 3.6 12.5 - - + +
395A LEU* 3.7 35.2 - - + -
396A VAL* 4.1 10.7 - - + +
399A ILE* 4.3 2.5 - - + -
454A LEU 3.1 5.8 + - - +
455A TYR 3.7 7.4 - - - +
457A CYS* 1.3 76.5 - - - +
459A ALA* 1.3 61.4 + - - +
461A LEU* 3.4 4.6 + - - +
462A VAL* 3.2 27.9 + - - +
504A LEU* 3.9 13.7 - - + -
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Residues in contact with ALA 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455A TYR 3.1 17.4 + - - +
456A VAL 3.8 1.6 - - - +
458A ALA* 1.3 74.3 - - - +
460A PHE* 1.3 62.8 + - - +
462A VAL* 3.9 6.5 - - - +
463A ARG* 3.0 26.2 + - - +
497A LEU* 3.5 18.5 - - + +
500A GLU* 3.9 13.6 - - + +
501A ALA* 3.8 23.1 - - + +
504A LEU* 3.5 10.2 - - + +
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Residues in contact with PHE 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421A TRP* 3.8 19.3 - + - -
426A LEU* 3.6 21.3 - - + -
429A GLU* 3.7 31.2 - - + -
430A VAL* 4.0 19.3 - - + -
456A VAL 2.8 21.7 + - - +
457A CYS* 3.5 7.9 - - - +
459A ALA* 1.3 74.5 - - - +
461A LEU* 1.3 63.2 + - - +
463A ARG* 3.5 3.2 - - - +
464A TRP* 3.3 52.3 - + - -
484A LEU* 3.3 26.9 - - + +
486A THR* 4.1 5.4 - - + -
489A TRP* 3.9 12.8 - + - -
497A LEU* 3.4 23.3 - - + +
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Residues in contact with LEU 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A LEU* 5.3 2.9 - - + -
396A VAL* 4.1 21.3 - - + -
403A VAL* 4.3 5.6 - - + -
407A LEU* 4.4 8.3 - - + -
414A TYR* 3.9 28.7 - - + -
417A PHE* 3.9 13.0 - - + -
421A TRP* 3.8 18.5 - - + -
457A CYS 3.0 16.3 + - - +
458A ALA 3.7 5.4 - - - +
460A PHE* 1.3 78.7 - - - +
462A VAL* 1.3 61.8 + - + +
464A TRP* 3.2 12.9 + - - +
468A ILE* 3.4 33.3 - - + +
481A LEU* 3.4 33.0 - - + -
484A LEU* 5.6 1.3 - - + -
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Residues in contact with VAL 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A VAL* 4.7 6.7 - - + -
399A ILE* 4.1 17.9 - - + -
400A ASP* 3.2 42.2 - - + +
403A VAL* 4.6 8.3 - - + -
458A ALA 3.2 17.8 + - - +
459A ALA* 4.0 10.3 - - - +
461A LEU* 1.3 77.5 - - + +
463A ARG* 1.3 64.9 + - - +
464A TRP 3.2 1.6 - - - -
465A ARG* 3.2 29.4 + - - +
500A GLU* 6.5 0.2 - - + -
503A ARG* 5.9 3.4 - - - +
504A LEU* 4.9 3.6 - - + -
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Residues in contact with ARG 463 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459A ALA 3.0 18.4 + - - +
460A PHE* 3.5 9.6 - - - +
461A LEU 3.2 0.2 - - - -
462A VAL* 1.3 76.4 - - - +
464A TRP* 1.3 97.1 + - + +
465A ARG* 3.4 2.6 + - - +
466A LYS* 5.2 0.5 + - - +
467A GLU* 4.7 4.8 + - - +
488A HIS* 5.7 3.0 + - - -
489A TRP* 3.8 27.5 - - + +
493A ASP* 5.1 6.3 + - - -
497A LEU* 4.9 3.6 - - + -
1008A UNX 3.8 17.7 - - - -
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Residues in contact with TRP 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460A PHE* 3.3 44.2 - + - -
461A LEU 3.2 11.3 + - - +
462A VAL 3.2 1.2 - - - -
463A ARG* 1.3 99.5 - - + +
465A ARG* 1.3 66.6 + - - +
466A LYS 3.1 3.7 + - - -
467A GLU* 3.3 34.9 + - - +
468A ILE* 3.0 23.7 + - + +
480A PHE* 3.9 24.2 - + + -
484A LEU* 3.6 23.8 - - + -
485A PRO* 3.9 34.1 + - + +
486A THR* 3.6 16.6 - - + -
489A TRP* 3.3 34.3 - + - -
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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