Contacts of the helix formed by residues 419 - 433 (chain A) in PDB entry 3Q36
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 419 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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413A ASP 5.2 0.4 - - - -
414A LEU* 3.0 44.3 + - + +
417A GLY* 3.1 36.9 + - - -
418A THR* 1.3 75.8 - - - +
420A TYR* 1.3 62.4 - - - +
421A GLN* 3.4 3.8 - - - -
422A VAL* 3.0 23.4 + - + +
423A ALA* 3.0 12.0 + - - +
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Residues in contact with TYR 420 (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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371A ILE* 3.7 28.9 - - + -
384A CYS* 4.5 3.4 - - - -
386A PHE* 3.6 45.4 - - + -
387A ARG* 3.7 35.8 + - + -
415A VAL* 3.9 17.0 + - + -
418A THR* 2.9 55.4 + - + +
419A HIS* 1.3 71.6 - - - +
421A GLN* 1.3 71.5 + - - +
423A ALA* 3.1 8.1 + - - +
424A CYS* 3.0 20.6 + - - +
458A SF4 4.6 2.7 - - - -
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Residues in contact with GLN 421 (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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367A CYS* 4.0 25.1 - - + +
368A LEU* 4.3 21.6 - - - +
371A ILE* 3.6 17.5 - - - +
418A THR 4.7 1.6 - - - +
419A HIS* 3.4 1.1 - - - -
420A TYR* 1.3 88.6 + - - +
422A VAL* 1.3 59.8 + - + +
424A CYS* 3.3 3.5 + - - +
425A GLN* 3.0 33.4 + - - +
441A LEU* 3.6 29.9 + - + +
442A ASN* 5.5 2.8 - - - +
458A SF4 4.1 10.3 - - - -
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Residues in contact with VAL 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A LEU* 3.5 28.0 - - + -
419A HIS* 3.0 20.6 + - + +
421A GLN* 1.3 76.8 - - + +
423A ALA* 1.3 61.3 + - - +
424A CYS 3.1 1.3 - - - -
425A GLN* 3.0 23.6 + - + +
426A LYS* 2.9 27.9 + - + +
436B ASP* 4.5 28.3 - - + +
438B GLY* 6.2 1.1 - - - -
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Residues in contact with ALA 423 (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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386A PHE* 3.7 24.0 - - + -
411A ILE* 3.7 20.8 - - + +
414A LEU* 3.8 17.5 - - + +
415A VAL* 4.2 10.1 - - + -
419A HIS 3.0 11.8 + - - +
420A TYR 3.4 8.7 - - - +
422A VAL* 1.3 76.4 - - - +
424A CYS* 1.3 58.4 + - - +
426A LYS* 3.1 3.7 + - - +
427A TYR* 2.9 28.2 + - - +
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Residues in contact with CYS 424 (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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286A PRO* 3.9 8.5 - - - -
386A PHE* 3.5 21.2 - - + -
420A TYR 3.0 5.2 + - - +
421A GLN 3.5 7.4 - - - +
422A VAL 3.1 0.2 - - - -
423A ALA* 1.3 80.1 - - - +
425A GLN* 1.3 56.7 + - - +
427A TYR* 3.3 2.4 + - - +
428A PHE* 2.9 25.5 + - - +
441A LEU* 3.6 5.4 - - + -
447A PHE* 3.5 28.2 - - - -
458A SF4 2.2 46.2 - - - -
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Residues in contact with GLN 425 (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 GLN* 3.0 22.0 + - - +
422A VAL* 3.0 25.4 + - + +
424A CYS* 1.3 73.6 - - - +
426A LYS* 1.3 56.2 + - - +
428A PHE* 2.9 10.9 + - - +
429A GLU* 2.7 43.2 + - - +
437A CYS* 3.7 24.5 - - - -
439A PHE* 3.7 11.5 + - + +
440A SER* 3.7 6.5 + - - +
441A LEU* 2.8 42.1 + - + +
436B ASP* 5.2 5.7 + - - -
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Residues in contact with LYS 426 (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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407A GLY* 5.1 2.2 - - - -
410A GLN* 2.9 51.0 + - + +
411A ILE* 4.2 10.8 - - + -
414A LEU* 4.7 4.5 - - + -
422A VAL* 2.9 13.7 + - + +
423A ALA* 3.4 10.5 - - - +
425A GLN* 1.3 77.7 - - - +
427A TYR* 1.3 61.2 + - - +
429A GLU* 3.2 25.8 + - - +
430A MET* 3.0 59.6 + - + +
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Residues in contact with TYR 427 (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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281A THR 4.6 0.9 + - - -
284A PHE 4.5 4.9 + - - -
286A PRO* 3.4 32.5 - - + +
289A ARG* 3.3 31.7 + - - -
386A PHE* 4.1 9.4 - - + -
398A LEU* 3.9 15.9 - - + -
401A TYR* 3.8 24.1 - + - -
403A ILE* 3.9 17.0 - - + -
411A ILE* 4.2 5.6 - - + +
423A ALA 2.9 13.0 + - - +
424A CYS 3.5 8.1 - - - +
425A GLN 3.2 0.2 - - - -
426A LYS* 1.3 75.5 - - - +
428A PHE* 1.3 65.7 + - - +
430A MET* 3.3 10.7 + - - +
431A ILE* 3.0 61.0 + - + +
447A PHE* 3.9 11.4 - + - -
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Residues in contact with PHE 428 (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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424A CYS 2.9 14.4 + - - +
425A GLN* 3.0 15.0 - - - +
427A TYR* 1.3 77.9 - - - +
429A GLU* 1.3 65.0 + - - +
431A ILE* 3.6 1.0 + - - +
432A HIS* 2.9 59.8 + + + +
434A VAL* 4.7 2.2 - - + -
437A CYS* 3.6 29.2 - - + -
439A PHE* 4.0 9.2 - + + -
447A PHE* 3.5 45.1 - + + -
450A GLU* 3.8 18.4 - - + -
451A SER* 3.6 27.4 - - - -
454A ILE* 4.0 16.6 - - + -
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Residues in contact with GLU 429 (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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425A GLN* 2.7 23.6 + - - +
426A LYS* 3.2 31.6 + - + +
428A PHE* 1.3 72.3 - - - +
430A MET* 1.3 61.2 + - + +
432A HIS 3.6 0.2 - - - -
433A ASN* 2.8 24.4 + - - -
434A VAL* 3.1 33.6 + - + +
435A ASP* 3.4 19.1 - - - +
436A ASP* 3.5 8.5 - - - +
437A CYS* 3.1 42.3 + - + +
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Residues in contact with MET 430 (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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403A ILE* 3.4 29.8 - - + -
404A SER* 3.9 11.7 - - - +
407A GLY* 3.2 42.2 - - - +
411A ILE* 4.0 6.5 - - + -
426A LYS* 3.0 57.0 + - + +
427A TYR* 3.8 3.8 - - - +
428A PHE 3.3 0.2 - - - -
429A GLU* 1.3 73.6 - - - +
431A ILE* 1.3 63.9 + - - +
432A HIS 3.0 6.2 + - - -
433A ASN* 3.1 15.7 + - - +
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Residues in contact with ILE 431 (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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281A THR 4.2 10.3 - - - +
282A LYS* 3.5 25.1 - - - +
284A PHE 5.2 1.1 - - - +
289A ARG* 5.7 2.5 - - - +
401A TYR 5.3 3.4 - - - +
403A ILE* 3.3 28.9 - - + -
427A TYR* 3.0 53.7 + - + +
428A PHE 3.7 6.5 - - - +
430A MET* 1.3 75.1 - - - +
432A HIS* 1.3 71.6 + - + +
433A ASN* 5.3 0.4 - - - -
447A PHE* 4.7 4.0 - - + -
455A LEU* 5.7 1.4 - - - +
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Residues in contact with HIS 432 (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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282A LYS 3.5 15.8 + - - -
428A PHE* 2.9 56.7 + + + +
429A GLU 4.2 1.3 - - - +
430A MET 3.0 0.4 - - - -
431A ILE* 1.3 87.2 - - + +
433A ASN* 1.3 72.9 + - - +
434A VAL* 3.5 18.9 + - + +
447A PHE* 4.6 1.3 - + - -
451A SER* 2.8 32.4 + - - -
454A ILE* 4.3 23.2 - - + +
455A LEU* 3.9 25.5 - - + +
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Residues in contact with ASN 433 (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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429A GLU 2.8 11.1 + - - -
430A MET* 3.1 10.9 + - - +
431A ILE 5.3 0.7 - - - +
432A HIS* 1.3 81.7 - - - +
434A VAL* 1.3 59.8 + - - +
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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