Contacts of the helix formed by residues 419 - 433 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414B LEU* 2.7 39.6 + - + +
417B GLY* 3.2 33.9 + - - -
418B THR* 1.3 74.2 - - + +
420B TYR* 1.3 62.7 + - - +
421B GLN 3.6 1.6 - - - -
422B VAL* 4.0 23.1 - - + +
423B ALA* 3.2 21.0 + - - +
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Residues in contact with TYR 420 (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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371B ILE* 4.0 29.4 - - + -
384B CYS* 4.5 2.5 - - - -
386B PHE* 3.4 45.5 - - + -
387B ARG* 3.0 53.2 + - + -
415B VAL* 3.8 24.1 + - + -
418B THR* 2.9 40.5 + - + -
419B HIS* 1.3 71.9 - - - +
421B GLN* 1.3 59.6 + - - +
423B ALA* 3.0 11.4 - - - +
424B CYS* 2.8 25.8 + - - +
458B SF4 4.6 2.5 - - - -
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Residues in contact with GLN 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B CYS* 3.5 30.5 - - + +
368B LEU* 4.0 23.8 - - - +
371B ILE* 4.2 9.2 - - + +
420B TYR* 1.3 73.2 - - - +
422B VAL* 1.3 56.6 + - + +
424B CYS* 3.0 5.8 + - - +
425B GLN* 2.7 40.4 + - - +
441B LEU* 2.8 39.9 + - + +
442B ASN* 3.5 16.0 - - - +
458B SF4 4.1 7.0 - - - -
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Residues in contact with VAL 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A ASP* 3.6 32.8 - - + +
438A GLY* 5.4 6.1 - - - -
414B LEU* 3.7 24.2 - - + -
419B HIS* 3.7 21.7 + - + +
420B TYR 3.3 0.6 - - - -
421B GLN* 1.3 77.5 - - + +
423B ALA* 1.3 52.9 + - - +
425B GLN* 2.9 24.0 + - - +
426B LYS* 2.7 36.5 + - + +
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Residues in contact with ALA 423 (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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386B PHE* 3.8 21.3 - - + -
411B ILE* 4.0 13.4 - - + +
414B LEU* 3.5 25.8 - - + +
415B VAL* 4.4 2.5 - - + -
419B HIS 3.2 12.5 + - - +
420B TYR* 3.0 15.7 + - - +
422B VAL* 1.3 79.6 - - - +
424B CYS* 1.3 55.3 + - - -
426B LYS* 3.0 5.1 + - - +
427B TYR* 2.8 27.4 + - - +
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Residues in contact with CYS 424 (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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286B PRO* 3.7 17.7 - - - -
386B PHE* 3.7 12.8 - - + -
420B TYR 2.8 6.6 + - - +
421B GLN 3.0 8.9 + - - +
423B ALA* 1.3 75.8 - - - +
425B GLN* 1.3 56.7 + - - +
427B TYR* 3.3 3.5 - - - +
428B PHE* 2.8 26.3 + - - +
441B LEU* 3.5 4.9 - - + -
447B PHE* 3.5 28.1 - - - -
458B SF4 2.1 45.3 - - - -
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Residues in contact with GLN 425 (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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436A ASP* 5.4 5.3 + - - -
421B GLN* 2.7 18.8 + - - +
422B VAL* 3.2 26.0 - - - +
424B CYS* 1.3 74.3 - - - +
426B LYS* 1.3 59.8 + - + +
428B PHE* 3.2 8.6 + - - +
429B GLU* 2.9 37.5 + - - +
437B CYS* 3.7 23.3 - - - -
439B PHE* 3.8 11.6 + - + -
440B SER* 3.6 7.6 + - - -
441B LEU* 2.8 43.1 + - + +
447B PHE* 6.2 0.2 - - - -
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Residues in contact with LYS 426 (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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435A ASP* 2.5 45.2 + - - -
436A ASP* 5.2 4.0 - - - +
410B GLN* 2.8 32.5 + - + +
411B ILE* 3.8 10.1 - - + -
414B LEU* 4.0 15.9 - - + -
422B VAL* 2.7 13.4 + - + +
423B ALA* 3.0 12.8 - - - +
425B GLN* 1.3 77.5 - - + +
427B TYR* 1.3 63.6 + - - +
429B GLU* 3.2 21.7 + - - +
430B MET* 3.1 48.4 + - + +
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Residues in contact with TYR 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B THR 5.0 0.9 + - - -
284B PHE 4.6 4.6 + - - -
286B PRO* 3.6 35.7 - - + -
289B ARG* 3.1 32.9 + - - -
386B PHE* 4.0 5.6 - - + -
398B LEU* 4.0 18.6 - - + -
401B TYR* 3.8 23.4 - + + -
403B ILE* 4.1 14.4 - - + -
411B ILE* 4.0 10.7 - - + +
423B ALA 2.8 11.3 + - - +
424B CYS* 3.3 12.1 - - - +
426B LYS* 1.3 76.9 - - - +
428B PHE* 1.3 63.0 + - - +
430B MET* 3.1 8.3 + - - +
431B ILE* 3.0 58.8 + - + +
447B PHE* 3.9 11.2 - + - -
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Residues in contact with PHE 428 (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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424B CYS 2.8 14.7 + - - +
425B GLN* 3.2 13.6 + - - +
427B TYR* 1.3 78.1 - - - +
429B GLU* 1.3 63.0 + - - +
431B ILE* 4.5 0.9 - - - -
432B HIS* 2.9 59.9 + + + +
434B VAL* 4.5 1.3 - - + -
437B CYS* 3.5 33.7 - - + -
439B PHE* 4.0 16.8 - + + -
447B PHE* 3.4 46.0 - + + -
450B GLU* 3.7 11.4 - - + -
451B SER* 3.6 26.2 - - - -
454B ILE* 3.9 17.5 - - + -
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Residues in contact with GLU 429 (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 GLN* 2.9 17.9 + - - +
426B LYS* 3.2 37.8 + - - +
428B PHE* 1.3 75.7 - - - +
430B MET* 1.3 56.0 + - + +
433B ASN* 2.7 29.8 + - - -
434B VAL* 2.9 34.8 + - - +
435B ASP* 3.3 8.8 - - - +
436B ASP* 3.0 29.4 - - - +
437B CYS* 3.5 21.5 + - - +
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Residues in contact with MET 430 (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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403B ILE* 3.5 39.9 - - + -
404B SER* 5.2 3.4 - - - +
407B GLY* 4.2 14.8 - - - +
410B GLN* 4.2 9.0 - - - +
411B ILE* 3.6 16.4 - - + -
426B LYS* 3.1 45.7 + - + +
427B TYR* 3.1 7.7 + - - +
429B GLU* 1.3 75.8 - - + +
431B ILE* 1.3 61.1 + - - +
432B HIS 3.1 6.0 + - - -
433B ASN* 3.4 18.6 + - - +
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Residues in contact with ILE 431 (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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281B THR 4.3 10.5 - - - +
282B LYS* 3.6 29.5 - - - +
284B PHE 5.0 2.5 - - - +
289B ARG* 5.7 1.3 - - - +
401B TYR 5.2 4.5 - - - +
403B ILE* 4.2 12.1 - - + -
427B TYR* 3.0 60.3 + - + +
428B PHE* 4.0 0.7 - - - +
429B GLU 3.6 0.2 - - - -
430B MET* 1.3 75.0 - - - +
432B HIS* 1.3 79.5 + - + +
433B ASN* 4.8 2.5 - - - +
447B PHE* 4.4 6.5 - - + -
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Residues in contact with HIS 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B LYS* 3.3 17.3 + - + +
428B PHE* 2.9 48.6 + + + +
429B GLU 4.3 0.2 - - - +
430B MET 3.1 0.2 - - - -
431B ILE* 1.3 93.2 - - + +
433B ASN* 1.3 75.6 + - - +
434B VAL* 3.6 17.1 - - + +
447B PHE* 4.4 1.1 - + - -
451B SER* 2.8 49.3 + - - -
454B ILE* 4.2 17.4 - - + +
455B LEU 4.4 10.9 + - - -
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Residues in contact with ASN 433 (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 GLU 2.7 11.8 + - - -
430B MET* 3.4 13.4 + - - +
431B ILE 4.8 1.7 - - - +
432B HIS* 1.3 84.6 + - - +
434B VAL* 1.3 61.0 + - - +
435B ASP* 5.5 0.9 - - - -
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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