Contacts of the helix formed by residues 419 - 433 (chain B) in PDB entry 2A72
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 PHE 419 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362A PHE* 4.0 17.9 - + + -
366A VAL* 3.8 31.1 - - + +
369A LEU* 3.9 28.7 - - + -
381A VAL* 3.5 27.8 - - + -
384A ILE* 3.7 24.0 - - + -
385A TRP 4.2 3.8 - - - -
389A LEU* 3.9 12.3 - - + -
407A THR* 3.5 28.5 - - + -
411A VAL* 4.1 8.5 - - + -
416B ARG 5.1 0.4 + - - -
417B TYR 3.2 0.8 - - - -
418B THR* 1.3 89.6 - - + +
420B GLU* 1.3 53.6 + - - +
421B ASP 3.5 2.7 - - - -
422B ALA* 3.3 6.2 + - + -
423B GLN* 2.7 35.8 + - - +
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Residues in contact with GLU 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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366A VAL* 5.9 0.7 - - - -
370A LYS* 6.4 0.9 - - - +
406B LYS* 3.6 40.5 + - - +
409B HIS* 5.5 1.7 - - - +
410B ASN* 5.2 2.1 - - - +
417B TYR* 3.2 47.1 + - + +
418B THR 3.5 1.4 + - - -
419B PHE* 1.3 76.5 - - - +
421B ASP* 1.3 68.9 + - - +
423B GLN* 3.5 8.8 + - - +
424B GLU* 3.1 23.4 + - + +
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Residues in contact with ASP 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A LYS* 6.0 0.3 - - - +
403A SER* 3.4 21.0 + - - +
406A LYS* 3.4 40.2 + - + +
407A THR* 5.8 0.2 - - - +
421A ASP* 5.1 1.2 - - - +
406B LYS* 4.2 17.6 - - - +
418B THR 5.4 0.2 + - - -
419B PHE 3.5 0.2 - - - -
420B GLU* 1.3 84.0 - - - +
422B ALA* 1.3 61.5 + - - +
424B GLU* 3.4 6.2 + - - +
425B HIS* 3.0 23.6 + - - +
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Residues in contact with ALA 422 (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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362A PHE* 3.9 17.0 - - + -
399A LEU* 3.7 25.3 - - + +
403A SER* 3.8 10.6 + - - -
407A THR* 3.6 24.2 + - + +
419B PHE* 3.3 10.4 + - - +
421B ASP* 1.3 78.3 - - - +
423B GLN* 1.3 57.4 + - - +
425B HIS* 3.2 4.2 + - - +
426B ILE* 2.9 31.4 + - - +
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Residues in contact with GLN 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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362A PHE* 4.0 10.3 - - + -
363A TRP* 3.3 47.0 + - + +
366A VAL* 3.4 26.5 - - + +
367A GLU* 2.7 27.3 + - - +
370A LYS* 3.3 22.0 + - - -
419B PHE 2.7 21.0 + - - +
420B GLU* 3.8 7.3 - - - +
422B ALA* 1.3 69.5 - - - +
424B GLU* 1.3 60.4 + - - +
426B ILE* 3.4 2.6 + - - +
427B TYR* 2.9 28.4 + - - +
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Residues in contact with GLU 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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420B GLU* 3.1 17.2 + - + +
421B ASP* 3.8 7.0 - - - +
423B GLN* 1.3 73.5 - - - +
425B HIS* 1.3 65.6 + - - +
427B TYR* 3.7 17.5 - - - +
428B LYS* 3.1 57.2 + - - +
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Residues in contact with HIS 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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398A ASN 4.6 1.1 - - - -
399A LEU* 4.3 14.5 - - + +
400A ASP* 3.1 44.7 + - + +
403A SER* 3.8 9.9 - - - +
421B ASP 3.0 14.1 + - - +
422B ALA* 3.4 9.0 - - - +
424B GLU* 1.3 78.9 - - - +
426B ILE* 1.3 65.0 + - - +
428B LYS* 3.3 10.2 + - + +
429B LEU* 3.1 54.2 + - + +
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Residues in contact with ILE 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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359A ASN* 3.2 63.5 - - + +
362A PHE* 3.9 21.8 - - + -
363A TRP* 4.4 4.3 - - + -
397A ILE* 4.3 5.4 - - + -
398A ASN 3.8 20.6 - - - +
399A LEU* 4.0 11.2 - - + -
422B ALA 2.9 18.3 + - - +
423B GLN* 3.9 3.6 - - - +
425B HIS* 1.3 72.0 - - - +
427B TYR* 1.3 66.6 + - - +
429B LEU* 3.3 11.8 + - + +
430B MET* 3.0 31.1 + - + +
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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
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334A MET* 3.4 27.2 - - + +
335A ASP* 2.6 34.7 + - - -
338A LEU* 4.8 1.6 - - + -
363A TRP* 3.7 32.5 - + - +
423B GLN 2.9 18.8 + - - +
424B GLU* 3.7 24.2 - - - +
426B ILE* 1.3 76.6 - - - +
428B LYS* 1.3 67.0 + - + +
430B MET* 3.4 9.1 + - + -
431B LYS* 3.2 50.0 + - + +
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Residues in contact with LYS 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 GLU* 3.1 50.1 + - + +
425B HIS* 3.6 12.8 - - + +
426B ILE 3.3 0.2 - - - -
427B TYR* 1.3 79.2 - - + +
429B LEU* 1.3 66.5 + - + +
431B LYS* 3.4 15.6 + - + +
432B SER* 3.5 12.0 + - - -
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Residues in contact with LEU 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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359A ASN* 4.2 22.4 - - - +
398A ASN* 4.8 5.2 - - + +
425B HIS* 3.1 46.3 + - + +
426B ILE* 3.3 14.8 + - + +
428B LYS* 1.3 78.1 - - + +
430B MET* 1.3 58.2 + - - +
432B SER* 2.8 34.9 + - - +
433B ASP* 3.0 13.7 + - + +
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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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334A MET* 3.7 24.7 - - + +
338A LEU* 5.3 1.3 - - + -
347A PHE* 4.9 1.6 - - - -
359A ASN* 4.0 14.1 - - + +
360A LEU* 3.6 44.6 - - + -
363A TRP* 3.7 38.6 - - + -
426B ILE* 3.0 21.9 + - + +
427B TYR* 3.8 6.7 - - - +
429B LEU* 1.3 76.1 - - - +
431B LYS* 1.3 61.0 + - - +
432B SER 3.3 0.3 + - - -
433B ASP 3.4 0.2 + - - -
434B SER* 3.4 29.3 + - - +
435B TYR* 2.9 28.1 + - - +
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Residues in contact with LYS 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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333A GLY* 5.3 1.2 - - - -
334A MET* 3.5 45.5 - - + +
335A ASP* 4.1 6.4 + - - +
427B TYR* 3.2 48.6 + - + +
428B LYS* 3.6 12.3 - - + +
429B LEU 3.2 0.8 - - - -
430B MET* 1.3 75.4 - - - +
432B SER* 1.3 57.5 + - - +
435B TYR* 4.6 7.4 - - + -
436B PRO* 3.4 17.1 - - - +
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Residues in contact with SER 432 (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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428B LYS 3.5 6.7 + - - -
429B LEU* 2.8 32.3 + - - +
431B LYS* 1.3 78.8 - - - +
433B ASP* 1.3 58.6 + - - +
436B PRO* 3.7 11.5 - - - +
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Residues in contact with ASP 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 LEU* 3.0 14.4 + - + +
430B MET* 3.4 1.8 + - - -
431B LYS 3.6 0.2 - - - -
432B SER* 1.3 81.8 - - - +
434B SER* 1.3 71.8 + - - +
435B TYR 3.4 1.1 - - - -
436B PRO* 3.2 3.2 - - - +
437B ARG* 2.7 67.3 + - - +
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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