Contacts of the helix formed by residues 419 - 433 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416A ARG 5.0 0.8 + - - -
417A TYR* 3.1 1.2 - - - +
418A THR* 1.3 90.7 - - + +
420A GLU* 1.3 54.5 + - - +
421A ASP 3.5 1.3 - - - -
422A ALA* 3.2 7.7 + - + -
423A GLN* 2.7 35.6 + - - +
362B PHE* 4.0 17.3 - + + -
366B VAL* 3.8 32.7 - - + +
369B LEU* 3.8 28.0 - - + -
381B VAL* 3.5 28.5 - - + -
384B ILE* 3.7 23.8 - - + -
385B TRP* 4.1 4.7 - - - -
389B LEU* 3.9 13.0 - - + -
407B THR* 3.6 28.9 - - + -
411B VAL* 4.3 6.1 - - + -
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Residues in contact with GLU 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A LYS* 3.1 47.2 + - - +
409A HIS* 5.1 4.4 + - - +
410A ASN* 5.3 1.9 - - - +
417A TYR* 3.2 44.5 + - + +
418A THR 3.5 1.2 + - - -
419A PHE* 1.3 76.5 - - - +
421A ASP* 1.3 60.9 + - - +
423A GLN* 3.5 8.3 + - - +
424A GLU* 3.1 28.0 + - + +
366B VAL* 5.8 0.7 - - - -
370B LYS* 6.5 0.9 - - - +
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Residues in contact with ASP 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A LYS* 2.5 34.3 + - - -
418A THR 5.4 0.2 + - - -
419A PHE 3.5 0.4 - - - -
420A GLU* 1.3 76.5 - - - +
422A ALA* 1.3 64.1 + - - +
424A GLU* 3.5 6.2 + - - +
425A HIS* 3.1 22.2 + - - +
403B SER* 4.0 17.9 - - - +
406B LYS* 3.3 39.3 + - + +
407B THR* 5.8 0.4 - - - +
421B ASP* 5.1 2.1 - - - +
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Residues in contact with ALA 422 (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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419A PHE* 3.2 10.3 + - - +
421A ASP* 1.3 74.7 - - - +
423A GLN* 1.3 60.9 + - - +
425A HIS* 3.2 4.3 + - - +
426A ILE* 3.0 31.5 + - - +
362B PHE* 4.0 16.6 - - + -
399B LEU* 3.8 23.8 - - + -
403B SER* 3.9 11.5 - - - +
407B THR* 3.7 23.3 + - + +
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Residues in contact with GLN 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A PHE 2.7 21.4 + - - +
420A GLU* 3.8 7.0 - - - +
422A ALA* 1.3 73.8 - - - +
424A GLU* 1.3 56.2 + - - +
426A ILE* 3.8 1.8 - - - +
427A TYR* 2.9 28.9 + - + +
362B PHE* 4.0 10.7 - - + -
363B TRP* 3.4 49.4 + - + +
366B VAL* 3.5 20.4 - - + +
367B GLU* 2.7 29.8 + - - +
370B LYS* 3.1 25.0 + - - -
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Residues in contact with GLU 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A GLU* 3.1 17.3 + - + +
421A ASP* 3.8 6.7 - - - +
422A ALA 3.2 0.2 - - - -
423A GLN* 1.3 74.5 - - - +
425A HIS* 1.3 64.8 + - - +
427A TYR* 3.4 19.4 + - - +
428A LYS* 3.1 55.2 + - - +
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Residues in contact with HIS 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A ASP 3.1 14.2 + - - +
422A ALA* 3.3 10.8 - - - +
424A GLU* 1.3 79.8 - - - +
426A ILE* 1.3 62.6 + - + +
428A LYS* 3.4 8.6 + - - +
429A LEU* 3.0 45.3 + - + +
398B ASN 4.1 10.3 + - - -
399B LEU* 4.0 19.2 - - + -
400B ASP* 3.1 45.8 + - + +
403B SER* 4.4 0.4 - - - +
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Residues in contact with ILE 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A ALA 3.0 19.8 + - - +
423A GLN* 3.9 4.0 - - - +
425A HIS* 1.3 79.9 - - + +
427A TYR* 1.3 66.4 + - - +
429A LEU* 3.3 6.4 + - + +
430A MET* 3.0 30.0 + - + +
359B ASN* 3.4 61.0 - - + +
362B PHE* 3.9 22.0 - - + -
363B TRP* 4.5 3.8 - - + -
397B ILE* 4.2 5.2 - - + -
398B ASN 3.9 20.2 - - - +
399B LEU* 3.9 11.4 - - + -
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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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423A GLN 2.9 18.9 + - - +
424A GLU* 3.6 22.7 - - - +
426A ILE* 1.3 77.7 - - - +
428A LYS* 1.3 67.7 + - + +
430A MET* 3.5 9.3 + - + +
431A LYS* 3.1 49.1 + - + +
334B MET* 3.4 31.8 - - + +
335B ASP* 2.6 37.4 + - - -
338B LEU* 4.7 5.4 - - + -
363B TRP* 3.7 29.1 - + - +
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Residues in contact with LYS 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 GLU* 3.1 54.5 + - - +
425A HIS* 3.8 7.4 - - - +
427A TYR* 1.3 81.9 - - + +
429A LEU* 1.3 65.2 + - - +
431A LYS* 3.5 23.3 + - + +
432A SER* 3.5 9.2 + - - -
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Residues in contact with LEU 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 HIS* 3.0 39.6 + - + +
426A ILE* 3.5 14.1 - - + +
428A LYS* 1.3 74.3 - - - +
430A MET* 1.3 58.2 + - - +
432A SER* 3.0 16.9 + - - +
433A ASP* 2.9 37.6 + - + +
359B ASN* 3.5 26.0 - - - +
398B ASN* 4.9 6.3 - - + +
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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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426A ILE* 3.0 22.7 + - + +
427A TYR* 3.8 10.5 - - + +
428A LYS 3.4 0.4 - - - -
429A LEU* 1.3 74.7 - - - +
431A LYS* 1.3 61.4 + - - +
432A SER 3.3 0.7 + - - -
433A ASP* 3.3 2.5 + - - -
434A SER* 4.0 25.6 - - - +
435A TYR* 2.8 28.4 + - - +
334B MET* 3.6 26.0 - - + +
338B LEU* 5.3 1.1 - - + -
347B PHE* 5.0 1.8 - - - -
359B ASN* 4.0 12.8 - - + +
360B LEU* 3.6 44.9 - - + -
363B TRP* 3.8 34.1 - - + -
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Residues in contact with LYS 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A TYR* 3.1 54.5 + - + +
428A LYS* 3.5 17.4 - - + +
429A LEU 3.3 0.2 - - - -
430A MET* 1.3 78.1 - - - +
432A SER* 1.3 56.6 + - - +
435A TYR* 4.4 8.9 - - + +
436A PRO* 3.4 16.3 - - - +
334B MET* 3.8 23.5 - - + +
335B ASP* 4.5 7.6 + - - -
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Residues in contact with SER 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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428A LYS 3.5 7.4 + - - -
429A LEU* 3.0 24.4 + - - +
431A LYS* 1.3 78.0 - - - +
433A ASP* 1.3 59.9 + - - +
436A PRO* 3.8 12.5 - - - +
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Residues in contact with ASP 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 LEU* 2.9 23.6 + - + +
430A MET 3.3 1.8 + - - -
432A SER* 1.3 80.7 - - - +
434A SER* 1.3 75.4 + - - +
435A TYR 3.2 1.7 + - - -
436A PRO* 3.3 3.9 - - - +
437A ARG* 3.1 33.3 + - - +
440A ARG* 5.2 1.2 + - - -
359B ASN* 5.0 8.0 + - - +
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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