Contacts of the helix formed by residues 420 - 430 (chain A) in PDB entry 2W3C
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 SER 420 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366A VAL* 4.5 3.8 - - - -
406A THR* 2.8 29.8 + - - +
419A VAL* 1.3 77.6 - - - +
421A ALA* 1.3 63.8 - - - +
423A GLN* 3.3 16.0 + - - +
424A LEU* 3.1 28.7 + - - +
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Residues in contact with ALA 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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365A ILE* 4.2 6.5 - - + -
366A VAL* 4.3 6.5 - - + +
369A LEU* 3.7 26.6 - - + +
403A ILE* 3.8 30.5 - - + -
406A THR* 3.6 9.3 + - + +
420A SER* 1.3 72.2 - - - +
422A GLY* 1.3 64.3 + - - +
424A LEU* 3.2 5.8 + - - +
425A LEU* 3.0 29.8 + - - +
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Residues in contact with GLY 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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403A ILE 4.4 0.6 + - - -
406A THR* 2.7 30.0 - - - +
407A LEU* 3.6 29.6 - - - +
421A ALA* 1.3 73.0 - - - +
423A GLN* 1.3 55.3 + - - -
425A LEU* 3.4 4.2 + - - +
426A CYS* 2.9 34.9 + - - +
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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
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406A THR* 4.2 1.7 + - - +
419A VAL* 4.3 14.5 - - + +
420A SER* 3.3 21.8 + - - +
421A ALA 3.3 0.8 - - - -
422A GLY* 1.3 72.5 - - - +
424A LEU* 1.3 60.9 + - - +
426A CYS* 3.4 7.3 + - - +
427A GLY* 3.0 25.5 + - - -
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Residues in contact with LEU 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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366A VAL* 4.0 15.9 - - + +
369A LEU* 4.1 23.6 - - + +
370A MET* 3.7 40.8 - - + -
373A VAL* 3.9 20.8 - - + +
419A VAL* 3.8 26.5 - - + -
420A SER 3.1 19.9 + - - +
421A ALA* 3.7 5.6 - - - +
423A GLN* 1.3 76.0 - - - +
425A LEU* 1.3 57.7 + - - +
427A GLY* 3.4 2.5 + - - -
428A GLY* 3.0 22.0 + - - -
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Residues in contact with LEU 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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369A LEU* 4.1 20.6 - - + -
372A MET* 4.3 3.4 - - + -
373A VAL* 5.5 0.9 - - + -
389A PHE* 4.7 7.9 - - + -
403A ILE* 3.9 28.0 - - + -
407A LEU* 5.0 2.2 - - + -
421A ALA 3.0 22.1 + - - +
422A GLY* 3.8 6.1 - - - +
424A LEU* 1.3 74.6 - - - +
426A CYS* 1.3 60.7 + - - +
428A GLY 3.2 0.6 + - - +
429A LEU* 2.9 34.0 + - - +
440A ALA* 3.6 21.1 - - + +
443A ALA* 3.8 26.2 - - + -
444A LEU* 4.2 28.0 - - + +
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Residues in contact with CYS 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 LEU* 3.7 25.8 - - - -
422A GLY 2.9 21.0 + - - +
423A GLN* 3.9 8.1 - - - +
425A LEU* 1.3 76.2 - - - +
427A GLY* 1.3 62.4 + - - +
428A GLY 3.4 0.3 + - - -
429A LEU* 3.6 7.1 + - - -
430A PHE* 3.1 35.2 + - + +
444A LEU* 5.9 0.2 - - - -
461A VAL* 5.1 2.7 - - - -
463A LEU* 4.3 22.4 - - + -
474A LEU* 4.4 10.8 - - - -
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Residues in contact with GLY 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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373A VAL* 5.1 4.8 - - - +
423A GLN* 3.0 16.8 + - - -
424A LEU 3.8 2.9 - - - -
426A CYS* 1.3 77.6 - - - +
428A GLY* 1.3 56.6 + - - +
430A PHE* 3.8 1.3 + - - -
431A SER* 3.2 27.2 + - - -
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Residues in contact with GLY 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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373A VAL* 4.3 13.4 - - - +
424A LEU 3.0 14.2 + - - -
425A LEU 3.2 3.6 + - - -
426A CYS 3.2 0.2 - - - -
427A GLY* 1.3 73.6 - - - +
429A LEU* 1.3 52.5 + - - +
430A PHE 3.1 2.3 + - - -
431A SER* 3.3 9.8 + - - -
436A SER* 3.9 6.7 - - - -
437A ASN* 2.7 37.2 + - - -
440A ALA* 3.8 14.4 - - - -
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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 LEU 2.9 18.9 + - - +
426A CYS* 3.8 9.9 - - - +
428A GLY* 1.3 75.7 - - - +
430A PHE* 1.3 77.3 + - + +
437A ASN* 2.9 21.7 + - - +
440A ALA* 3.6 3.5 - - + +
441A ALA* 3.9 28.3 - - + +
444A LEU* 3.6 23.3 - - + -
474A LEU* 3.6 30.5 - - + -
478A CYS* 4.2 6.7 - - - -
481A ILE* 5.3 2.9 - - - +
490A THR* 5.6 0.2 + - - -
494A LEU* 3.9 32.3 - - + +
497A LEU* 4.2 4.9 - - + -
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Residues in contact with PHE 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 CYS* 3.1 30.2 + - + +
427A GLY* 3.9 3.1 - - - -
428A GLY 3.1 0.4 - - - -
429A LEU* 1.3 96.6 - - + +
431A SER* 1.3 66.5 + - - +
432A THR* 5.6 0.2 - - - +
463A LEU* 3.7 35.4 - - + -
474A LEU* 3.9 16.6 - - + -
477A GLN* 3.4 19.7 - - + -
478A CYS* 4.5 6.5 - - - -
481A ILE* 3.3 36.3 - - + -
494A LEU* 5.9 1.3 - - + -
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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