Contacts of the helix formed by residues 422 - 429 (chain B) in PDB entry 2WSC
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 LEU 422 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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418B ILE 2.9 28.1 + - - +
419B ILE* 4.0 2.2 - - - -
420B SER 2.9 4.4 - - - +
421B HIS* 1.3 76.6 - - - +
423B SER* 1.3 61.1 + - - +
424B TRP 3.2 0.9 - - - -
425B ALA* 2.9 28.8 + - - +
426B SER* 3.4 5.9 + - - -
528B HIS* 3.9 15.4 + - - +
531B THR* 3.6 23.3 - - - +
532B LEU* 4.1 12.8 - - + -
535B VAL* 3.2 33.2 - - + -
1769B CLA 3.5 45.8 - - + -
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Residues in contact with SER 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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703A LEU* 5.0 1.8 - - - -
707A ILE* 4.1 8.7 - - - +
1813A CLA 4.0 20.6 - - - -
419B ILE* 4.9 1.6 - - - -
420B SER* 2.8 18.7 + - - +
422B LEU* 1.3 81.0 - - - +
424B TRP* 1.3 62.8 + - - +
426B SER* 3.4 3.6 + - - +
427B LEU* 3.1 28.2 + - - +
532B LEU* 4.4 21.3 - - - +
1735B CLA 3.2 24.8 + - - -
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Residues in contact with TRP 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 SER 2.3 32.0 + - - +
421B HIS* 4.4 7.6 - - + -
423B SER* 1.3 67.6 + - - +
425B ALA* 1.3 89.4 + - + +
427B LEU* 4.7 2.0 - - - +
428B PHE* 3.3 41.7 + + - +
1735B CLA 2.9 53.9 + - + +
1761B CLA 3.2 51.0 - + + +
1762B CLA 2.7 24.8 + - + -
1768B CLA 3.8 27.6 - - + -
1769B CLA 3.6 33.9 - + + -
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Residues in contact with ALA 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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421B HIS 4.8 3.1 - - - +
422B LEU* 2.9 16.3 + - - +
424B TRP* 1.3 98.8 - - + +
426B SER* 1.3 52.4 + - - +
428B PHE* 3.5 2.8 - - - +
429B LEU* 2.6 41.9 + - + +
528B HIS* 3.8 34.5 - - + +
1768B CLA 6.1 3.6 - - + -
1769B CLA 4.8 5.6 - - + +
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Residues in contact with SER 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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1813A CLA 3.8 18.6 - - - -
422B LEU 3.4 2.5 + - - -
423B SER 3.4 7.7 + - - -
425B ALA* 1.3 77.9 - - - +
427B LEU* 1.3 51.1 + - - +
429B LEU* 2.7 10.7 + - - -
430B GLY* 2.3 37.9 + - - -
525B LEU* 4.2 1.7 - - - +
528B HIS* 3.6 8.7 + - - +
529B THR* 2.9 46.4 + - - -
532B LEU* 4.1 8.4 - - - +
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Residues in contact with LEU 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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1813A CLA 3.5 43.2 - - + +
423B SER 3.1 11.3 + - - +
424B TRP* 4.7 2.2 - - - +
426B SER* 1.3 76.3 - - - +
428B PHE* 1.3 63.7 + - - +
431B PHE* 3.1 61.3 + - + -
1735B CLA 2.9 60.8 - - + +
1762B CLA 3.2 13.5 - - - +
1778B BCR 4.4 13.5 - - + -
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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 TRP* 3.3 32.0 + + + +
425B ALA* 3.4 3.7 + - - +
426B SER 3.1 0.6 - - - -
427B LEU* 1.3 75.9 - - - +
429B LEU* 1.3 66.5 + - + +
430B GLY 2.7 14.5 + - - -
432B HIS* 3.2 48.9 + + + +
1762B CLA 2.8 74.2 - + + +
1768B CLA 3.8 57.4 - - + -
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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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425B ALA* 2.6 24.8 + - + +
426B SER* 3.0 4.0 - - - +
428B PHE* 1.3 80.3 - - + +
430B GLY* 1.3 62.7 + - - +
432B HIS* 5.2 2.2 - - + -
433B THR* 3.1 24.0 + - - +
521B HIS* 3.9 15.3 - - + +
524B ALA* 3.4 11.4 - - + +
525B LEU* 3.4 45.1 - - + +
528B HIS* 4.0 5.4 - - + -
1768B CLA 3.4 55.2 - - + -
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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