Contacts of the helix formed by residues 424 - 430 (chain B) in PDB entry 2QCU
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 ASN 424 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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426A GLU* 4.0 13.5 + - - -
157B GLN* 3.6 12.1 + - - +
387B PRO 4.1 0.3 - - - -
388B GLY* 3.7 15.9 + - - +
421B TYR* 3.1 18.9 + - + +
423B SER* 1.3 76.8 + - - +
425B SER* 1.3 65.0 + - - +
426B GLU 3.1 3.4 - - - -
427B LEU* 3.1 19.0 + - + +
428B LEU* 3.2 11.4 + - - +
453B TYR* 3.3 25.1 + - + +
458B GLU* 5.6 0.7 - - - +
810B TAM 3.1 41.0 + - - +
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Residues in contact with SER 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B TYR* 4.7 0.7 - - - -
402B LEU* 3.9 27.1 - - - +
417B TYR* 3.3 34.7 + - - +
421B TYR* 3.7 9.0 - - - +
422B GLY 2.9 20.4 + - - -
423B SER 3.2 0.6 - - - -
424B ASN* 1.3 77.9 - - - +
426B GLU* 1.3 57.0 + - - +
428B LEU* 3.1 8.2 + - - +
429B LEU* 2.9 37.3 + - - +
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Residues in contact with GLU 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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161A ARG* 5.1 9.8 + - - +
424A ASN* 4.9 3.8 + - - -
427A LEU* 4.1 17.3 - - + +
821A IMD 4.2 23.0 + - - -
398B TYR* 4.7 11.2 - - - +
402B LEU* 5.3 0.9 - - + -
405B ARG* 4.7 9.2 + - - -
406B TYR* 3.3 32.2 + - + +
423B SER 4.1 8.9 + - - +
424B ASN 3.1 1.0 - - - -
425B SER* 1.3 78.9 - - - +
427B LEU* 1.3 55.8 + - - +
429B LEU* 3.9 0.9 - - - +
430B GLY* 3.0 26.7 + - - +
802B SO4 3.0 25.8 + - - +
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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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426A GLU* 3.6 44.4 - - + +
427A LEU* 4.2 16.3 - - + +
430A GLY* 4.2 15.3 - - - -
424B ASN* 3.1 15.7 + - - +
426B GLU* 1.3 75.3 - - - +
428B LEU* 1.3 67.5 + - - +
430B GLY* 3.6 8.7 + - - -
453B TYR* 3.7 24.9 - - + +
457B HIS* 3.9 15.6 - - + +
810B TAM 3.7 28.5 - - + +
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Residues in contact with LEU 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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417B TYR* 3.9 32.3 - - + +
421B TYR* 3.4 43.5 - - + -
424B ASN 3.2 7.8 + - - +
425B SER* 3.1 10.4 + - - +
427B LEU* 1.3 82.2 - - - +
429B LEU* 1.3 69.3 + - + +
430B GLY* 3.4 0.7 + - - -
449B ALA* 4.2 20.9 - - + +
450B GLU* 4.0 22.4 - - + -
453B TYR* 3.6 33.4 - - + +
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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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402B LEU* 4.8 0.9 - - + -
406B TYR* 3.5 51.8 - - + -
408B PHE* 4.2 14.8 - - + -
409B LEU* 4.2 15.0 - - + -
417B TYR* 3.8 27.6 - - + -
425B SER* 2.9 23.8 + - - +
426B GLU 4.1 0.7 - - - +
428B LEU* 1.3 83.8 - - + +
430B GLY* 1.3 66.8 + - - +
431B ASN 3.2 0.3 + - - -
432B ALA* 2.9 24.7 + - + +
438B LEU* 3.8 23.8 - - + -
449B ALA* 5.9 0.7 - - - +
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Residues in contact with GLY 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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427A LEU* 4.2 11.8 - - - +
457A HIS* 3.4 19.7 - - - -
405B ARG* 5.0 1.0 + - - -
406B TYR* 4.8 7.8 + - - -
426B GLU 3.0 16.3 + - - +
427B LEU 4.1 7.0 - - - -
428B LEU 3.2 3.4 - - - -
429B LEU* 1.3 80.7 - - - +
431B ASN* 1.3 58.5 + - - -
432B ALA 3.4 3.8 + - - +
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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