Contacts of the helix formed by residues 400 - 410 (chain A) in PDB entry 2QFZ
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 ASP 400 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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396A VAL* 3.0 15.2 + - + +
398A ARG 3.5 0.2 - - - -
399A ILE* 1.3 81.5 - - + +
401A GLU* 1.3 64.7 + - - +
402A GLN* 3.3 3.3 + - - +
403A VAL* 3.3 19.5 + - + +
404A HIS 3.1 17.8 + - - -
462A VAL* 3.2 37.3 - - + +
465A ARG* 3.1 40.7 + - - -
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Residues in contact with GLU 401 (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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397A SER 3.5 21.3 + - - +
398A ARG 5.1 1.1 - - - +
399A ILE 4.1 0.2 - - - -
400A ASP* 1.3 76.1 + - - +
402A GLN* 1.3 62.2 + - - +
404A HIS* 3.4 7.4 + - + +
405A ARG* 3.1 44.8 + - - +
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Residues in contact with GLN 402 (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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400A ASP* 3.1 1.5 - - - +
401A GLU* 1.3 76.3 - - - +
403A VAL* 1.3 66.3 + - - +
405A ARG* 4.0 5.0 - - - +
406A HIS* 3.1 24.9 + - - +
465A ARG* 3.0 29.0 + - - +
469A LEU* 3.9 24.0 - - + +
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Residues in contact with VAL 403 (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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396A VAL* 4.5 4.3 - - + -
400A ASP* 3.3 27.0 + - + +
402A GLN* 1.3 77.3 - - - +
404A HIS* 1.3 62.4 + - - +
406A HIS* 3.3 2.4 + - - +
407A LEU* 3.1 35.8 + - + +
461A LEU* 4.3 15.3 - - + -
462A VAL* 4.6 4.0 - - + -
465A ARG* 3.5 37.0 - - + +
468A ILE* 4.2 24.9 - - + +
469A LEU* 4.3 15.0 - - + -
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Residues in contact with HIS 404 (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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393A GLU* 3.6 35.6 + - + -
396A VAL* 4.1 1.7 - - - +
397A SER* 3.8 35.6 - - - -
400A ASP 3.1 13.3 + - - +
401A GLU* 3.5 9.9 - - + +
403A VAL* 1.3 78.0 - - - +
405A ARG* 1.3 65.7 + - + +
407A LEU* 3.6 4.8 + - - +
408A ASP* 3.3 26.9 + - + +
414A TYR* 2.9 32.4 + + - +
275B ASP* 5.8 1.0 + - - -
278B ARG* 4.8 12.2 + - - -
279B GLN* 6.1 2.8 - - - -
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Residues in contact with ARG 405 (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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401A GLU* 3.1 29.5 + - - +
402A GLN* 4.1 4.5 - - - +
404A HIS* 1.3 78.2 - - + +
406A HIS* 1.3 56.5 + - - +
407A LEU 3.2 0.4 - - - -
408A ASP* 3.5 7.3 - - - +
409A GLN* 2.7 37.6 + - - +
275B ASP* 3.7 11.5 + - - -
278B ARG* 3.3 59.0 - - - +
282B ILE* 5.8 1.7 - - + +
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Residues in contact with HIS 406 (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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402A GLN 3.1 17.7 + - - +
403A VAL* 3.7 4.0 - - - +
405A ARG* 1.3 78.4 - - - +
407A LEU* 1.3 61.9 + - - +
409A GLN* 3.4 5.6 + - - -
410A HIS* 2.9 53.6 + + - +
468A ILE* 2.6 40.4 + - + -
469A LEU* 3.4 37.9 + - + +
471A GLU 2.7 22.5 + - - -
472A LYS* 4.4 4.9 - - - -
477A LEU* 4.1 9.2 - - + +
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Residues in contact with LEU 407 (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 VAL* 3.1 30.2 + - + +
404A HIS 3.8 5.6 - - - +
406A HIS* 1.3 76.2 - - - +
408A ASP* 1.3 60.4 + - - +
410A HIS 3.3 1.0 + - - -
411A GLU 3.1 3.8 + - - -
412A VAL* 2.9 46.0 + - + +
414A TYR* 3.9 38.1 - - + +
417A PHE* 4.2 14.6 - - + -
461A LEU* 4.4 3.8 - - + -
468A ILE* 4.4 13.2 - - + -
477A LEU* 4.2 16.4 - - + -
481A LEU* 3.7 28.7 - - + -
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Residues in contact with ASP 408 (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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404A HIS* 3.3 15.6 + - + +
405A ARG* 3.3 10.7 + - - +
406A HIS 3.3 0.2 - - - -
407A LEU* 1.3 77.0 - - - +
409A GLN* 1.3 64.5 + - - +
411A GLU* 3.1 14.9 + - - +
412A VAL 4.3 3.1 + - - -
278B ARG* 4.1 7.8 + - - +
279B GLN* 4.6 16.0 - - - +
282B ILE* 3.5 28.9 - - - +
283B ASP* 5.4 0.5 - - - +
286B ARG* 3.6 9.4 + - - -
320B GLN* 5.5 0.5 - - - +
1011B UNX 2.6 27.7 - - - -
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Residues in contact with GLN 409 (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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405A ARG 2.7 21.3 + - - +
406A HIS* 3.6 8.5 - - - +
408A ASP* 1.3 74.4 + - - +
410A HIS* 1.3 76.8 + - + +
411A GLU* 4.5 0.2 - - - +
282B ILE* 4.0 25.4 - - - +
286B ARG* 2.5 55.8 + - - +
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Residues in contact with HIS 410 (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 HIS* 2.9 58.1 + + - +
409A GLN* 1.3 95.9 - - + +
411A GLU* 1.3 69.1 + - - +
412A VAL* 3.2 3.1 + - - +
472A LYS* 3.2 46.1 + - + +
474A PHE* 3.1 31.3 - - - +
477A LEU* 3.8 21.1 - - + -
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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