Contacts of the helix formed by residues 400 - 410 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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396B VAL* 2.8 17.9 + - + +
399B ILE* 1.3 80.0 - - + +
401B GLU* 1.3 65.8 + - - +
402B GLN* 2.9 8.7 + - - +
403B VAL* 3.0 34.6 + - + +
404B HIS 3.1 9.2 + - - -
462B VAL* 3.8 30.3 - - + +
465B ARG* 3.2 41.3 + - - +
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Residues in contact with GLU 401 (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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396B VAL 3.7 0.8 + - - -
397B SER 3.5 21.1 + - - +
398B ARG 4.9 1.3 + - - +
399B ILE 4.0 0.8 - - - -
400B ASP* 1.3 74.1 - - - +
402B GLN* 1.3 57.1 + - - +
404B HIS* 3.6 6.3 + - + +
405B ARG* 3.0 49.4 + - - +
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Residues in contact with GLN 402 (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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400B ASP* 3.0 9.5 - - - +
401B GLU* 1.3 76.8 - - - +
403B VAL* 1.3 63.2 + - - +
405B ARG* 4.3 4.7 - - - +
406B HIS* 3.3 14.0 + - - +
465B ARG* 3.3 22.8 + - - +
469B LEU* 3.3 36.2 - - + +
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Residues in contact with VAL 403 (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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396B VAL* 4.7 5.2 - - + -
400B ASP* 3.0 31.5 + - + +
402B GLN* 1.3 76.9 - - - +
404B HIS* 1.3 63.5 + - - +
406B HIS* 3.2 4.4 + - - +
407B LEU* 3.1 27.9 + - + +
461B LEU* 4.3 22.7 - - + +
462B VAL* 5.5 2.7 - - + +
465B ARG* 3.6 29.2 - - + -
468B ILE* 4.1 27.3 - - + +
469B LEU* 4.2 17.0 - - + -
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Residues in contact with HIS 404 (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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279A GLN* 6.3 1.4 - - - -
393B GLU* 3.6 34.9 + - + -
396B VAL* 4.1 1.3 - - + +
397B SER* 3.6 37.6 - - - +
400B ASP 3.1 15.2 + - - +
401B GLU* 3.7 4.9 - - + +
403B VAL* 1.3 78.5 - - - +
405B ARG* 1.3 71.1 + - + +
407B LEU* 3.5 6.4 + - - +
408B ASP* 3.2 24.6 + - + +
414B TYR* 2.6 35.7 + + - +
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Residues in contact with ARG 405 (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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275A ASP* 4.4 13.1 + - - -
278A ARG* 3.5 53.6 - - - +
401B GLU* 3.0 33.0 + - - +
402B GLN* 4.3 4.3 - - - +
404B HIS* 1.3 83.2 - - + +
406B HIS* 1.3 61.0 + - - +
408B ASP* 3.4 6.4 + - - +
409B GLN* 2.8 33.0 + - - +
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Residues in contact with HIS 406 (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 GLN 3.3 18.5 + - - +
403B VAL 3.2 4.8 + - - +
405B ARG* 1.3 80.1 - - - +
407B LEU* 1.3 55.9 + - - +
409B GLN* 4.1 4.5 - - - -
410B HIS* 2.8 65.8 + + - +
468B ILE* 2.8 35.3 + - + -
469B LEU* 3.5 30.5 + - + +
471B GLU 2.8 24.7 + - - -
472B LYS* 4.7 3.8 - - + -
477B LEU* 4.2 8.1 - - + +
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Residues in contact with LEU 407 (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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403B VAL* 3.1 22.1 + - + +
404B HIS* 3.6 5.8 - - - +
405B ARG 3.3 0.2 - - - -
406B HIS* 1.3 73.4 - - - +
408B ASP* 1.3 60.4 + - - +
410B HIS 3.3 1.7 + - - -
411B GLU 3.0 8.7 + - - -
412B VAL* 2.9 49.3 + - + +
414B TYR* 3.6 42.0 - - + +
417B PHE* 4.2 15.3 - - + -
461B LEU* 4.4 9.9 - - + -
468B ILE* 4.5 12.6 - - + -
477B LEU* 4.5 11.4 - - + -
481B LEU* 3.8 27.1 - - + -
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Residues in contact with ASP 408 (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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278A ARG* 5.6 0.5 + - - -
279A GLN* 4.8 16.5 - - - +
282A ILE* 4.3 22.8 - - - +
283A ASP* 5.1 0.2 - - - -
286A ARG* 4.1 9.0 + - - -
320A GLN* 4.0 0.9 - - - +
1012A UNX 2.4 29.1 - - - -
404B HIS* 3.2 17.3 + - + +
405B ARG* 3.8 8.7 - - - +
407B LEU* 1.3 78.4 - - - +
409B GLN* 1.3 64.4 + - - +
411B GLU* 3.2 15.0 + - - +
412B VAL 4.3 3.8 + - - -
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Residues in contact with GLN 409 (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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278A ARG* 5.1 6.2 + - - -
282A ILE* 3.9 35.6 - - - +
286A ARG* 3.7 23.3 + - - +
405B ARG 2.8 19.2 + - - +
406B HIS* 3.7 8.5 - - - +
407B LEU 3.2 0.2 - - - -
408B ASP* 1.3 79.6 + - - +
410B HIS* 1.3 73.0 + - + +
411B GLU* 3.6 1.0 + - - +
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Residues in contact with HIS 410 (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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406B HIS* 2.8 57.6 + + - +
408B ASP 3.3 0.4 - - - -
409B GLN* 1.3 90.9 - - + +
411B GLU* 1.3 65.7 + - - +
412B VAL* 3.3 3.4 + - - +
471B GLU 4.3 0.2 - - - -
472B LYS* 3.0 53.1 + - + +
473B ASP 4.7 1.6 - - - -
474B PHE* 3.0 29.7 - - - +
477B LEU* 3.6 21.5 - - + -
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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