Contacts of the helix formed by residues 402 - 413 (chain C) in PDB entry 2QPA
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 THR 402 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318C VAL* 5.9 0.2 - - - -
319C LEU* 3.9 3.4 - - + -
400C ASP* 3.4 10.2 + - - +
401C LEU* 1.3 75.2 - - - +
403C ILE* 1.3 58.4 + - - +
404C LYS* 2.7 23.5 + - + +
405C ASP* 2.6 45.7 + - - +
406C PHE* 4.1 2.9 + - - -
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Residues in contact with ILE 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319C LEU* 3.2 41.7 - - + +
323C ASP* 4.2 17.3 - - + +
327C LEU* 5.3 6.8 - - + +
402C THR* 1.3 74.1 - - + +
404C LYS* 1.3 57.2 + - - +
405C ASP 3.2 0.7 - - - -
406C PHE* 3.9 8.7 + - - +
407C LEU* 3.0 32.8 + - + +
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Residues in contact with LYS 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402C THR* 3.6 20.3 - - + +
403C ILE* 1.3 79.0 - - - +
405C ASP* 1.3 64.3 + - - +
407C LEU* 3.2 16.6 - - + +
408C LYS* 3.0 22.5 + - - +
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Residues in contact with ASP 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346C ALA* 3.9 11.8 - - + +
349C GLN* 3.2 36.9 - - + +
350C PRO* 4.5 2.5 - - - +
400C ASP 4.0 2.4 - - - +
401C LEU* 3.4 20.1 - - + -
402C THR* 2.6 50.7 + - - +
404C LYS* 1.3 69.1 - - - +
406C PHE* 1.3 67.6 + - + +
408C LYS* 3.2 15.5 + - - +
409C ALA* 3.2 11.4 + - - +
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Residues in contact with PHE 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308C PHE* 4.3 20.2 - + - -
312C VAL* 3.4 33.9 - - + -
317C SER* 6.2 1.8 - - - -
319C LEU* 3.9 23.8 - - + -
324C TYR* 5.5 3.1 - + - -
327C LEU* 4.0 31.6 - - + -
342C VAL* 4.8 5.2 - - + -
343C VAL* 4.2 19.7 - - + -
346C ALA* 3.6 26.0 - - + -
347C LEU* 5.3 3.1 - - + -
401C LEU* 5.1 15.7 - - + -
402C THR 4.2 11.7 - - - -
403C ILE* 4.2 3.8 - - - +
404C LYS 3.4 0.2 - - - -
405C ASP* 1.3 77.5 - - + +
407C LEU* 1.3 52.0 + - - +
409C ALA* 2.6 25.5 + - - +
410C ILE* 2.6 20.9 + - - +
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Residues in contact with LEU 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327C LEU* 5.3 5.2 - - + -
330C MET* 4.8 21.5 - - + -
403C ILE* 3.0 27.3 + - + +
404C LYS* 3.2 19.7 - - + +
406C PHE* 1.3 79.6 - - + +
408C LYS* 1.3 61.9 + - - +
410C ILE* 3.4 14.4 + - + +
411C LYS* 3.2 27.4 + - - +
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Residues in contact with LYS 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349C GLN* 5.3 10.3 - - + +
404C LYS 3.0 11.8 + - - +
405C ASP* 3.5 10.5 - - - +
406C PHE 3.1 0.2 - - - -
407C LEU* 1.3 76.9 - - - +
409C ALA* 1.3 58.1 + - - +
411C LYS* 3.5 9.5 + - - +
412C SER* 3.0 25.0 + - - -
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Residues in contact with ALA 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342C VAL* 3.6 25.8 - - + +
345C ASP* 3.2 29.1 - - + +
346C ALA* 4.2 2.2 - - + -
349C GLN* 5.8 0.2 - - - +
405C ASP 3.2 7.9 + - - +
406C PHE* 2.6 19.8 + - - +
408C LYS* 1.3 72.9 - - - +
410C ILE* 1.3 62.7 + - - +
412C SER* 3.0 9.1 + - - -
413C THR* 2.8 25.3 + - - -
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Residues in contact with ILE 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308C PHE* 4.5 7.0 - - + -
327C LEU* 3.5 30.1 - - + -
330C MET* 3.9 27.1 - - + +
331C THR* 4.5 5.6 - - + -
334C TYR* 3.7 22.7 + - + +
342C VAL* 3.7 21.8 - - + -
406C PHE 2.6 19.5 + - - +
407C LEU* 3.8 14.8 - - + +
409C ALA* 1.3 70.3 - - - +
411C LYS* 1.3 65.2 + - + +
413C THR 2.3 31.4 - - - +
414C ARG* 4.4 0.3 - - - -
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Residues in contact with LYS 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407C LEU 3.2 13.0 + - - +
408C LYS* 3.5 13.0 - - - +
410C ILE* 1.3 82.2 - - + +
412C SER* 1.3 62.9 + - - +
413C THR* 3.1 3.5 + - - -
414C ARG* 4.4 3.5 + - - +
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Residues in contact with SER 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345C ASP* 5.3 7.4 - - - -
408C LYS 3.0 14.9 + - - -
409C ALA* 3.0 14.9 + - - -
411C LYS* 1.3 75.6 - - - +
413C THR* 1.3 63.1 + - - +
414C ARG 4.2 0.6 + - - -
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Residues in contact with THR 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334C TYR* 3.0 14.4 + - + -
338C ASP* 5.4 7.2 - - + +
341C VAL* 4.7 20.3 - - + +
342C VAL* 4.6 17.2 - - + +
345C ASP* 6.1 1.4 - - - +
409C ALA 2.8 12.5 + - - -
410C ILE* 2.3 23.5 - - - +
411C LYS 4.1 0.4 - - - -
412C SER* 1.3 82.0 + - - +
414C ARG* 1.3 71.0 + - - +
416C THR* 6.0 0.4 - - - +
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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