Contacts of the helix formed by residues 418 - 431 (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 ASN 418 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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416C THR 4.2 1.3 + - - +
417C VAL* 1.3 76.0 - - - +
419C GLU* 1.3 68.6 + - - +
420C ASP* 2.5 41.6 + - - +
421C ASP* 2.8 34.3 + - - +
422C LEU* 3.1 12.2 + - - +
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Residues in contact with GLU 419 (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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417C VAL 4.4 0.2 + - - -
418C ASN* 1.3 71.5 - - - +
420C ASP* 1.3 57.3 + - - +
422C LEU* 2.7 32.8 + - - +
423C LEU* 2.8 30.0 + - + +
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Residues in contact with ASP 420 (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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418C ASN* 2.5 30.8 + - - +
419C GLU* 1.3 80.7 + - - +
421C ASP* 1.3 63.4 + - - +
423C LEU* 3.5 22.5 + - - +
424C LYS* 3.5 12.5 + - - +
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Residues in contact with ASP 421 (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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174C PRO* 6.3 2.7 - - + -
278C ILE* 5.7 1.4 - - - +
280C TRP* 3.7 27.9 + - + -
417C VAL* 5.2 9.9 - - + -
418C ASN* 2.8 30.5 + - - +
420C ASP* 1.3 80.2 - - - +
422C LEU* 1.3 60.3 + - - +
423C LEU 3.2 0.4 - - - -
424C LYS* 3.6 8.0 + - - +
425C GLN* 3.2 28.3 + - - +
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Residues in contact with LEU 422 (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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174C PRO* 5.0 3.8 - - + -
295C TYR* 3.5 17.8 + - - +
298C LEU* 3.4 39.5 - - + -
333C GLY* 6.3 2.5 - - - -
417C VAL* 5.8 6.5 - - + +
418C ASN 3.1 10.8 + - - +
419C GLU* 2.7 15.7 + - - +
421C ASP* 1.3 75.1 - - - +
423C LEU* 1.3 63.1 + - + +
425C GLN* 3.9 8.0 + - + +
426C GLU* 3.5 16.8 + - - +
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Residues in contact with LEU 423 (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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419C GLU* 2.8 31.2 + - + +
420C ASP* 3.7 20.2 - - - +
421C ASP 3.2 0.2 - - - -
422C LEU* 1.3 77.3 - - + +
424C LYS* 1.3 59.5 + - - +
425C GLN 3.1 1.8 - - - -
426C GLU* 2.9 23.1 + - + +
427C GLN* 2.9 14.7 + - - +
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Residues in contact with LYS 424 (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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280C TRP* 3.8 39.4 - - + +
420C ASP 3.5 9.6 + - - +
421C ASP* 3.9 8.1 - - - +
422C LEU 3.5 0.2 - - - -
423C LEU* 1.3 78.2 - - - +
425C GLN* 1.3 62.0 + - - +
427C GLN* 3.6 7.1 + - - +
428C PHE* 3.4 22.0 + - - +
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Residues in contact with GLN 425 (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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172C TYR* 3.8 9.0 - - - -
173C GLY* 2.8 12.9 + - - -
174C PRO* 2.8 45.8 - - + +
175C PRO* 5.1 0.2 - - - +
277C ASN 3.2 14.1 + - - -
279C PRO* 3.3 27.8 - - - +
280C TRP* 4.6 3.8 - - - +
295C TYR* 3.9 20.4 - - + +
421C ASP 3.2 18.5 + - - +
422C LEU* 3.9 8.3 - - + +
423C LEU 3.1 0.6 - - - -
424C LYS* 1.3 77.8 - - - +
426C GLU* 1.3 61.3 + - - +
428C PHE* 3.6 3.7 + - - +
429C THR* 2.9 28.4 + - - -
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Residues in contact with GLU 426 (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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295C TYR* 5.4 2.4 + - - -
422C LEU 3.5 12.0 + - - +
423C LEU* 2.9 16.2 + - + +
425C GLN* 1.3 78.8 - - - +
427C GLN* 1.3 63.9 + - - +
429C THR* 3.5 8.5 + - - -
430C ARG* 3.4 15.1 + - - +
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Residues in contact with GLN 427 (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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423C LEU 2.9 12.2 + - - +
424C LYS* 4.1 7.4 - - - +
425C GLN 3.3 0.2 - - - -
426C GLU* 1.3 72.4 - - - +
428C PHE* 1.3 56.7 + - - +
429C THR 3.0 3.8 - - - -
430C ARG* 2.6 36.7 + - - +
431C ASP* 3.2 9.6 + - - +
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Residues in contact with PHE 428 (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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170C LEU* 4.2 16.2 - - + -
172C TYR* 3.3 38.1 - + - -
279C PRO* 3.3 52.7 - - + -
280C TRP* 4.5 9.0 - - + -
282C LEU* 5.2 0.9 - - + -
287C ARG* 4.1 27.4 - - + -
293C ARG* 4.9 4.3 - - + -
424C LYS 3.4 14.8 + - - +
425C GLN* 3.9 3.1 - - - +
426C GLU 3.5 0.2 - - - -
427C GLN* 1.3 77.9 - - - +
429C THR* 1.3 60.1 + - - +
430C ARG 3.3 0.2 - - - -
431C ASP* 3.2 11.2 - - + +
432C PHE* 3.2 34.3 + - - -
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Residues in contact with THR 429 (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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172C TYR* 2.8 29.1 + - - +
295C TYR* 4.2 17.0 - - + -
425C GLN 2.9 18.2 + - - -
426C GLU* 3.7 9.3 - - - -
427C GLN 3.0 1.2 - - - -
428C PHE* 1.3 73.4 - - - +
430C ARG* 1.3 67.1 + - - +
431C ASP 3.1 2.8 + - - -
432C PHE* 3.3 22.0 + - + +
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Residues in contact with ARG 430 (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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426C GLU 3.4 9.6 + - - +
427C GLN* 2.6 22.6 + - - +
429C THR* 1.3 74.9 - - - +
431C ASP* 1.3 67.1 + - - +
432C PHE* 3.7 2.5 + - - -
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Residues in contact with ASP 431 (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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287C ARG* 4.2 14.2 + - - +
427C GLN* 3.2 11.8 + - - +
428C PHE* 3.2 12.9 - - - +
429C THR 3.1 0.2 - - - -
430C ARG* 1.3 95.3 - - - +
432C PHE* 1.3 68.9 + - - +
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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