Contacts of the helix formed by residues 422 - 431 (chain A) 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 LEU 422 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A PRO* 5.1 2.0 - - + -
295A TYR* 4.8 10.5 - - - +
298A LEU* 3.5 36.6 - - + -
417A VAL* 4.6 12.6 - - + -
418A ASN 3.2 20.6 - - - +
419A GLU* 4.1 10.3 - - - +
420A ASP 2.6 2.8 + - - -
421A ASP* 1.3 74.8 - - - +
423A LEU* 1.3 65.3 + - - +
424A LYS 3.4 1.3 - - - -
425A GLN* 3.6 25.6 - - + +
426A GLU* 4.0 4.7 + - + +
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Residues in contact with LEU 423 (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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419A GLU 3.7 13.1 + - - +
420A ASP* 2.8 12.4 + - - +
422A LEU* 1.3 79.4 - - - +
424A LYS* 1.3 65.2 + - - +
425A GLN 3.1 2.0 + - - -
426A GLU* 3.3 9.8 + - + +
427A GLN* 3.1 24.5 + - + +
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Residues in contact with LYS 424 (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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280A TRP* 3.1 44.3 + - + +
420A ASP 3.9 5.1 + - - +
421A ASP* 5.4 1.3 - - - -
422A LEU 3.4 2.0 - - - +
423A LEU* 1.3 77.1 - - - +
425A GLN* 1.3 65.2 + - - +
427A GLN* 3.5 8.3 - - - +
428A PHE* 2.9 23.7 + - - +
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Residues in contact with GLN 425 (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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172A TYR* 4.2 6.8 - - - -
173A GLY* 3.1 26.0 + - - -
174A PRO* 3.6 27.2 - - + +
175A PRO* 5.3 0.6 - - - +
277A ASN 3.3 24.7 + - - -
279A PRO* 4.2 9.6 - - - +
280A TRP* 4.6 8.1 - - - +
295A TYR* 3.7 21.2 - - + +
421A ASP* 4.2 9.5 + - - -
422A LEU* 3.6 25.8 - - + +
424A LYS* 1.3 76.5 - - - +
426A GLU* 1.3 66.0 + - - +
428A PHE* 2.8 20.3 + - - +
429A THR* 2.8 16.4 + - - -
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Residues in contact with GLU 426 (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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295A TYR* 5.2 2.1 + - - -
422A LEU* 4.0 4.0 + - + +
423A LEU* 3.3 16.2 + - + +
425A GLN* 1.3 77.5 - - - +
427A GLN* 1.3 65.8 + - - +
429A THR* 3.0 12.1 + - - -
430A ARG* 2.8 23.0 + - - +
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Residues in contact with GLN 427 (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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423A LEU* 3.1 16.4 + - + +
424A LYS* 3.5 13.0 - - - +
426A GLU* 1.3 76.7 - - - +
428A PHE* 1.3 58.0 + - - +
430A ARG* 2.9 10.7 + - - +
431A ASP* 2.8 39.2 + - - +
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Residues in contact with PHE 428 (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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170A LEU* 4.5 15.9 - - + -
172A TYR* 3.8 28.9 - + - -
279A PRO* 3.0 56.3 - - + -
280A TRP* 3.7 11.2 - + + -
282A LEU* 5.4 1.1 - - + -
287A ARG* 4.6 21.1 - - + -
293A ARG* 4.9 3.1 - - - -
424A LYS 2.9 12.6 + - - +
425A GLN* 2.8 13.8 + - - +
427A GLN* 1.3 74.8 - - - +
429A THR* 1.3 62.6 + - - -
430A ARG 2.9 1.2 + - - -
431A ASP* 3.1 3.3 + - - +
432A PHE* 2.9 54.4 + - + +
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Residues in contact with THR 429 (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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172A TYR* 2.9 36.0 + - - +
295A TYR* 4.0 14.9 - - + -
425A GLN 2.8 18.3 + - - -
426A GLU* 3.0 10.8 + - - -
428A PHE* 1.3 73.8 - - - +
430A ARG* 1.3 55.7 + - - +
432A PHE* 2.8 31.5 - - + -
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Residues in contact with ARG 430 (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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426A GLU 2.8 11.0 + - - +
427A GLN* 2.9 16.1 + - - +
429A THR* 1.3 79.4 - - - +
431A ASP* 1.3 71.6 + - - +
432A PHE* 4.1 3.3 - - - -
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Residues in contact with ASP 431 (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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427A GLN* 2.8 23.9 + - - +
428A PHE* 3.1 2.8 + - - +
430A ARG* 1.3 83.8 - - - +
432A PHE* 1.3 75.3 + - - +
433A GLY* 2.8 8.6 + - - +
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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