Contacts of the helix formed by residues 413 - 424 (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 ARG 413 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411A GLU 5.0 3.8 - - - +
412A VAL* 1.3 81.2 - - - +
414A TYR* 1.3 66.9 + - - +
415A LEU* 3.0 23.4 + - + +
416A GLN* 3.0 55.5 + - + +
417A PHE* 3.8 1.5 - - - -
415B LEU 5.1 1.6 + - - -
416B GLN* 5.5 1.8 + - - +
419B PHE* 3.2 55.7 - - - +
420B ARG* 5.5 1.6 - - - +
1003B UNX 3.9 15.0 - - - -
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Residues in contact with TYR 414 (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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389A VAL* 3.8 19.7 - - + +
392A LEU* 4.0 19.1 - - + -
393A GLU* 3.7 44.5 + - + +
396A VAL* 3.3 25.7 - - + +
404A HIS* 2.9 40.0 + + - -
407A LEU* 3.9 19.4 - - + +
412A VAL 5.2 1.6 - - - -
413A ARG* 1.3 73.9 - - - +
415A LEU* 1.3 57.6 + - - +
416A GLN 3.1 0.7 + - - -
417A PHE* 3.2 22.2 + + + -
418A ALA* 2.8 32.5 + - + +
461A LEU* 3.9 20.2 - - + -
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Residues in contact with LEU 415 (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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386A GLN* 3.5 36.3 - - + +
389A VAL* 3.7 29.8 - - + +
413A ARG* 3.0 26.3 + - + +
414A TYR* 1.3 76.9 - - - +
416A GLN* 1.3 61.7 + - - +
417A PHE 3.3 0.7 + - - -
419A PHE* 3.3 39.1 + - + +
413B ARG* 5.0 2.3 + - - -
415B LEU* 4.3 18.8 - - + +
419B PHE* 4.2 21.8 - - + -
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Residues in contact with GLN 416 (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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411A GLU 3.7 10.9 + - - +
412A VAL* 3.7 3.3 - - - +
413A ARG* 3.0 67.5 + - - +
415A LEU* 1.3 77.8 - - - +
417A PHE* 1.3 57.7 + - - +
419A PHE* 5.6 0.4 - - - -
474A PHE* 4.0 11.9 - - - -
478A LEU* 3.9 32.6 - - + +
482A GLN* 3.0 23.6 + - - -
413B ARG* 5.2 7.1 + - - +
416B GLN* 5.7 2.3 + - - -
482B GLN* 5.3 8.7 - - - +
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Residues in contact with PHE 417 (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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392A LEU* 5.0 0.7 - - + -
407A LEU* 4.2 10.1 - - + -
412A VAL* 3.8 12.3 - - + -
413A ARG 3.8 7.4 - - - -
414A TYR* 3.7 38.6 - + - -
416A GLN* 1.3 79.9 - - - +
418A ALA* 1.3 81.6 + - + +
419A PHE 3.4 2.5 + - - -
420A ARG* 3.8 4.9 + - - +
421A TRP* 3.2 47.4 - + - -
461A LEU* 3.9 18.8 - - + -
478A LEU* 4.1 7.4 - - + -
481A LEU* 3.6 40.4 - - + +
482A GLN* 4.1 3.4 - - + -
1006A UNX 2.5 29.6 - - - -
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Residues in contact with ALA 418 (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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389A VAL* 4.0 11.0 - - + -
392A LEU* 3.7 29.4 - - + -
414A TYR* 2.8 20.5 + - + +
417A PHE* 1.3 84.2 - - + +
419A PHE* 1.3 63.1 + - - +
420A ARG 3.3 2.0 - - - -
421A TRP* 3.2 14.5 + - + +
422A MET* 3.2 27.1 + - + +
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Residues in contact with PHE 419 (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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382A GLN* 3.5 29.4 - - + -
385A ILE* 3.5 31.2 - - + +
386A GLN* 3.9 13.5 - - - -
389A VAL* 4.1 5.1 - - - +
415A LEU* 3.3 25.8 + - + +
416A GLN 5.6 0.2 - - - -
417A PHE 3.4 0.6 - - - -
418A ALA* 1.3 75.7 - - - +
420A ARG* 1.3 60.8 + - + +
422A MET* 3.9 1.6 - - - +
423A ASN* 2.9 55.2 + - + +
413B ARG* 3.6 43.7 - - - +
415B LEU* 3.8 24.5 - - + -
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Residues in contact with ARG 420 (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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417A PHE 3.8 1.8 + - - +
418A ALA 3.3 0.2 - - - -
419A PHE* 1.3 81.9 - - + +
421A TRP* 1.3 63.2 + - - +
423A ASN* 4.3 1.3 - - - -
424A ASN* 3.1 40.9 + - - +
428A ARG* 3.6 22.8 + - + +
429A GLU* 3.2 24.7 + - - +
482A GLN* 2.8 37.2 + - - +
483A ASN* 5.3 0.6 + - - -
1004A UNX 2.9 13.4 - - - -
1006A UNX 3.6 18.9 - - - -
413B ARG* 5.3 3.5 - - - +
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Residues in contact with TRP 421 (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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392A LEU* 4.6 4.3 - - + -
417A PHE* 3.2 49.8 + + - -
418A ALA* 3.2 17.8 + - + +
420A ARG* 1.3 76.3 - - - +
422A MET* 1.3 57.0 + - - +
425A LEU 3.3 1.7 + - - -
426A LEU* 3.0 37.6 + - + +
429A GLU* 3.4 28.9 + - + +
453A HIS* 3.0 13.8 + - - -
457A CYS* 3.5 47.6 - - + -
460A PHE* 3.8 22.4 - + - -
461A LEU* 3.8 24.5 - - + -
481A LEU* 3.7 16.9 + - + -
484A LEU* 3.9 8.3 - - + -
1004A UNX 3.7 5.8 - - - -
1006A UNX 3.5 6.7 - - - -
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Residues in contact with MET 422 (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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377A ASN* 4.0 9.5 + - - -
378A TYR* 4.3 0.7 + - - -
385A ILE* 3.8 20.6 - - + -
388A LYS* 3.7 42.0 - - + +
389A VAL* 3.9 14.1 - - + +
392A LEU* 4.2 20.4 - - + -
418A ALA* 3.2 14.5 + - + +
419A PHE 3.9 4.3 - - - +
421A TRP* 1.3 76.1 - - - +
423A ASN* 1.3 64.3 + - - +
424A ASN 3.3 0.4 - - - -
425A LEU* 3.4 21.3 + - - +
453A HIS* 3.6 26.0 - - - -
454A LEU* 4.0 14.1 - - + -
457A CYS* 3.9 20.0 - - + -
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Residues in contact with ASN 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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320A GLN 3.0 26.3 + - - +
321A GLY* 3.6 10.6 - - - +
325A LEU* 4.9 0.9 - - - +
378A TYR* 2.5 33.8 + - - -
382A GLN* 2.9 31.2 + - - +
385A ILE* 3.7 10.3 - - + +
419A PHE* 2.9 38.8 + - + +
420A ARG* 4.3 0.2 - - - -
422A MET* 1.3 75.7 - - - +
424A ASN* 1.3 77.9 + - - +
413B ARG* 6.2 0.8 - - - +
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Residues in contact with ASN 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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320A GLN* 6.2 0.4 - - - +
321A GLY* 3.7 23.1 - - - -
323A ASN* 5.4 0.2 + - - -
324A ASP* 2.8 27.4 + - - +
325A LEU* 4.2 3.8 - - - -
420A ARG* 3.1 28.0 + - - +
423A ASN* 1.3 93.5 + - - +
425A LEU* 1.3 68.8 + - - +
426A LEU 3.3 0.2 - - - -
427A MET* 3.0 25.3 + - - +
428A ARG* 3.5 19.6 - - + +
1004A UNX 3.7 9.0 - - - -
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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