Contacts of the helix formed by residues 413 - 424 (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 ARG 413 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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415A LEU 5.0 3.2 + - - -
416A GLN* 5.2 6.3 + - - +
419A PHE* 3.6 43.4 - - - +
420A ARG* 5.3 3.4 - - - +
423A ASN* 6.2 0.4 - - - +
411B GLU 4.0 3.6 + - - +
412B VAL* 1.3 77.4 - - - +
414B TYR* 1.3 67.1 + - - +
415B LEU* 3.5 35.6 - - + +
416B GLN* 3.0 56.3 + - + +
417B PHE* 3.7 7.9 - - - -
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Residues in contact with TYR 414 (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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389B VAL* 3.7 21.1 - - + +
392B LEU* 4.3 11.2 - - + -
393B GLU* 3.5 52.4 + - + +
396B VAL* 3.4 24.9 - - + +
404B HIS* 2.6 41.3 + + - +
407B LEU* 3.6 25.0 - - + +
412B VAL 5.1 2.2 - - - -
413B ARG* 1.3 71.9 - - - +
415B LEU* 1.3 54.6 + - - +
417B PHE* 3.1 22.7 + + + -
418B ALA* 2.7 35.7 + - + +
461B LEU* 4.0 14.6 - - + -
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Residues in contact with LEU 415 (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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386A GLN* 3.9 13.2 - - - +
413A ARG* 5.1 1.9 + - - -
415A LEU* 4.3 15.9 - - + -
419A PHE* 3.8 27.4 - - + -
386B GLN* 5.1 9.0 - - - -
389B VAL* 3.5 30.5 - - + +
413B ARG* 3.5 27.8 - - + +
414B TYR* 1.3 78.4 - - - +
416B GLN* 1.3 60.2 + - - +
419B PHE* 3.3 44.5 + - + +
1003B UNX 3.8 0.3 - - - -
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Residues in contact with GLN 416 (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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413A ARG* 5.5 1.3 + - - +
416A GLN* 5.7 2.5 + - - -
482A GLN* 5.2 10.1 - - - +
411B GLU 3.9 6.2 + - - +
412B VAL* 3.6 10.4 - - - +
413B ARG* 3.0 69.0 + - - +
415B LEU* 1.3 78.1 - - - +
417B PHE* 1.3 57.3 + - - +
478B LEU* 4.0 26.2 - - + +
482B GLN* 3.3 21.0 + - - -
1003B UNX 3.4 6.9 - - - -
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Residues in contact with PHE 417 (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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392B LEU* 5.1 0.7 - - + -
407B LEU* 4.2 8.7 - - + -
412B VAL* 3.8 13.2 - - + -
413B ARG 3.7 8.7 - - - -
414B TYR* 3.1 37.2 + + - -
416B GLN* 1.3 77.2 - - - +
418B ALA* 1.3 78.9 + - + +
420B ARG* 3.9 5.5 + - - +
421B TRP* 3.4 57.1 + + - -
461B LEU* 4.1 21.3 - - + -
478B LEU* 4.1 6.3 - - + -
481B LEU* 3.6 41.3 - - + +
482B GLN* 4.5 10.6 - - + +
1003B UNX 3.0 16.8 - - - -
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Residues in contact with ALA 418 (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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389B VAL* 3.9 10.3 - - + -
392B LEU* 3.6 30.7 - - + -
414B TYR* 2.7 27.4 + - - +
417B PHE* 1.3 81.8 - - + +
419B PHE* 1.3 63.0 + - - +
420B ARG 3.2 2.5 - - - -
421B TRP* 3.1 11.9 + - + +
422B MET* 3.1 25.2 + - + +
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Residues in contact with PHE 419 (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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413A ARG* 3.2 49.1 - - - +
415A LEU* 4.2 17.3 - - + -
382B GLN* 3.8 24.2 - - + -
385B ILE* 3.4 27.8 - - + +
389B VAL* 4.0 10.8 - - - +
415B LEU* 3.3 29.6 + - + +
417B PHE 3.5 0.4 - - - -
418B ALA* 1.3 75.5 - - - +
420B ARG* 1.3 56.2 + - + +
422B MET* 3.3 3.6 + - - +
423B ASN* 2.8 64.7 + - + +
424B ASN* 5.7 0.2 - - - -
1003B UNX 3.6 4.5 - - - -
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Residues in contact with ARG 420 (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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413A ARG* 5.5 1.1 - - - +
417B PHE 3.9 4.9 + - - +
419B PHE* 1.3 83.4 - - + +
421B TRP* 1.3 56.1 + - - +
424B ASN* 3.0 38.8 + - - +
428B ARG* 3.8 27.6 + - + +
429B GLU* 2.8 37.1 + - - +
482B GLN* 3.1 39.7 + - - +
1002B UNX 2.8 20.6 - - - -
1003B UNX 3.1 13.8 - - - -
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Residues in contact with TRP 421 (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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392B LEU* 4.4 9.4 - - + -
417B PHE* 3.4 49.5 + + - +
418B ALA* 3.1 14.0 + - + +
420B ARG* 1.3 74.6 - - - +
422B MET* 1.3 59.1 + - + +
425B LEU* 3.3 0.3 - - - -
426B LEU* 2.9 32.1 + - + -
429B GLU* 3.3 34.9 + - + +
453B HIS* 2.9 20.9 + - - -
457B CYS* 3.6 42.4 - - + -
460B PHE* 3.8 24.9 - + - -
461B LEU* 4.0 24.2 - - + -
481B LEU* 4.1 13.0 + - + -
482B GLN* 5.9 0.4 - - - +
484B LEU* 4.1 12.3 - - + -
1002B UNX 3.7 4.9 - - - -
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Residues in contact with MET 422 (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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377B ASN* 4.3 6.8 + - - -
378B TYR* 4.4 0.5 + - - -
385B ILE* 3.9 22.6 - - + +
388B LYS* 4.0 32.5 - - + +
389B VAL* 3.8 15.0 - - + +
392B LEU* 3.9 28.5 - - + -
418B ALA 3.1 12.7 + - - +
419B PHE 3.8 4.7 - - - +
421B TRP* 1.3 77.6 - - + +
423B ASN* 1.3 65.4 + - - +
425B LEU* 3.4 20.4 + - - +
453B HIS* 3.6 22.6 - - + -
454B LEU* 4.8 9.9 - - - -
457B CYS* 3.5 30.7 - - + -
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Residues in contact with ASN 423 (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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320B GLN 2.8 26.8 + - - +
321B GLY* 3.6 10.8 - - - +
325B LEU* 4.9 0.9 - - - +
378B TYR* 2.6 33.9 + - - -
382B GLN* 2.8 29.9 + - - -
385B ILE* 3.7 8.7 - - + +
419B PHE* 2.8 46.3 + - + +
422B MET* 1.3 73.9 - - - +
424B ASN* 1.3 76.8 + - - +
425B LEU 3.9 0.3 + - - -
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Residues in contact with ASN 424 (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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320B GLN* 5.9 1.0 - - - +
321B GLY* 3.3 29.0 - - - +
323B ASN* 5.8 0.2 - - - -
324B ASP* 2.9 28.5 + - - +
325B LEU* 4.3 3.5 - - - +
419B PHE* 5.7 0.2 - - - -
420B ARG* 3.0 26.5 + - - +
423B ASN* 1.3 91.5 + - - +
425B LEU* 1.3 67.0 + - - +
426B LEU 3.4 1.1 - - - -
427B MET* 3.0 24.4 + - - +
428B ARG* 3.9 15.8 - - + +
1002B UNX 3.6 8.3 - - - -
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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