Contacts of the helix formed by residues 447 - 461 (chain A) in PDB entry 2QLU
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 HIS 447 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284A TRP* 3.6 41.6 - + - +
401A LYS 5.4 1.4 + - - -
402A ALA* 4.2 9.6 - - - +
403A ALA* 3.6 36.9 + - + +
443A HIS 4.5 0.8 + - - +
444A TRP* 3.2 12.2 + - - +
445A LEU 4.5 0.2 - - - -
446A LYS* 1.3 78.0 - - - +
448A PRO* 1.4 70.0 - - + +
449A GLY* 3.4 8.0 + - - -
450A LEU* 3.1 34.2 + - + +
451A ALA* 2.8 31.0 + - - +
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Residues in contact with PRO 448 (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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445A LEU 5.5 0.2 - - - +
446A LYS 4.0 6.9 - - - +
447A HIS* 1.4 88.8 - - + +
449A GLY* 1.3 60.2 + - - +
451A ALA* 3.8 6.6 + - + +
452A GLN* 3.2 37.4 + - - +
484A SER* 5.9 4.5 - - - -
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Residues in contact with GLY 449 (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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284A TRP* 3.2 31.3 - - - -
447A HIS* 3.3 8.2 + - - -
448A PRO* 1.3 75.5 - - - +
450A LEU* 1.3 59.7 + - - +
452A GLN* 3.4 1.1 + - - -
453A LEU* 2.9 28.8 + - - +
481A ILE* 3.6 17.3 - - - +
484A SER* 5.9 1.9 - - - -
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Residues in contact with LEU 450 (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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284A TRP* 3.8 22.0 - - + -
287A LEU* 3.8 23.6 - - + -
397A VAL* 4.1 26.9 - - + +
400A CYS* 4.6 7.2 - - + -
402A ALA* 3.4 36.6 - - + -
444A TRP* 3.6 26.9 - - + +
447A HIS* 3.1 17.2 + - + +
449A GLY* 1.3 70.5 - - - +
451A ALA* 1.3 61.8 + - - +
452A GLN 3.2 0.4 - - - -
453A LEU* 3.7 3.8 - - + +
454A CYS* 2.9 40.5 + - - -
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Residues in contact with ALA 451 (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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444A TRP 4.2 1.8 + - - -
445A LEU* 3.6 36.1 - - + +
447A HIS 2.8 17.4 + - - +
448A PRO* 3.8 7.9 - - + +
450A LEU* 1.3 78.4 - - - +
452A GLN* 1.3 61.7 + - + +
454A CYS* 3.4 2.6 + - - +
455A VAL* 3.2 26.9 + - - +
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Residues in contact with GLN 452 (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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448A PRO* 3.2 28.8 + - - +
449A GLY 3.9 1.1 - - - +
450A LEU 3.2 0.6 - - - -
451A ALA* 1.3 74.8 - - + +
453A LEU* 1.3 67.7 + - - +
455A VAL* 3.4 12.6 + - + +
456A THR* 3.2 24.3 + - - -
480A LEU 5.1 0.9 - - - +
481A ILE* 3.7 31.5 - - + +
484A SER* 3.3 27.9 + - - -
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Residues in contact with LEU 453 (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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284A TRP* 5.6 2.9 - - + -
287A LEU* 4.0 22.2 - - + -
288A CYS* 6.4 1.1 - - - -
291A ALA* 5.0 1.8 - - + -
393A LEU* 4.5 19.7 - - + +
396A LEU* 5.9 0.2 - - + -
397A VAL* 3.5 29.4 - - + -
449A GLY 2.9 18.1 + - - +
450A LEU* 4.1 7.4 - - + +
452A GLN* 1.3 77.4 - - - +
454A CYS* 1.3 55.4 + - - +
456A THR* 3.3 11.2 + - + -
457A ILE* 3.0 39.1 + - + +
478A VAL* 3.5 35.9 - - + -
481A ILE* 3.9 16.7 - - + +
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Residues in contact with CYS 454 (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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397A VAL* 4.1 12.1 - - - -
440A ILE* 3.9 33.8 - - + +
444A TRP* 4.1 18.8 - - - -
445A LEU* 4.4 13.0 - - + -
450A LEU* 2.9 33.7 + - - +
451A ALA 3.9 3.8 - - - +
452A GLN 3.2 0.4 - - - -
453A LEU* 1.3 69.8 - - - +
455A VAL* 1.3 66.9 + - - +
456A THR 3.1 1.3 - - - -
457A ILE* 3.5 10.6 - - - +
458A GLU* 2.9 29.2 + - - +
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Residues in contact with VAL 455 (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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451A ALA 3.2 18.8 + - - +
452A GLN* 3.4 14.1 - - + +
454A CYS* 1.3 77.3 - - - +
456A THR* 1.3 63.1 + - - +
458A GLU* 3.3 9.3 + - - +
459A GLU* 3.2 38.9 + - + +
477A ARG* 4.6 4.5 - - - +
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Residues in contact with THR 456 (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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393A LEU* 5.1 4.7 - - + -
452A GLN 3.2 12.6 + - - -
453A LEU* 3.4 19.7 - - + +
454A CYS 3.1 0.4 - - - -
455A VAL* 1.3 76.0 - - - +
457A ILE* 1.3 59.4 + - - +
459A GLU* 3.2 3.7 + - - +
460A CYS* 3.0 29.2 + - - -
469A LEU* 3.8 17.0 - - + +
474A VAL* 4.1 24.2 - - + -
477A ARG* 3.3 39.3 + - + +
481A ILE* 4.4 3.5 - - - +
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Residues in contact with ILE 457 (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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390A GLY* 3.5 9.2 - - - +
393A LEU* 3.5 26.7 - - + -
394A TRP* 3.5 27.6 - - + +
397A VAL* 3.9 19.3 - - + -
440A ILE* 4.6 4.0 - - + -
453A LEU* 3.0 18.2 + - + +
454A CYS* 3.5 16.4 - - - +
456A THR* 1.3 73.7 - - - +
458A GLU* 1.3 64.5 + - - +
460A CYS* 3.0 11.7 + - - +
461A TRP* 2.9 61.2 + - + -
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Residues in contact with GLU 458 (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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440A ILE* 4.0 25.3 - - + +
454A CYS* 2.9 21.9 + - - +
455A VAL* 3.8 8.1 - - - +
456A THR 3.3 0.2 - - - -
457A ILE* 1.3 77.7 - - - +
459A GLU* 1.3 60.1 + - + +
461A TRP* 3.6 24.1 + - - +
462A ASP* 3.6 20.3 + - - +
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Residues in contact with GLU 459 (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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455A VAL* 3.3 22.0 - - + +
456A THR 3.2 3.0 + - - +
457A ILE 3.1 0.8 - - - -
458A GLU* 1.3 75.3 - - + +
460A CYS* 1.3 66.2 + - - +
462A ASP* 3.4 17.4 + - - +
467A ALA 3.8 8.8 - - - +
468A ARG* 3.4 20.0 - - - -
469A LEU* 3.7 23.9 - - + +
477A ARG* 2.5 41.9 + - - -
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Residues in contact with CYS 460 (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 MET* 3.8 19.2 - - - +
387A TYR* 3.4 10.0 + - - -
390A GLY* 3.7 19.1 - - - -
393A LEU* 4.6 11.7 - - - -
456A THR 3.0 18.2 + - - +
457A ILE* 3.2 9.6 - - - +
459A GLU* 1.3 77.6 - - - +
461A TRP* 1.3 57.7 + - - +
462A ASP 3.3 0.2 - - - -
468A ARG* 3.2 29.7 - - - +
469A LEU* 4.3 7.0 - - - -
474A VAL* 3.6 30.5 - - - -
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Residues in contact with TRP 461 (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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387A TYR* 3.7 32.7 - - + +
390A GLY* 4.0 8.3 - - - -
391A LEU* 3.5 27.4 - - + -
394A TRP* 3.9 21.3 - + + -
437A ARG* 3.0 56.9 + - + +
438A PRO* 3.7 25.4 - - + -
440A ILE* 4.0 14.4 - - + -
457A ILE* 2.9 43.5 + - + +
458A GLU* 3.6 29.0 + - + +
459A GLU 3.3 0.4 - - - -
460A CYS* 1.3 76.1 - - - +
462A ASP* 1.3 59.4 + - - +
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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