Contacts of the helix formed by residues 432 - 446 (chain A) in PDB entry 5Q0R
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 GLN 432 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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430A ASN* 3.1 11.1 + - - +
431A PRO* 1.3 92.1 + - + +
433A HIS* 1.4 62.2 + - - +
434A PHE 3.4 2.0 - - - -
435A ALA* 3.2 23.8 + - + +
436A CYS* 3.0 32.7 + - - -
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Residues in contact with HIS 433 (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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379A LEU* 3.9 31.4 - - + +
385A GLU* 2.8 33.0 + - - -
423A CYS* 3.5 30.7 - - + -
427A GLN* 3.2 39.5 + - + +
430A ASN* 3.1 31.1 + - - +
431A PRO 3.3 1.2 - - - -
432A GLN* 1.4 76.7 - - - +
434A PHE* 1.3 61.8 + - - +
436A CYS* 3.3 10.7 + - - +
437A LEU* 3.2 28.8 + - + +
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Residues in contact with PHE 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A LEU* 3.9 25.6 - - + -
419A LEU* 3.9 27.1 - - + -
420A GLN* 3.6 53.8 - - + +
423A CYS* 3.8 18.5 - - + +
431A PRO 4.6 5.8 + - - +
432A GLN 3.4 0.4 - - - -
433A HIS* 1.3 75.8 - - - +
435A ALA* 1.4 57.6 + - - +
437A LEU* 3.1 8.1 + - + +
438A LEU* 3.0 59.9 + - + +
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Residues in contact with ALA 435 (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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431A PRO 5.3 0.4 + - - -
432A GLN* 3.2 32.1 + - + +
434A PHE* 1.4 77.3 - - - +
436A CYS* 1.3 57.7 + - - +
438A LEU* 3.3 17.2 + - - +
439A GLY* 3.0 23.4 + - - -
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Residues in contact with CYS 436 (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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379A LEU* 3.7 27.8 - - + +
430A ASN* 5.8 3.4 - - - -
432A GLN* 3.0 27.6 + - - -
433A HIS* 3.3 12.1 + - - +
435A ALA* 1.3 73.2 - - - +
437A LEU* 1.3 64.5 + - - +
439A GLY* 3.2 9.6 + - - +
440A ARG* 3.2 30.5 + - - +
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Residues in contact with LEU 437 (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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379A LEU* 3.8 11.4 - - + -
381A MET* 3.8 42.8 - - + -
385A GLU* 3.7 16.2 - - + +
389A LEU* 4.3 16.7 - - + +
419A LEU* 3.8 30.7 - - + -
423A CYS* 3.6 30.1 - - - -
433A HIS* 3.2 18.0 + - + +
434A PHE* 3.1 9.9 + - + +
436A CYS* 1.3 74.6 - - - +
438A LEU* 1.4 63.8 + - - +
440A ARG* 3.1 15.3 + - + +
441A LEU* 3.3 10.6 + - - +
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Residues in contact with LEU 438 (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 LEU* 6.3 1.3 - - + -
416A LEU* 4.7 10.1 - - + -
419A LEU* 6.1 1.6 - - + -
434A PHE* 3.0 52.7 + - + +
435A ALA* 3.4 14.6 - - + +
437A LEU* 1.4 75.1 - - - +
439A GLY* 1.3 57.1 + - - +
441A LEU* 3.1 38.0 + - + +
442A THR* 3.2 20.4 + - + +
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Residues in contact with GLY 439 (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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435A ALA 3.0 14.0 + - - -
436A CYS* 3.2 7.3 + - - -
438A LEU* 1.3 77.2 - - - +
440A ARG* 1.3 68.0 + - - +
442A THR* 3.1 19.9 + - - -
443A GLU* 3.2 15.8 + - - +
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Residues in contact with ARG 440 (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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372A PHE* 3.7 3.3 - - + -
375A SER* 3.2 46.0 + - - -
376A ILE* 3.7 31.2 - - + -
378A GLU* 5.5 2.8 + - - +
379A LEU* 3.5 36.7 - - + +
381A MET* 5.3 0.9 - - - -
389A LEU* 4.8 8.1 - - + -
436A CYS* 3.2 31.9 + - - +
437A LEU* 3.1 7.9 + - - +
439A GLY* 1.3 83.6 + - - +
441A LEU* 1.3 60.4 + - - +
443A GLU* 3.5 13.5 + - - +
444A LEU* 2.9 33.3 + - + +
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Residues in contact with LEU 441 (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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330A GLU* 5.2 1.3 - - - +
389A LEU* 3.8 31.4 - - + +
392A ILE* 4.0 22.4 - - + -
393A VAL* 3.7 29.8 - - + -
412A GLN* 5.9 0.4 - - - +
416A LEU* 5.4 1.8 - - + -
437A LEU 3.3 5.2 + - - +
438A LEU* 3.1 31.1 + - + +
440A ARG* 1.3 74.5 - - - +
442A THR* 1.3 64.3 + - + +
444A LEU* 3.4 10.2 - - + +
445A ARG* 3.3 25.1 + - + +
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Residues in contact with THR 442 (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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438A LEU* 3.2 12.7 + - + +
439A GLY* 3.1 17.8 + - - -
441A LEU* 1.3 74.2 - - + +
443A GLU* 1.3 64.0 + - - +
445A ARG* 3.1 24.9 + - + +
446A THR* 3.5 11.5 + - - +
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Residues in contact with GLU 443 (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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368A PRO 5.0 1.0 - - - +
371A SER* 4.5 5.5 + - - -
372A PHE* 3.5 33.2 + - + +
375A SER* 3.2 26.6 + - - -
439A GLY 3.2 13.7 + - - +
440A ARG* 3.7 20.4 + - - +
442A THR* 1.3 80.8 + - - +
444A LEU* 1.4 56.1 + - - +
446A THR* 2.7 32.6 + - + +
447A PHE* 3.4 12.0 - - + -
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Residues in contact with LEU 444 (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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330A GLU* 3.3 46.4 - - + +
333A PHE* 3.8 17.5 - - + -
334A LEU* 3.9 21.5 - - + +
372A PHE* 3.6 23.8 - - + -
389A LEU* 5.8 1.3 - - + -
393A VAL* 3.8 28.9 - - + -
440A ARG 2.9 16.5 + - - +
441A LEU* 3.4 16.6 - - + +
443A GLU* 1.4 74.0 - - - +
445A ARG* 1.3 63.3 + - - +
447A PHE* 3.1 25.2 + - + +
448A ASN 4.2 0.2 + - - -
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Residues in contact with ARG 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A GLU* 3.5 22.9 + - - +
396A SER* 3.7 15.8 + - - -
398A ASP* 2.8 35.2 + - - -
399A ARG* 3.3 32.5 - - - +
441A LEU* 3.5 13.7 - - + +
442A THR* 3.1 14.7 + - + +
444A LEU* 1.3 78.3 - - - +
446A THR* 1.3 61.5 + - + +
448A ASN* 3.2 27.2 + - - +
449A HIS 4.4 0.5 + - - -
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Residues in contact with THR 446 (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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442A THR 3.7 13.7 - - - +
443A GLU* 2.7 23.3 + - + +
444A LEU 3.2 0.2 - - - -
445A ARG* 1.3 75.7 - - + +
447A PHE* 1.3 65.0 + - - +
448A ASN 3.1 1.7 + - - -
449A HIS* 2.8 38.8 + - + +
450A HIS* 3.2 21.7 + - - -
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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