Contacts of the helix formed by residues 436 - 449 (chain A) in PDB entry 2OIV
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 PRO 436 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434A LYS* 6.0 1.3 - - + -
435A ASP* 1.3 88.9 - - + +
437A GLN* 1.3 62.8 + - + +
438A GLN 3.5 1.1 + - - -
439A ARG* 3.7 7.6 + - + +
440A TYR* 3.1 23.3 + - + +
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Residues in contact with GLN 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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405A GLN* 3.3 35.3 + - + +
406A PRO* 5.6 2.8 - - - +
435A ASP* 3.1 17.1 + - - +
436A PRO* 1.3 75.9 - - - +
438A GLN* 1.3 65.6 + - - +
440A TYR* 3.2 16.0 + - - +
441A LEU* 3.0 44.2 + - + +
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Residues in contact with GLN 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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403A ILE* 3.2 32.2 + - - +
405A GLN* 2.8 44.9 + - - +
409A HIS* 3.4 29.6 + - + -
411A SER* 2.9 30.3 + - - +
427A HIS* 4.2 2.0 - - + -
429A ASP* 3.4 24.7 - - - +
434A LYS* 6.0 2.5 - - + -
435A ASP* 4.2 5.8 + - - +
436A PRO 3.5 0.4 - - - -
437A GLN* 1.3 79.2 - - - +
439A ARG* 1.3 62.6 + - - +
441A LEU* 3.2 8.5 + - - +
442A ALA* 3.1 20.6 + - - +
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Residues in contact with ARG 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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427A HIS* 3.8 15.6 - - + +
429A ASP* 5.0 0.6 + - - +
434A LYS* 5.5 11.9 - - + +
435A ASP 5.3 0.4 + - - -
436A PRO* 3.7 8.3 + - + +
437A GLN 3.3 0.4 - - - -
438A GLN* 1.3 75.9 - - - +
440A TYR* 1.3 55.9 + - - +
442A ALA* 3.2 3.6 + - - +
443A ASP* 2.7 66.4 + - - +
453A TYR* 3.2 23.4 + - - -
454A GLN* 4.8 3.6 + - - +
456A THR* 3.2 38.0 + - - +
457A HIS 4.5 0.2 - - - -
458A GLU* 3.2 44.2 + - - +
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Residues in contact with TYR 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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436A PRO* 3.1 17.2 + - + +
437A GLN* 3.2 22.0 + - - +
439A ARG* 1.3 78.3 - - - +
441A LEU* 1.3 69.0 + - + +
443A ASP* 3.2 9.0 + - + -
444A MET* 2.8 70.0 + - + +
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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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376A SER* 5.4 3.8 + - - +
403A ILE* 3.6 17.5 - - + +
404A ASN 3.6 26.0 - - - +
405A GLN* 4.2 15.5 - - + -
406A PRO* 5.2 1.6 - - + -
437A GLN* 3.0 41.6 + - + +
438A GLN* 3.2 9.2 + - - +
440A TYR* 1.3 89.1 - - + +
442A ALA* 1.3 58.4 + - - +
444A MET* 3.4 7.6 + - + +
445A ALA* 3.0 28.6 + - - +
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Residues in contact with ALA 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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403A ILE* 4.3 16.3 - - + +
413A LEU* 3.6 12.2 - - + +
427A HIS* 3.6 45.3 - - + +
438A GLN 3.1 7.8 + - - +
439A ARG* 3.2 10.5 + - - +
441A LEU* 1.3 75.9 - - - +
443A ASP* 1.3 60.5 + - - +
445A ALA* 3.5 2.9 + - - +
446A ALA* 3.0 27.4 + - - +
456A THR* 5.8 0.9 - - + -
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Residues in contact with ASP 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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439A ARG* 2.7 59.9 + - - +
440A TYR* 3.6 10.9 - - + +
442A ALA* 1.3 75.5 - - - +
444A MET* 1.3 60.8 + - - +
446A ALA* 3.4 2.7 + - - +
447A TYR* 2.8 30.9 + - - +
453A TYR* 3.3 44.6 - - + +
456A THR* 4.6 4.0 + - - -
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Residues in contact with MET 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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376A SER* 3.4 23.8 - - - +
440A TYR* 2.8 65.3 + - + +
441A LEU* 3.8 9.9 - - + +
443A ASP* 1.3 69.9 - - - +
445A ALA* 1.3 60.0 + - - +
447A TYR* 3.4 15.1 + - + +
448A HIS* 2.9 62.6 + - + -
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Residues in contact with ALA 445 (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 VAL* 4.4 8.1 - - + +
375A LEU* 3.8 23.2 - - + +
376A SER* 4.6 1.7 + - - -
401A LEU* 5.8 0.4 - - + -
403A ILE* 4.2 14.1 - - + -
413A LEU* 4.0 13.2 - - + -
441A LEU 3.0 17.0 + - - +
442A ALA 3.6 5.2 - - - +
444A MET* 1.3 76.1 - - - +
446A ALA* 1.3 62.6 + - - +
448A HIS* 3.2 3.0 + - - -
449A LEU* 3.0 31.4 + - + +
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Residues in contact with ALA 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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413A LEU* 4.1 9.5 - - + +
442A ALA 3.0 17.4 + - - +
443A ASP* 3.6 4.5 - - - +
445A ALA* 1.3 76.4 - - - +
447A TYR* 1.3 63.4 + - - +
449A LEU* 3.1 8.3 + - - -
451A LEU* 3.0 46.9 + - + +
452A ASP 5.3 0.2 - - - +
453A TYR* 4.2 14.4 - - + -
456A THR* 4.1 19.5 - - - +
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Residues in contact with TYR 447 (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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443A ASP 2.8 21.4 + - - +
444A MET* 3.6 17.9 - - + +
446A ALA* 1.3 72.2 - - - +
448A HIS* 1.3 88.7 + + - +
450A GLY* 3.1 19.6 + - - -
451A LEU 3.7 13.6 + - - +
453A TYR* 4.7 14.1 - + + +
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Residues in contact with HIS 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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375A LEU* 3.2 32.8 + - + +
376A SER* 3.4 14.3 + - - -
383A GLN* 3.1 32.3 + - - -
387A GLN* 3.0 39.4 + - - +
391A ALA* 5.8 0.2 - - - +
444A MET* 2.9 49.5 + - + +
445A ALA 3.2 0.9 + - - +
447A TYR* 1.3 92.1 - + - +
449A LEU* 1.3 59.9 + - - +
450A GLY 3.2 6.3 + - - -
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Residues in contact with LEU 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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375A LEU* 3.9 19.5 - - + -
387A GLN* 5.3 0.9 - - - -
390A LEU* 3.7 31.6 - - + +
391A ALA* 3.9 27.9 - - + +
399A VAL* 5.9 0.9 - - + -
401A LEU* 3.9 36.3 - - + -
413A LEU* 5.1 0.7 - - + -
415A VAL* 4.3 12.8 - - + -
417A ARG* 4.7 8.6 + - - +
445A ALA 3.0 22.4 + - - +
446A ALA* 3.1 7.3 + - - +
448A HIS* 1.3 77.1 - - - +
450A GLY* 1.3 60.4 + - - +
451A LEU* 3.4 16.8 + - + +
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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