Contacts of the helix formed by residues 434 - 446 (chain A) in PDB entry 5OIV
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 434 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A LEU* 4.2 0.8 - - - +
31A ALA* 3.5 15.2 + - - +
32A ALA* 3.4 15.5 - - - +
36A TYR* 3.7 8.9 - - - -
417A PHE* 2.9 17.3 + - - +
419A GLU* 3.7 31.2 - - - +
431A SER* 3.5 15.6 - - - +
432A MET 3.2 0.8 - - - -
433A GLN* 1.3 77.3 - - - +
435A SER* 1.3 65.4 + - - +
436A TRP* 3.5 33.7 - - + +
437A THR* 3.1 13.6 + - - +
438A ALA* 3.3 11.1 + - - +
504A GOL 3.1 26.1 + - - -
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Residues in contact with SER 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 3.9 10.1 - - - -
20A LEU* 3.6 19.2 - - - +
23A ASN* 2.9 23.2 + - - +
29A THR* 3.8 0.9 - - - +
30A THR 2.6 28.7 + - - -
31A ALA* 2.8 15.2 + - - -
43A ALA* 6.4 0.2 - - - -
47A VAL* 3.8 14.1 - - - -
433A GLN 3.4 1.6 + - - -
434A GLN* 1.3 71.7 - - - +
436A TRP* 1.4 58.0 + - - +
438A ALA* 3.3 4.5 + - - +
439A ALA* 2.9 26.0 + - - +
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Residues in contact with TRP 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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31A ALA* 4.6 0.8 + - - +
42A TRP* 3.4 52.5 - + - -
43A ALA* 3.7 23.5 - - + +
46A PHE* 3.6 37.1 - + + +
47A VAL* 4.8 2.0 - - - +
180A GLY 5.6 0.4 - - - -
376A TRP* 5.1 2.0 - + - -
381A TRP* 3.9 25.2 - + - -
383A VAL* 3.6 41.0 - - + +
419A GLU 4.5 2.6 + - - -
434A GLN* 3.3 27.8 - - + +
435A SER* 1.4 78.4 - - - +
437A THR* 1.3 83.4 + - - +
439A ALA* 3.6 8.6 - - - +
440A ALA* 3.0 26.2 + - - +
504A GOL 3.8 21.8 - - - -
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Residues in contact with THR 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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382A PRO* 3.9 27.7 - - + +
412A ALA* 5.3 4.3 - - + -
417A PHE* 3.6 24.7 - - + -
418A ALA 2.7 30.1 + - - +
419A GLU* 4.2 1.7 + - - -
421A TYR* 4.9 3.4 - - - +
434A GLN* 3.1 12.1 + - - +
436A TRP* 1.3 89.6 + - - +
438A ALA* 1.3 65.3 + - - +
440A ALA* 3.3 7.3 + - - +
441A VAL* 3.1 26.9 + - + +
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Residues in contact with ALA 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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16A ALA* 3.7 24.4 - - + +
19A LEU* 3.7 22.9 - - + -
20A LEU* 4.3 4.3 - - + -
417A PHE* 3.6 22.9 - - + -
434A GLN 3.3 3.8 + - - -
435A SER 3.6 7.2 - - - +
437A THR* 1.3 79.1 - - - +
439A ALA* 1.3 56.6 + - - +
441A VAL* 3.2 3.3 + - - +
442A LEU* 2.9 33.9 + - - +
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Residues in contact with ALA 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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20A LEU* 4.7 2.4 - - + +
46A PHE* 3.1 35.2 - - + +
47A VAL* 4.3 3.8 - - - -
49A ILE* 5.0 2.1 - - + +
50A GLY* 3.7 20.5 + - - -
435A SER 2.9 17.9 + - - +
436A TRP* 3.6 6.7 - - - +
437A THR 3.2 0.2 - - - -
438A ALA* 1.3 75.8 - - - +
440A ALA* 1.3 63.0 + - - +
442A LEU* 3.3 3.0 + - - +
443A ASP* 2.9 25.5 + - - +
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Residues in contact with ALA 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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382A PRO* 4.4 9.6 - - + +
383A VAL* 5.4 0.7 - - - -
386A TRP* 3.8 36.3 - - + -
436A TRP 3.0 17.5 + - - +
437A THR* 3.6 8.1 - - - +
438A ALA 3.3 0.4 - - - -
439A ALA* 1.3 77.2 - - - +
441A VAL* 1.3 62.4 + - - +
443A ASP* 3.3 1.9 + - - +
444A TRP* 2.9 42.5 + - + -
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Residues in contact with VAL 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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12A LEU* 3.8 19.3 - - + +
16A ALA* 4.2 13.5 - - + -
409A LEU* 4.3 6.7 - - + -
412A ALA* 3.6 31.2 - - + -
417A PHE* 4.1 11.9 - - + -
437A THR* 3.1 14.6 + - + +
438A ALA 3.6 7.4 - - - +
440A ALA* 1.3 77.0 - - - +
442A LEU* 1.3 59.2 + - - +
444A TRP* 3.2 12.9 + - + +
445A LEU* 2.8 53.4 + - + +
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Residues in contact with LEU 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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13A ALA* 3.6 31.4 - - + +
16A ALA* 3.6 9.0 - - + -
17A ALA* 3.9 25.4 - - + +
20A LEU* 3.6 30.3 - - + -
50A GLY* 3.7 16.8 - - - +
53A PRO* 4.4 13.5 - - + +
54A LEU* 4.1 14.1 - - + -
438A ALA 2.9 21.8 + - - +
439A ALA* 3.8 3.4 - - - +
441A VAL* 1.3 78.4 - - - +
443A ASP* 1.3 64.1 + - - +
445A LEU* 3.5 9.5 + - - +
446A GLY* 3.7 9.0 + - - +
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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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49A ILE* 3.5 25.6 - - + +
50A GLY* 5.0 0.4 - - - -
53A PRO* 5.0 4.4 - - - +
125A ARG* 2.8 42.1 + - - +
129A HIS* 4.7 2.5 + - - -
386A TRP* 2.8 36.7 + - - +
390A TRP* 5.4 1.6 - - - -
439A ALA 2.9 17.0 + - - +
440A ALA 3.8 0.2 - - - +
442A LEU* 1.3 78.1 - - - +
444A TRP* 1.3 66.7 + - - +
446A GLY* 3.7 7.6 + - - -
501A GOL 5.1 1.9 + - - -
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Residues in contact with TRP 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A PRO* 4.3 8.7 - - + -
385A THR* 3.8 28.5 - - + -
386A TRP* 3.4 46.3 - + + +
389A SER* 4.2 10.5 + - - -
405A ARG* 2.7 68.3 + - + +
408A GLY* 3.7 25.8 - - - -
409A LEU* 3.8 25.6 - - + -
412A ALA* 5.3 0.7 - - + -
440A ALA* 2.9 35.8 + - + +
441A VAL* 3.7 9.6 - - + +
443A ASP* 1.3 79.7 - - - +
445A LEU* 1.3 67.1 + - - +
446A GLY* 3.1 1.2 + - - -
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Residues in contact with LEU 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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9A PRO* 3.6 43.7 - - + +
12A LEU* 4.3 7.9 - - + -
13A ALA* 3.6 23.1 - - + +
405A ARG* 3.7 10.9 + - - +
409A LEU* 3.8 28.0 - - + -
441A VAL* 2.8 42.9 + - + +
442A LEU* 3.5 3.6 + - - +
443A ASP 3.4 0.2 - - - -
444A TRP* 1.3 75.0 - - - +
446A GLY* 1.3 69.6 - - - +
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Residues in contact with GLY 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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13A ALA* 5.9 1.0 - - - +
53A PRO* 6.5 0.7 - - - -
129A HIS* 6.5 0.4 - - - -
442A LEU 3.7 10.4 + - - +
443A ASP 3.7 6.0 + - - -
444A TRP 3.0 5.8 - - - -
445A LEU* 1.3 87.3 - - - +
501A GOL 4.6 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