Contacts of the helix formed by residues 384 - 396 (chain A) in PDB entry 3OVA
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 THR 384 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313A PHE* 3.4 11.7 - - - -
336A LYS 3.5 13.5 - - - +
337A GLU* 4.3 11.4 - - + +
383A THR* 1.3 91.2 + - - +
385A PRO* 1.3 74.2 - - - +
386A GLU* 3.5 12.7 + - - +
387A GLU* 3.1 36.0 + - - +
388A GLY* 3.0 18.4 + - - -
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Residues in contact with PRO 385 (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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277A ALA* 3.7 17.5 - - + -
279A PHE* 3.7 18.8 - - + -
308A LEU* 3.8 14.7 - - + +
313A PHE* 3.5 22.8 - - + -
333A CYS* 4.0 5.6 - - + -
335A ILE 3.2 27.1 - - - +
336A LYS 3.4 10.5 - - - +
384A THR* 1.3 86.2 - - - +
386A GLU* 1.3 65.4 + - - +
388A GLY* 3.3 1.0 + - - -
389A VAL* 2.9 34.7 + - - +
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Residues in contact with GLU 386 (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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277A ALA* 4.5 8.5 - - - +
278A VAL 4.7 1.2 + - - +
279A PHE* 3.8 30.4 - - + +
336A LYS 4.6 1.6 - - - +
384A THR* 3.6 11.3 + - - +
385A PRO* 1.3 90.6 - - - +
387A GLU* 1.3 64.8 + - + +
389A VAL 3.4 0.3 + - - -
390A ARG* 3.0 22.7 + - - +
414A ILE* 3.2 39.8 - - + +
416A SER* 4.3 14.7 + - - +
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Residues in contact with GLU 387 (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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340A ARG* 5.2 2.4 + - - -
382A PHE* 3.6 17.7 - - + +
383A THR* 2.9 30.0 + - - -
384A THR* 3.1 29.8 + - - +
386A GLU* 1.3 75.6 - - + +
388A GLY* 1.3 64.0 - - - +
390A ARG* 3.5 33.7 + - - +
391A SER* 3.1 23.4 + - - -
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Residues in contact with GLY 388 (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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307A PHE* 3.3 26.8 - - - -
313A PHE* 4.9 1.6 - - - -
382A PHE* 3.7 23.0 - - - +
384A THR 3.0 12.1 + - - -
385A PRO 3.6 3.8 - - - -
386A GLU 3.2 0.4 - - - -
387A GLU* 1.3 76.7 - - - +
389A VAL* 1.3 55.0 + - - +
391A SER* 3.2 4.5 + - - -
392A TYR 2.8 23.9 + - - -
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Residues in contact with VAL 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A PHE* 3.9 13.7 - - + -
281A VAL* 3.7 30.3 - - + -
304A ILE* 3.6 35.2 - - + -
307A PHE* 4.3 2.7 - - + -
308A LEU* 3.7 18.4 - - + -
385A PRO 2.9 20.7 + - - +
386A GLU 3.4 0.2 + - - -
388A GLY* 1.3 71.6 - - - +
390A ARG* 1.3 58.9 + - - +
392A TYR* 4.2 5.6 - - + -
393A ALA* 2.7 38.1 + - + +
414A ILE* 4.0 12.1 - - + -
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Residues in contact with ARG 390 (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 GLU 3.0 18.1 + - - +
387A GLU* 3.6 39.2 + - - +
389A VAL* 1.3 77.0 - - - +
391A SER* 1.3 60.4 + - - +
394A SER* 2.7 37.0 + - - +
412A PHE* 3.7 16.8 - - + -
414A ILE* 3.4 12.0 - - + +
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Residues in contact with SER 391 (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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307A PHE* 6.1 0.2 - - - -
382A PHE* 4.2 22.3 - - - -
387A GLU 3.1 10.6 + - - -
388A GLY 3.4 7.9 - - - -
390A ARG* 1.3 83.1 - - - +
392A TYR* 1.3 63.1 + - - +
394A SER* 3.8 2.7 - - - -
395A THR* 3.0 33.4 + - - +
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Residues in contact with TYR 392 (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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303A LYS* 3.4 29.0 + - - +
304A ILE* 3.8 31.0 - - + -
307A PHE* 3.7 37.2 - + + -
310A ARG* 3.8 12.3 - - - -
388A GLY 2.8 16.8 + - - +
389A VAL* 3.2 4.0 + - - +
391A SER* 1.3 77.4 - - - +
393A ALA* 1.3 56.5 + - - +
395A THR* 3.4 3.6 + - - -
396A HIS* 2.7 71.8 + + + +
399A THR* 3.6 6.8 - - - +
400A LEU* 3.8 12.6 - - + -
22C A 2.5 30.1 + - - -
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Residues in contact with ALA 393 (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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281A VAL* 5.2 3.6 - - + -
304A ILE* 5.1 4.3 - - + -
389A VAL* 2.7 29.9 + - + +
392A TYR* 1.3 79.6 - - + +
394A SER* 1.3 58.6 + - - +
396A HIS 4.6 0.2 - - - +
397A TRP* 3.4 24.8 + - - +
400A LEU* 4.4 13.9 - - + -
408A ILE* 3.8 16.5 - - + +
412A PHE* 3.7 24.8 - - + -
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Residues in contact with SER 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ARG* 2.7 28.2 + - - +
391A SER* 3.8 5.2 - - - -
393A ALA* 1.3 77.1 - - - +
395A THR* 1.3 63.2 + - - +
397A TRP* 3.5 17.2 + - - -
412A PHE* 3.4 18.7 - - - -
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Residues in contact with THR 395 (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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391A SER* 3.0 22.0 + - - +
392A TYR* 4.2 0.2 - - - -
394A SER* 1.3 84.0 - - - +
396A HIS* 1.3 79.4 + - - +
397A TRP* 3.5 9.6 + - - -
398A HIS* 5.2 0.9 + - - +
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Residues in contact with HIS 396 (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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392A TYR* 2.7 55.5 + + + +
393A ALA 4.2 0.4 - - - -
395A THR* 1.3 100.8 + - - +
397A TRP* 1.3 64.4 + - - +
398A HIS* 3.1 4.1 + - - +
399A THR* 3.2 20.1 + - + +
400A LEU* 3.4 8.4 - - - +
21C C 2.8 33.5 + - + -
22C A 3.0 34.0 + - - -
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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