Contacts of the helix formed by residues 384 - 396 (chain B) in PDB entry 3OVS
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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B PHE* 3.7 6.6 - - - -
336B LYS 3.4 15.0 - - - +
337B GLU* 3.8 16.8 - - + +
382B PHE* 4.5 0.2 - - - +
383B THR* 1.3 85.8 + - - +
385B PRO* 1.4 62.1 - - - +
386B GLU* 3.7 10.8 + - - +
387B GLU* 2.9 39.6 + - - +
388B GLY* 2.8 31.9 + - - -
390B ARG* 5.3 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ALA* 4.2 10.3 - - + -
279B PHE* 3.7 22.7 - - + -
308B LEU* 4.0 13.4 - - + +
313B PHE* 3.5 27.5 - - + -
333B CYS* 4.2 4.0 - - + -
335B ILE 3.1 22.9 - - - +
336B LYS* 3.2 18.2 - - - +
384B THR* 1.4 86.4 - - - +
386B GLU* 1.3 63.0 + - - +
388B GLY* 3.1 0.9 + - - -
389B VAL* 2.8 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ALA* 4.3 11.1 - - - +
278B VAL 4.6 2.4 + - - +
279B PHE* 3.6 41.2 - - + +
336B LYS 4.5 2.1 - - - +
384B THR* 3.7 11.3 + - - +
385B PRO* 1.3 90.9 - - - +
387B GLU* 1.3 63.5 + - - +
389B VAL* 4.0 1.1 - - - +
390B ARG* 3.1 31.5 + - - +
414B ILE* 3.6 24.2 - - + +
416B SER* 4.0 19.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B ARG* 3.9 9.4 + - - -
381B LYS 3.8 6.3 - - - +
382B PHE* 3.5 25.7 - - + +
383B THR* 3.3 27.4 + - - -
384B THR* 2.9 32.7 + - - +
386B GLU* 1.3 78.1 - - - +
388B GLY* 1.3 61.8 + - - +
390B ARG* 3.5 33.2 + - - +
391B SER* 3.5 17.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B PHE* 3.4 21.2 - - - -
313B PHE* 4.9 1.1 - - - -
382B PHE* 3.8 23.3 - - - -
384B THR 2.8 13.4 + - - -
385B PRO* 3.1 4.5 + - - -
386B GLU 3.1 0.4 - - - -
387B GLU* 1.3 77.0 - - - +
389B VAL* 1.3 58.6 + - - +
391B SER* 3.2 7.1 + - - -
392B TYR 3.0 21.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B PHE* 4.0 16.2 - - + -
281B VAL* 3.9 26.7 - - + -
304B ILE* 3.8 39.5 - - + -
307B PHE* 4.3 6.3 - - + -
308B LEU* 3.9 21.1 - - + -
385B PRO 2.8 22.6 + - - +
386B GLU 4.2 2.2 - - - +
388B GLY* 1.3 70.3 - - - +
390B ARG* 1.3 65.4 + - - +
392B TYR* 4.3 3.1 - - + +
393B ALA* 2.9 30.5 + - + +
414B ILE* 4.2 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B THR* 5.3 0.4 + - - -
386B GLU* 3.1 16.5 + - - +
387B GLU* 3.5 49.8 + - - +
388B GLY 3.3 0.2 - - - -
389B VAL* 1.3 75.7 - - - +
391B SER* 1.3 59.9 + - - +
394B SER* 3.3 26.5 + - - +
412B PHE* 3.6 16.0 - - + -
414B ILE* 3.5 23.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B PHE* 4.3 21.2 - - - -
387B GLU 3.5 7.9 + - - -
388B GLY 3.2 9.7 + - - -
389B VAL 3.1 0.6 - - - -
390B ARG* 1.3 77.8 - - - +
392B TYR* 1.3 63.9 + - - +
394B SER* 3.1 7.8 + - - -
395B THR* 2.9 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 392 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B LYS* 3.5 28.0 + - - +
304B ILE* 3.8 31.6 - - + -
307B PHE* 3.4 44.4 - + + -
310B ARG* 3.6 13.5 - - - -
388B GLY 3.0 10.7 + - - +
389B VAL* 3.3 3.8 + - + +
391B SER* 1.3 76.6 - - - +
393B ALA* 1.3 56.4 + - - +
395B THR* 3.2 4.8 + - - -
396B HIS* 2.7 73.4 + + + +
399B THR* 3.6 8.5 - - - +
400B LEU* 4.0 10.8 - - + -
22D A 2.5 29.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 393 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B VAL* 5.5 3.6 - - + -
304B ILE* 5.1 4.0 - - + -
389B VAL* 2.9 25.8 + - + +
392B TYR* 1.3 83.4 - - + +
394B SER* 1.3 62.0 + - - +
397B TRP* 3.2 26.9 + - - +
400B LEU* 4.4 13.0 - - + -
408B ILE* 3.8 19.5 - - + +
412B PHE* 4.0 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 394 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B ARG* 3.3 20.3 + - - +
391B SER* 3.1 8.8 + - - -
393B ALA* 1.3 78.7 - - - +
395B THR* 1.3 62.5 + - - +
397B TRP* 3.1 20.3 + - - -
412B PHE* 3.9 16.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B SER* 2.9 24.8 + - - +
392B TYR* 3.8 0.9 - - - -
394B SER* 1.3 81.1 - - - +
396B HIS* 1.3 84.5 + - - +
397B TRP* 3.5 4.5 + - - +
398B HIS* 3.2 21.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ARG* 5.3 0.4 + - - -
392B TYR* 2.7 55.1 + + + +
393B ALA 4.0 0.4 - - - -
395B THR* 1.3 106.5 + - - +
397B TRP* 1.3 62.4 + - - -
398B HIS* 3.2 9.7 + - - -
399B THR* 3.2 21.7 - - + +
400B LEU* 3.3 9.0 - - - +
21D C 2.8 33.6 + - + -
22D A 3.2 31.6 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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