Contacts of the helix formed by residues 434 - 447 (chain F) in PDB entry 6V3O
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 GLY 434 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219E ARG* 3.4 28.2 - - - +
261F ARG* 3.3 7.3 + - - -
431F ILE 2.9 10.6 + - - -
433F ASP* 1.3 76.9 - - - +
435F SER* 1.3 65.0 + - - -
436F LEU 3.2 1.6 - - - -
437F LEU 3.2 10.0 + - - -
438F ASP* 3.2 18.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 435 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322F GLN* 5.5 1.4 - - - +
326F LEU* 3.7 14.8 - - - +
329F GLU* 2.5 36.6 + - - -
431F ILE 4.4 2.0 + - - -
434F GLY* 1.3 71.7 - - - -
436F LEU* 1.3 56.9 + - - +
438F ASP* 3.4 13.4 + - - +
439F LEU* 3.0 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 436 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326F LEU* 3.9 31.5 - - + +
330F LEU* 4.9 7.4 - - + -
375F LEU* 6.0 0.7 - - + -
416F LEU* 4.2 26.9 - - + +
419F CYS* 4.0 9.2 - - + -
420F TYR* 3.7 43.7 - - + +
423F LEU* 3.9 20.2 - - + -
431F ILE 4.9 2.1 + - - +
432F ALA* 3.5 11.9 - - + +
434F GLY 3.2 0.8 - - - -
435F SER* 1.3 76.5 - - - +
437F LEU* 1.3 65.4 + - - +
439F LEU* 3.3 5.7 + - + +
440F LEU* 3.0 24.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 437 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261F ARG* 3.9 6.5 - - - +
275F ARG* 3.9 24.5 - - + -
276F LEU 5.5 0.2 - - - +
278F TYR* 3.8 36.1 - - + +
420F TYR* 4.6 9.2 - - + +
432F ALA 3.0 18.6 + - - +
433F ASP* 3.8 22.0 - - - +
434F GLY 3.2 7.4 + - - +
436F LEU* 1.3 73.1 - - - +
438F ASP* 1.3 65.3 + - - +
440F LEU* 3.1 8.6 + - - +
441F ARG* 2.8 62.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 438 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257F PRO* 3.8 30.3 - - + +
261F ARG* 2.8 34.6 + - - -
322F GLN* 5.4 1.8 - - - +
434F GLY 3.2 8.7 + - - -
435F SER* 3.4 14.0 - - - +
437F LEU* 1.3 76.1 - - - +
439F LEU* 1.3 57.6 + - - +
441F ARG* 3.2 8.5 + - - +
442F GLN* 2.9 40.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 439 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319F TYR* 4.0 27.8 - - + -
322F GLN* 4.1 25.1 + - + +
323F ILE* 3.6 31.4 - - + +
326F LEU* 3.7 23.1 - - + -
412F PHE* 5.3 0.2 - - + -
416F LEU* 3.7 21.5 - - + -
435F SER 3.0 14.4 + - - +
436F LEU* 3.6 10.5 - - + +
437F LEU 3.2 0.2 - - - -
438F ASP* 1.3 74.8 - - - +
440F LEU* 1.3 62.5 + - - +
442F GLN* 3.1 13.3 + - - +
443F VAL* 3.1 25.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 440 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278F TYR* 3.9 36.1 - - + +
413F LEU* 3.9 26.5 - - + -
416F LEU* 4.0 23.6 - - + +
417F GLU* 4.2 10.8 - - + -
420F TYR* 3.9 35.2 - - + -
436F LEU* 3.0 24.1 + - + +
437F LEU* 3.6 7.9 - - - +
439F LEU* 1.3 77.1 - - - +
441F ARG* 1.3 62.6 + - - +
443F VAL* 3.2 8.0 - - + +
444F PHE* 3.1 28.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 441 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256F VAL* 5.3 1.1 - - - -
257F PRO* 4.7 11.3 + - + -
260F LEU* 3.7 38.6 + - + +
261F ARG* 4.0 21.2 - - - +
264F ASP* 2.8 37.9 + - - -
275F ARG* 4.2 5.3 - - - +
276F LEU* 2.9 32.3 + - - +
277F PRO 5.3 0.2 + - - -
278F TYR* 4.2 22.8 - - + +
280F VAL* 6.4 0.2 - - - +
437F LEU* 2.8 43.9 + - + +
438F ASP* 3.6 10.2 + - - +
440F LEU* 1.3 76.8 - - - +
442F GLN* 1.3 57.0 + - - +
444F PHE* 3.5 2.0 + - - +
445F THR* 2.3 35.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 442 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253F TRP* 3.0 51.3 + - + +
254F LYS* 5.4 1.4 - - - +
256F VAL* 5.7 0.4 - - - -
257F PRO* 3.5 30.3 - - + +
319F TYR* 4.0 5.4 - - + -
322F GLN* 3.1 25.7 + - - +
438F ASP* 2.9 26.8 + - - +
439F LEU* 3.1 12.4 + - + +
441F ARG* 1.3 78.2 - - - +
443F VAL* 1.3 57.5 + - - +
445F THR* 4.2 1.1 - - - -
446F PHE* 2.8 49.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 443 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319F TYR* 3.3 35.0 - - + +
409F ILE* 4.4 10.0 - - + +
412F PHE* 3.5 25.1 - - + -
413F LEU* 3.5 33.9 - - + -
416F LEU* 4.9 4.0 - - + -
439F LEU* 3.1 16.5 + - + +
440F LEU* 3.2 15.0 - - + +
442F GLN* 1.3 76.9 - - - +
444F PHE* 1.3 63.7 + - + +
445F THR 3.1 0.2 - - - -
447F GLY* 3.0 26.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 444 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278F TYR* 3.2 49.4 - + - +
279F ASN* 3.5 36.3 - - + -
280F VAL 4.7 3.4 - - - +
281F SER* 2.7 34.5 + - - +
284F ARG* 5.2 0.9 - - - +
409F ILE* 6.1 0.9 - - + -
413F LEU* 3.5 38.8 - - + -
417F GLU* 4.6 4.7 - - - -
440F LEU 3.1 18.8 + - - +
441F ARG 4.1 3.1 - - - +
442F GLN 3.3 0.2 - - - -
443F VAL* 1.3 84.6 - - + +
445F THR* 1.3 58.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 445 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256F VAL* 3.5 34.2 - - + +
260F LEU* 4.6 4.2 - - - +
281F SER* 5.4 1.5 - - - +
283F ILE 3.2 27.0 + - - +
284F ARG* 4.0 20.1 - - - +
285F PHE* 4.3 10.4 + - + -
441F ARG 2.3 26.1 + - - -
442F GLN 3.6 3.4 - - - -
443F VAL 3.1 0.2 - - - -
444F PHE* 1.3 80.8 - - - +
446F PHE* 1.3 75.9 + - + +
447F GLY 3.7 0.4 - - - -
450F LEU 4.7 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 446 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248F ILE* 3.8 20.2 - - + -
252F VAL* 3.9 23.6 - - + -
253F TRP* 3.6 41.7 - + + -
256F VAL* 3.9 15.5 - - + -
285F PHE* 3.8 22.0 - + + -
319F TYR* 4.2 3.6 - - - +
442F GLN* 2.8 30.1 + - + +
445F THR* 1.3 86.7 - - + +
447F GLY* 1.3 64.5 + - - +
449F SER* 3.7 4.2 + - - -
450F LEU* 3.1 62.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 447 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315F ALA* 4.6 0.3 - - - +
319F TYR* 2.7 31.1 + - - -
409F ILE* 4.6 15.9 - - - -
412F PHE* 6.0 0.2 - - - -
443F VAL* 3.0 20.6 + - - -
445F THR 3.7 0.4 - - - -
446F PHE* 1.3 82.0 - - - +
448F LEU* 1.3 62.6 + - - -
449F SER* 3.6 1.0 + - - -
450F LEU 4.3 1.4 + - - -
----------------------------------------------------------
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