Contacts of the helix formed by residues 315 - 323 (chain B) in PDB entry 3UXO
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 SER 315 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B TYR* 3.8 16.8 - - - +
313B VAL* 3.3 2.9 + - - +
314B ASP* 1.3 80.9 + - - +
316B GLU* 1.3 63.9 + - - +
317B GLN* 3.1 24.6 + - - +
318B ASP* 3.4 23.6 + - - +
319B ILE* 4.2 6.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ARG* 2.8 38.5 + - - +
266B TYR* 3.8 11.1 - - + +
269B VAL* 3.8 19.1 - - + -
270B LEU* 3.3 21.7 + - + +
315B SER* 1.3 73.2 - - - +
317B GLN* 1.3 63.7 + - - +
319B ILE* 3.0 29.2 + - - +
320B PHE* 3.6 9.7 - - - -
327B TYR* 3.8 10.9 + - + +
330B PRO* 4.6 0.2 - - - +
333B ARG* 2.5 49.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B SER* 3.1 13.2 + - - +
316B GLU* 1.3 78.5 - - - +
318B ASP* 1.3 64.4 + - - +
319B ILE 3.2 0.2 + - - -
320B PHE* 3.3 4.5 + - - +
321B ASP* 3.0 56.0 + - - +
327B TYR* 3.2 52.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B PRO 4.2 5.6 - - - +
313B VAL* 3.7 4.6 - - + -
314B ASP* 2.9 34.1 + - - +
315B SER* 3.4 19.7 + - - +
316B GLU 3.2 0.4 + - - -
317B GLN* 1.3 77.1 - - - +
319B ILE* 1.3 57.3 + - - +
321B ASP* 3.2 14.5 + - - +
322B TYR* 2.9 52.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B TYR 4.1 7.2 - - - +
267B CYS* 3.8 35.0 - - - +
270B LEU* 3.7 23.6 - - + -
282B MET* 3.5 21.8 - - + -
293B ILE* 3.8 22.2 - - + -
298B ILE* 4.7 7.4 - - + -
313B VAL* 4.1 18.8 - - + -
315B SER 4.2 4.3 - - - +
316B GLU* 3.0 17.2 + - - +
318B ASP* 1.3 74.0 - - - +
320B PHE* 1.3 65.3 + - - +
322B TYR* 3.2 20.3 + - - +
323B ILE* 3.3 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B LEU* 3.8 13.9 - - + -
278B PHE* 3.4 36.6 - + - -
282B MET* 3.7 17.9 - - + -
316B GLU 3.6 13.7 - - - -
317B GLN 3.3 6.6 + - - +
319B ILE* 1.3 77.4 - - - +
321B ASP* 1.3 62.9 + - - +
323B ILE* 3.3 5.5 + - - +
324B GLN 3.0 4.9 + - - -
325B TRP* 2.9 48.7 + + + +
326B ARG 3.5 16.4 - - - -
327B TYR* 3.7 22.0 - + - -
328B ARG* 3.8 21.8 - - + -
333B ARG* 3.5 30.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B GLN* 3.0 40.4 + - - +
318B ASP* 3.3 19.4 - - - +
320B PHE* 1.3 77.3 - - - +
322B TYR* 1.3 65.1 + - + +
324B GLN* 3.0 26.5 + - - +
325B TRP 4.6 6.5 - - - +
327B TYR 5.5 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B LYS* 5.5 0.9 - - - +
291B PHE* 3.2 30.9 - + + -
298B ILE* 3.6 29.4 - - + -
311B LEU* 3.6 31.8 - - + +
312B PRO* 2.8 37.2 + - - +
313B VAL* 4.0 8.5 - - + -
318B ASP* 2.9 33.2 + - + +
319B ILE* 3.2 11.4 + - - +
321B ASP* 1.3 78.9 - - + +
323B ILE* 1.3 59.8 + - - +
324B GLN* 3.5 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B MET* 3.6 50.3 - - + +
285B HIS* 3.5 27.5 - - + +
286B ALA* 3.6 28.9 - - + +
289B LYS* 4.4 7.0 - - + +
291B PHE* 4.3 8.7 - - + -
293B ILE* 4.3 3.1 - - + -
298B ILE* 4.3 14.4 - - + -
319B ILE 3.8 8.5 - - - +
320B PHE* 3.3 10.7 + - - +
321B ASP 3.2 0.2 - - - -
322B TYR* 1.3 78.4 - - - +
324B GLN* 1.3 69.6 + - - +
325B TRP* 3.7 20.3 - - + +
----------------------------------------------------------
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