Contacts of the helix formed by residues 325 - 331 (chain B) in PDB entry 6CNB
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 GLU 325 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ILE* 3.7 10.0 - - - +
302B LEU* 4.2 8.7 - - + +
305B ILE* 3.4 28.3 - - + -
306B GLY* 3.1 20.1 - - - +
309B VAL* 3.1 50.3 - - - +
322B GLU 4.2 0.6 + - - -
324B ILE* 1.3 81.0 - - - +
326B ALA* 1.3 54.0 + - - +
327B ILE 2.9 5.8 - - - -
328B ALA* 2.5 51.5 + - + +
329B THR* 3.0 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B LEU* 4.7 17.3 - - + +
322B GLU 4.6 1.6 + - - -
323B GLY* 3.5 22.7 + - - +
324B ILE 3.5 1.4 - - - -
325B GLU* 1.3 75.6 - - - +
327B ILE* 1.3 63.1 + - - +
329B THR* 3.9 10.2 + - - +
330B THR* 3.8 15.4 + - - +
342B PHE* 4.9 6.2 - - + -
230M SER* 4.3 3.1 + - - -
231M LEU* 3.3 25.3 - - + +
234M HIS* 5.0 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B MET* 6.2 7.2 - - + -
319B ILE* 4.9 9.0 - - + -
324B ILE 4.7 8.1 - - - +
325B GLU* 2.8 2.0 + - - +
326B ALA* 1.3 77.6 - - - +
328B ALA* 1.3 64.7 + - - +
330B THR* 2.8 24.3 + - - -
331B VAL* 2.9 25.4 + - + +
226M ARG* 6.3 3.6 - - + -
228M THR 5.2 10.3 - - - +
229M GLY* 6.1 1.1 - - - -
231M LEU* 3.4 36.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B SER* 6.0 0.4 - - - +
305B ILE* 5.6 0.7 - - + -
309B VAL* 5.6 0.4 - - + -
325B GLU* 2.5 44.7 + - + +
327B ILE* 1.3 77.7 - - + +
329B THR* 1.3 61.4 + - - +
331B VAL 2.8 13.6 - - - +
332B ILE* 2.7 47.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B VAL* 6.1 1.1 - - + -
259B ALA* 3.8 24.0 - - + +
260B CYS* 4.1 21.1 - - - +
302B LEU* 3.7 21.1 - - - +
305B ILE* 5.4 4.9 - - - +
325B GLU* 3.0 15.2 + - - +
326B ALA* 4.3 6.1 - - - -
327B ILE 3.3 0.4 + - - -
328B ALA* 1.3 75.6 - - - +
330B THR* 1.3 57.5 + - - +
332B ILE* 4.3 5.6 - - - +
342B PHE* 4.5 17.3 - - + -
345B LYS* 2.8 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ALA 3.8 5.9 + - - +
327B ILE* 2.8 11.4 + - - -
329B THR* 1.3 78.0 - - - +
331B VAL* 1.3 70.4 + - - +
332B ILE 3.8 0.4 + - - -
334B HIS 3.2 8.3 - - - +
338B GLU* 3.7 38.6 + - - +
339B ALA 4.1 7.6 - - - +
342B PHE* 3.7 29.6 - - + -
345B LYS* 3.0 28.3 + - + +
230M SER* 3.9 16.7 + - - +
231M LEU* 5.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B GLU* 3.8 31.0 - - - +
228B LYS* 4.4 3.0 + - - +
327B ILE* 2.9 27.8 + - + +
328B ALA* 2.8 18.3 - - - +
330B THR* 1.3 82.7 + - - +
332B ILE* 1.3 67.8 + - - +
333B ALA 4.7 7.4 - - - +
334B HIS 4.3 4.9 - - - +
335B LEU* 5.6 3.1 - - + -
338B GLU* 5.1 8.5 - - + -
----------------------------------------------------------
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