Contacts of the helix formed by residues 323 - 335 (chain D) in PDB entry 3BUW
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 PRO 323 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D GLN* 4.4 38.3 - - + +
250D PRO* 5.6 3.1 - - + -
322D LYS* 1.3 90.4 - - + +
324D LEU* 1.3 68.2 + - - +
325D PHE* 4.5 9.2 - - + +
326D GLN* 3.1 27.4 + - + +
327D ALA* 3.3 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 324 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247D LEU 4.9 2.5 + - - +
261D LEU* 3.9 22.4 - - + -
293D PHE* 3.8 25.4 - - + -
303D TRP* 3.5 56.6 - - + +
305D ILE* 3.6 30.7 - - + -
319D PRO* 4.8 3.3 - - + +
322D LYS 3.8 1.2 + - - -
323D PRO* 1.3 72.4 - - - +
325D PHE* 1.3 65.0 + - - +
327D ALA* 3.1 9.7 + - + -
328D LEU* 2.9 37.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 325 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D GLN 4.6 9.4 - - - -
250D PRO* 5.1 6.1 - - + -
257D ASN* 3.4 51.1 - - + -
260D SER* 4.4 7.4 - - - -
261D LEU* 3.9 25.5 - - + +
323D PRO* 3.1 8.9 + - + -
324D LEU* 1.3 79.1 - - - +
326D GLN* 1.3 57.6 + - - +
328D LEU* 3.4 4.3 + - - +
329D ILE* 2.9 43.1 + - + +
349D LEU* 3.9 44.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 326 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322D LYS* 3.6 15.9 - - + +
323D PRO* 3.1 24.1 + - + +
325D PHE* 1.3 76.7 - - - +
327D ALA* 1.3 61.2 + - - +
329D ILE* 4.4 16.0 - - - +
330D ASP* 2.8 73.4 + - - +
333D ARG* 5.0 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 327 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305D ILE* 5.6 0.9 - - + -
319D PRO* 4.0 28.9 - - + -
322D LYS* 3.6 19.6 - - + +
323D PRO 3.3 7.4 + - - +
324D LEU* 3.1 14.1 + - + +
326D GLN* 1.3 78.3 - - - +
328D LEU* 1.3 58.4 + - + +
330D ASP* 4.1 0.7 - - - +
331D GLY* 2.9 23.7 + - - -
337D TYR* 3.5 16.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 328 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261D LEU* 4.0 7.9 - - + -
265D HIS* 4.4 4.0 - - - +
291D TYR* 3.8 29.8 - - + +
293D PHE* 4.1 17.7 - - + -
305D ILE* 4.2 19.1 - - + -
324D LEU* 2.9 36.9 + - + +
325D PHE 3.8 3.1 - - - +
327D ALA* 1.3 75.9 - - - +
329D ILE* 1.3 59.7 + - - +
331D GLY 3.7 0.2 - - - -
332D PHE* 2.8 32.1 + - - +
337D TYR* 4.0 17.4 - - + +
349D LEU* 3.8 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 329 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325D PHE* 2.9 37.0 + - + +
326D GLN* 3.9 13.9 - - - +
328D LEU* 1.3 76.4 - - - +
330D ASP* 1.3 64.4 + - - +
332D PHE* 3.3 8.1 + - + +
333D ARG* 3.1 60.3 + - + +
349D LEU* 4.4 18.2 - - + +
350D THR* 3.9 36.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 330 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322D LYS* 2.7 30.2 + - - +
326D GLN* 2.8 41.2 + - - +
327D ALA 4.1 2.0 - - - +
329D ILE* 1.3 75.7 - - - +
331D GLY* 1.3 58.4 + - - +
333D ARG* 3.3 18.6 + - - +
334D GLU* 2.9 44.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 331 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327D ALA 2.9 12.0 + - - -
328D LEU 3.7 0.2 - - - -
330D ASP* 1.3 76.8 - - - +
332D PHE* 1.3 56.5 + - - +
334D GLU* 3.6 13.6 + - - +
335D GLY 3.0 6.9 + - - -
336D PHE* 2.9 31.3 + - - -
337D TYR* 3.1 31.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 332 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328D LEU 2.8 19.0 + - - +
329D ILE* 3.5 9.6 - - + +
330D ASP 3.2 0.2 - - - -
331D GLY* 1.3 74.9 - - - +
333D ARG* 1.3 75.7 + - + +
335D GLY* 3.2 9.2 + - - -
337D TYR 3.4 23.3 + - - +
338D LEU* 3.2 34.4 - - + +
346D ASN* 3.5 33.0 - - + +
350D THR* 5.9 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 333 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326D GLN* 5.0 2.8 - - - +
329D ILE* 3.1 38.7 + - - +
330D ASP* 3.3 18.6 + - - +
332D PHE* 1.3 91.0 - - + +
334D GLU* 1.3 65.8 + - + +
335D GLY* 3.3 0.9 + - - -
350D THR* 3.7 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 334 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330D ASP* 2.9 34.6 + - + +
331D GLY* 3.6 8.2 + - - +
333D ARG* 1.3 76.9 - - + +
335D GLY* 1.3 59.3 + - - +
336D PHE* 3.3 41.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 335 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D PRO 5.1 0.5 - - - -
289D GLY* 3.7 8.1 + - - -
331D GLY 3.0 4.0 + - - -
332D PHE 3.2 11.8 + - - -
333D ARG 4.2 1.1 - - - -
334D GLU* 1.3 79.0 - - - +
336D PHE* 1.3 66.1 + - - +
337D TYR 3.6 1.6 - - - -
338D LEU* 3.4 29.8 - - - +
----------------------------------------------------------
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