Contacts of the helix formed by residues 296 - 308 (chain D) in PDB entry 1A4Y
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 296 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294D GLU 3.6 1.4 - - - -
295D LEU* 1.3 74.7 - - - +
297D ASP* 1.3 64.8 + - - -
298D GLU* 2.9 9.0 + - - -
299D GLY 2.9 10.6 + - - -
300D ALA 3.0 8.5 + - - -
322D CYS 2.9 10.1 + - - -
323D SER* 3.3 21.7 - - - -
324D PHE* 3.3 10.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 297 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296D GLY* 1.3 71.9 - - - -
298D GLU* 1.3 56.0 + - - +
299D GLY 3.4 0.2 - - - -
300D ALA* 3.6 7.5 - - - +
301D ARG* 3.0 28.1 + - - +
323D SER 3.9 1.0 + - - -
324D PHE* 3.4 1.7 - - - -
325D THR* 2.6 56.8 + - - +
327D ALA* 3.6 17.7 - - + +
328D CYS* 3.3 22.1 - - + +
331D HIS* 5.8 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 298 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D ALA* 4.1 19.7 - - + -
295D LEU 4.2 2.5 - - - +
296D GLY* 2.9 0.9 - - - -
297D ASP* 1.3 76.9 - - - +
299D GLY* 1.3 63.6 + - - +
301D ARG* 2.7 44.2 + - - +
302D LEU* 3.2 28.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 299 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D ALA* 4.0 8.9 - - - +
272D CYS* 3.8 13.4 - - - -
295D LEU* 3.1 23.7 + - - -
296D GLY 2.9 7.2 + - - -
298D GLU* 1.3 73.2 - - - +
300D ALA* 1.3 60.2 + - - +
302D LEU* 3.3 5.9 + - - +
303D LEU* 3.0 33.8 + - - +
324D PHE* 4.5 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 300 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296D GLY 3.0 4.4 + - - -
297D ASP* 3.6 8.7 - - - +
298D GLU 3.3 0.2 - - - -
299D GLY* 1.3 77.7 - - - +
301D ARG* 1.3 55.3 + - - +
303D LEU* 3.4 5.7 + - - +
304D CYS* 2.9 35.7 + - - -
324D PHE* 3.2 39.3 - - + -
328D CYS* 3.6 22.0 - - + -
331D HIS* 5.6 0.4 - - - -
332D PHE* 4.0 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 301 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297D ASP 3.0 17.7 + - - +
298D GLU* 2.7 39.3 + - - +
299D GLY 3.2 0.2 - - - -
300D ALA* 1.3 74.0 - - - +
302D LEU* 1.3 80.7 + - - +
304D CYS* 3.5 5.0 + - - +
305D GLU* 2.9 67.7 + - + +
331D HIS* 4.2 33.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 302 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D ALA* 3.5 26.7 - - + +
272D CYS* 4.5 2.7 - - - -
273D GLY* 4.0 17.9 - - - +
276D CYS* 3.7 13.0 - - - -
280D ARG* 4.7 0.7 + - - -
298D GLU* 3.2 20.4 - - + +
299D GLY* 3.3 11.6 + - - +
301D ARG* 1.3 100.0 - - - +
303D LEU* 1.3 65.8 + - - +
305D GLU* 3.3 8.0 + - - +
306D THR* 2.9 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 303 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272D CYS* 4.0 16.4 - - - -
275D LEU* 5.7 1.1 - - + -
276D CYS* 4.2 12.6 - - - -
279D LEU* 4.5 15.5 - - + -
288D LEU* 5.4 0.2 - - + -
290D LEU* 4.0 27.4 - - + -
295D LEU* 4.2 8.1 - - + -
299D GLY 3.0 17.0 + - - +
300D ALA* 3.6 7.4 - - - +
301D ARG 3.3 0.2 - - - -
302D LEU* 1.3 76.2 - - - +
304D CYS* 1.3 59.6 - - - +
306D THR* 3.1 5.2 + - - -
307D LEU* 2.9 40.9 + - + +
314D LEU* 6.5 0.4 - - + -
317D LEU* 4.4 16.2 - - + -
319D VAL* 4.1 19.5 - - + -
324D PHE* 4.5 8.5 - - + -
332D PHE* 5.0 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 304 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300D ALA 2.9 21.2 + - - +
301D ARG 3.9 3.4 - - - +
303D LEU* 1.3 77.3 - - - +
305D GLU* 1.3 61.6 + - - +
307D LEU* 3.4 4.4 + - - +
308D LEU* 3.2 30.8 + - + +
331D HIS* 3.7 20.6 - - + +
332D PHE* 3.4 58.8 - - - -
335D VAL* 3.7 13.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 305 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D ARG* 4.8 4.2 + - - +
301D ARG* 2.9 57.0 + - + +
302D LEU* 3.6 7.9 - - - +
303D LEU 3.2 0.2 - - - -
304D CYS* 1.3 76.9 - - + +
306D THR* 1.3 61.7 + - - +
308D LEU* 3.3 9.2 + - - +
309D GLU* 3.2 31.1 + - - +
331D HIS* 5.7 5.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 306 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276D CYS* 3.2 38.2 - - - +
279D LEU* 3.6 22.2 - - + -
280D ARG* 2.9 37.2 + - + +
302D LEU 2.9 13.6 + - - -
303D LEU* 3.1 7.5 + - - -
305D GLU* 1.3 71.1 - - - +
307D LEU* 1.3 59.1 + - - +
308D LEU 3.0 4.3 - - - -
309D GLU* 2.8 28.9 + - - +
312D CYS* 3.6 9.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 307 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D LEU* 2.9 25.8 + - + +
304D CYS* 3.7 9.9 - - - +
305D GLU 3.3 0.2 - - - -
306D THR* 1.3 77.0 - - - +
308D LEU* 1.3 59.8 + - - +
309D GLU 4.3 2.9 - - - +
312D CYS* 3.9 23.1 - - - +
314D LEU* 4.2 12.6 - - + +
317D LEU* 4.0 24.5 - - + -
332D PHE* 4.7 8.1 - - + -
335D VAL* 3.9 23.6 - - + -
339D ASN* 2.7 42.0 + - - +
342D LEU* 4.1 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 308 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304D CYS* 3.2 19.4 + - + +
305D GLU* 3.7 8.7 - - - +
306D THR 3.0 0.8 - - - -
307D LEU* 1.3 80.8 - - - +
309D GLU* 1.3 64.9 + - - +
310D PRO* 3.7 4.0 - - - +
331D HIS 5.3 0.2 - - - +
334D SER* 4.1 22.9 - - - +
335D VAL* 3.8 27.1 - - + -
338D GLN* 3.8 35.3 + - + +
339D ASN* 4.5 3.4 - - + +
----------------------------------------------------------
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