Contacts of the helix formed by residues 253 - 271 (chain D) in PDB entry 1R4N
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 ASP 253 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D ASP* 2.8 33.7 + - + +
251D GLY 3.4 0.2 - - - -
252D ASP* 1.3 74.0 - - - +
254D PRO* 1.3 58.7 - - - +
255D GLU* 3.1 28.5 + - - +
256D HIS* 2.6 51.9 + - + +
257D ILE* 3.3 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 254 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C GLN* 5.6 7.4 - - - +
252D ASP 2.8 17.9 - - - +
253D ASP* 1.3 77.2 - - - +
255D GLU* 1.3 58.3 + - + +
256D HIS 2.9 1.0 + - - -
257D ILE* 2.9 7.1 + - + +
258D GLN* 2.6 37.3 + - - +
278D TYR* 3.8 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 255 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D PHE* 3.4 32.7 - - + -
253D ASP* 3.0 13.8 + - - +
254D PRO* 1.3 81.0 - - + +
256D HIS* 1.3 56.4 + - - +
258D GLN* 3.7 8.9 - - - +
259D TRP* 3.1 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 256 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D TRP* 3.4 13.3 - + - -
243D PHE* 3.2 40.7 - + - +
247D VAL* 5.0 5.6 - - + +
248D PRO 3.5 15.0 - - - -
249D LEU* 3.8 11.4 - - + -
250D ASP* 2.8 50.8 + - + +
253D ASP* 2.6 33.1 + - + +
255D GLU* 1.3 70.0 - - - +
257D ILE* 1.3 59.3 + - + +
259D TRP* 3.1 5.4 + - - +
260D ILE* 2.8 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 257 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251D GLY* 2.9 32.1 - - - +
252D ASP 4.7 7.6 - - - +
253D ASP 3.3 5.1 + - - +
254D PRO* 2.9 7.2 + - + +
256D HIS* 1.3 73.2 - - + +
258D GLN* 1.3 57.7 + - - +
260D ILE* 3.0 7.7 + - + -
261D PHE* 2.5 38.3 + - - +
278D TYR* 3.3 29.4 - - + +
281D THR* 4.0 17.0 - - + +
282D GLN* 3.5 44.0 - - + +
285D VAL* 5.1 9.2 - - + -
286D LYS* 4.3 3.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 258 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254D PRO 2.6 21.0 + - - +
255D GLU* 3.7 11.2 - - - +
257D ILE* 1.3 72.7 - - - +
259D TRP* 1.3 58.2 + - - +
261D PHE* 3.4 23.5 - - - +
262D GLN* 2.9 41.2 + - - +
278D TYR* 3.7 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 259 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232D VAL* 4.0 20.9 - - + -
236D GLN* 3.8 27.4 - - + -
237D TRP* 3.5 26.9 - + + -
240D GLU* 4.3 14.3 + - + -
242D PRO* 3.3 39.2 + - + +
243D PHE* 4.3 12.8 - + + -
255D GLU 3.1 14.8 + - - +
256D HIS 3.1 9.3 + - - +
257D ILE 3.1 0.4 - - - -
258D GLN* 1.3 75.5 - - - +
260D ILE* 1.3 70.0 + - + +
262D GLN* 2.9 11.0 + - + +
263D LYS* 2.7 65.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 260 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D ILE* 4.3 4.7 - - + +
232D VAL* 3.4 27.9 - - + +
233D ARG* 4.7 3.1 - - + +
237D TRP* 4.3 0.7 - - + -
249D LEU* 3.3 46.7 - - + -
256D HIS 2.8 20.1 + - - +
257D ILE* 3.5 7.4 - - - +
259D TRP* 1.3 88.6 - - + +
261D PHE* 1.3 52.0 + - - +
264D SER* 2.7 46.1 + - - +
281D THR* 3.7 17.0 - - + -
285D VAL* 3.9 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 261 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D ILE 2.5 20.8 + - - +
258D GLN* 3.4 24.9 - - - +
260D ILE* 1.3 73.3 - - - +
262D GLN* 1.3 57.1 + - - +
264D SER* 3.1 3.9 + - - -
265D LEU* 2.7 61.9 + - + +
276D VAL* 3.6 20.0 - - + -
277D THR* 3.5 5.8 - - - -
278D TYR* 3.2 44.9 - + + -
281D THR* 3.0 31.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 262 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258D GLN* 2.9 27.6 + - - +
259D TRP* 3.2 14.1 - - + +
261D PHE* 1.3 79.9 - - - +
263D LYS* 1.3 61.8 + - + +
265D LEU* 3.2 21.3 - - - +
266D GLU* 3.0 51.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 263 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232D VAL* 3.3 22.7 - - + +
236D GLN* 3.0 33.4 + - - +
240D GLU* 5.1 8.5 + - - -
259D TRP* 2.7 54.7 + - + +
262D GLN* 1.3 72.1 - - + +
264D SER* 1.3 60.6 + - - +
265D LEU 3.1 1.3 - - - -
266D GLU* 3.3 31.5 + - - +
267D ARG* 2.9 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 264 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D CYS* 3.8 4.4 - - - +
229D ILE* 3.0 47.9 - - - +
232D VAL* 3.3 14.6 - - - +
260D ILE* 2.7 31.1 + - - +
261D PHE* 3.6 4.0 - - - -
263D LYS* 1.3 72.6 - - - +
265D LEU* 1.3 58.5 + - - +
267D ARG* 3.7 4.0 - - - +
268D ALA* 2.9 30.5 + - - +
276D VAL* 4.1 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 265 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261D PHE* 2.7 49.2 + - + +
262D GLN* 3.2 26.2 - - - +
264D SER* 1.3 78.6 - - - +
266D GLU* 1.3 60.2 + - + +
268D ALA* 3.7 4.8 + - + +
269D SER* 3.3 20.4 + - - -
276D VAL* 4.3 17.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 266 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262D GLN* 3.0 39.6 + - - +
263D LYS* 3.6 38.8 + - + +
264D SER 3.3 0.2 - - - -
265D LEU* 1.3 76.5 - - - +
267D ARG* 1.3 65.7 + - - +
269D SER* 3.1 9.9 + - - -
270D GLN* 3.0 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 267 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D ILE 2.9 21.6 + - - -
219D ALA* 3.6 21.8 + - - +
222D PRO* 3.8 17.5 - - - +
227D HIS 3.9 6.9 + - - -
228D CYS* 3.9 15.3 - - + +
231D TYR* 3.0 57.3 - - + +
232D VAL* 4.4 3.6 - - + -
236D GLN* 5.2 1.8 - - - +
263D LYS 2.9 17.4 + - - +
264D SER* 3.7 6.5 - - - +
266D GLU* 1.3 73.8 - - - +
268D ALA* 1.3 67.0 + - - +
270D GLN* 2.9 39.1 + - - +
271D TYR* 3.3 24.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 268 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D CYS* 3.4 17.0 - - - -
264D SER 2.9 18.3 + - - +
265D LEU* 3.7 7.9 - - + +
267D ARG* 1.3 77.1 - - - +
269D SER* 1.3 51.4 + - - +
271D TYR 3.3 1.2 - - - -
272D ASN 2.6 31.2 + - - -
273D ILE* 2.8 31.8 + - + +
276D VAL* 3.6 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 269 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D LEU* 3.3 11.2 + - - -
266D GLU* 3.1 12.8 + - - -
268D ALA* 1.3 77.8 - - - +
270D GLN* 1.3 67.4 + - - +
272D ASN* 2.9 18.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 270 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266D GLU* 3.0 14.8 + - - +
267D ARG* 2.9 32.3 + - - +
269D SER* 1.3 78.1 - - - +
271D TYR* 1.3 80.4 + - + +
272D ASN* 3.3 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 271 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C SER* 2.8 31.1 + - - +
337C GLY* 6.0 0.3 - - - -
340C ILE* 3.1 15.4 - - - +
219D ALA 4.0 14.0 + - - -
220D SER 3.9 11.0 + - - -
222D PRO* 3.3 26.5 - - + -
228D CYS* 5.7 0.7 - - - -
267D ARG* 3.3 33.4 + - + +
268D ALA 3.3 2.2 - - - +
270D GLN* 1.3 96.2 + - + +
272D ASN* 1.3 79.3 + - - +
273D ILE* 3.3 16.3 + - + -
----------------------------------------------------------
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