Contacts of the helix formed by residues 288 - 305 (chain D) in PDB entry 7CR3
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 TRP 288 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A PHE* 3.9 31.5 - + + -
115A ILE* 6.4 0.2 - - + -
118A TYR* 3.6 40.0 + + + +
287D THR* 1.3 79.9 - - + +
289D ASN* 1.3 102.3 + - - +
290D GLY 3.4 0.2 - - - -
291D ARG* 4.5 2.2 - - - +
292D LEU* 3.1 36.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 289 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D ALA* 3.6 30.8 + - + +
287D THR* 4.2 1.9 - - - +
288D TRP* 1.3 125.1 - - - +
290D GLY* 1.3 58.1 + - - +
292D LEU* 3.4 5.4 + - - +
293D LEU* 3.0 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 290 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D VAL* 4.3 14.2 - - - +
253D ALA* 4.1 10.8 - - - +
254D GLU* 5.1 2.2 - - - -
285D PRO* 4.0 11.6 - - - +
287D THR* 3.3 18.2 + - - -
289D ASN* 1.3 79.2 - - - +
291D ARG* 1.3 57.8 + - - +
293D LEU* 3.3 4.6 + - - +
294D ALA* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 291 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284D TYR* 4.5 12.5 - - - -
285D PRO* 2.7 43.3 + - + +
286D GLN* 4.1 11.9 - - - +
287D THR 3.2 23.8 + - - +
288D TRP* 3.9 3.0 + - - +
289D ASN 3.4 0.2 - - - -
290D GLY* 1.3 74.9 - - - +
292D LEU* 1.3 57.0 + - - +
294D ALA* 3.8 2.3 - - - +
295D ALA* 2.9 31.0 + - - +
266G ASP* 3.3 25.1 + - - +
269G TRP* 3.8 51.0 - - + +
282G ASP* 4.6 3.2 + - - -
283G LYS* 4.7 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 292 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A VAL* 5.2 11.7 - - + -
112A PHE* 5.0 20.6 - - + -
288D TRP* 3.1 34.0 + - + +
289D ASN* 3.8 5.6 - - - +
291D ARG* 1.3 77.6 - - - +
293D LEU* 1.3 66.8 + - + +
295D ALA* 3.3 12.7 + - + +
296D THR* 3.2 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 293 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246D ALA 5.8 0.2 - - - +
249D LEU* 3.7 43.1 - - + +
250D VAL* 4.5 9.6 - - + -
253D ALA* 4.2 10.8 - - + -
289D ASN* 3.0 24.1 + - + +
290D GLY 3.8 2.9 - - - +
292D LEU* 1.3 82.5 - - + +
294D ALA* 1.3 61.0 + - - +
296D THR* 2.7 24.9 + - + +
297D PHE* 3.0 30.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 294 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246D ALA* 6.4 0.7 - - - -
250D VAL* 4.6 2.8 - - + +
270D TRP* 4.0 33.2 - - + -
285D PRO* 4.5 11.0 - - + -
290D GLY 2.9 17.9 + - - +
291D ARG 4.0 2.7 - - - +
293D LEU* 1.3 76.5 - - - +
295D ALA* 1.3 56.9 + - - +
297D PHE* 4.5 4.0 - - - +
298D THR* 2.9 37.3 + - - +
269G TRP* 4.6 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 295 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291D ARG 2.9 20.1 + - - +
292D LEU* 3.6 11.2 - - + +
293D LEU 3.2 0.4 - - - -
294D ALA* 1.3 76.3 - - - +
296D THR* 1.3 60.6 + - + +
298D THR* 3.5 10.7 - - - +
299D LEU* 4.5 10.4 - - - +
269G TRP* 4.8 3.5 - - + -
272G LEU* 3.6 30.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 296 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292D LEU* 3.2 24.5 - - + +
293D LEU* 2.7 20.5 + - + +
295D ALA* 1.3 80.3 - - + +
297D PHE* 1.3 76.7 + - - +
298D THR 3.3 1.4 + - - -
299D LEU* 3.9 11.9 + - - +
300D ILE* 4.1 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 297 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242D CYS* 4.3 19.1 - - - -
245D LEU* 3.8 24.7 - - + -
246D ALA* 3.7 32.0 - - + +
249D LEU* 3.8 31.0 - - + -
250D VAL* 6.4 0.4 - - + -
275D LEU* 4.4 4.8 - - + +
293D LEU* 3.0 40.0 + - + +
294D ALA* 4.5 3.1 - - - +
296D THR* 1.3 91.1 + - - +
298D THR* 1.3 59.1 + - - +
299D LEU 3.4 0.4 - - - -
300D ILE* 3.9 8.3 - - + +
301D GLY* 2.9 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 298 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275D LEU* 4.9 6.9 - - - +
294D ALA* 2.9 21.2 + - - +
295D ALA* 3.5 17.0 - - - +
297D PHE* 1.3 74.3 - - - +
299D LEU* 1.3 69.8 + - + +
300D ILE 3.0 2.5 - - - -
302D VAL* 3.0 36.5 + - - +
272G LEU* 3.8 26.4 - - + +
273G ILE* 6.6 0.2 - - + -
276G THR* 4.5 5.2 + - - +
278G ILE* 3.7 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 299 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295D ALA 4.5 9.2 - - - +
296D THR* 3.9 8.4 + - - +
297D PHE 3.4 0.4 - - - -
298D THR* 1.3 83.7 - - + +
300D ILE* 1.3 68.0 + - + +
302D VAL* 4.5 3.6 - - + -
303D SER* 3.1 24.8 + - - -
236G TRP* 4.4 25.8 + - + +
272G LEU* 4.5 6.7 - - + -
276G THR* 4.3 12.6 - - + -
305G PHE* 3.5 39.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 300 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242D CYS* 3.7 18.6 - - - -
296D THR 4.1 13.2 - - - +
297D PHE* 3.5 11.1 + - + +
298D THR 3.0 0.4 - - - -
299D LEU* 1.3 89.7 - - + +
301D GLY* 1.3 65.6 + - - +
303D SER* 3.4 3.6 + - - -
304D PHE* 3.0 52.0 + - + -
236G TRP* 4.8 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 301 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242D CYS* 4.2 7.5 - - - -
275D LEU* 3.6 36.6 - - - -
297D PHE 2.9 12.6 + - - -
300D ILE* 1.3 76.5 - - - +
302D VAL* 1.3 62.2 + - - +
304D PHE* 2.9 14.8 + - - -
305D PHE* 3.0 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 302 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D THR 3.9 14.6 - - - +
275D LEU* 3.5 13.3 - - + +
277D THR* 3.7 29.0 - - + +
298D THR* 3.0 35.6 + - - +
299D LEU* 4.4 5.2 - - + +
301D GLY* 1.3 74.4 - - - +
303D SER* 1.3 67.3 + - - +
305D PHE 4.2 0.6 - - - -
306D ALA* 3.5 24.4 + - - +
276G THR* 4.7 17.3 - - + +
278G ILE* 4.5 6.7 - - + -
305G PHE 5.4 6.5 - - - +
309G ALA* 5.0 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 303 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D LEU 3.1 20.9 + - - -
300D ILE* 3.4 6.1 + - - -
301D GLY 3.0 1.2 - - - -
302D VAL* 1.3 85.2 - - - +
304D PHE* 1.3 63.4 + - - +
306D ALA 4.0 0.2 + - - -
307D LEU* 3.4 24.8 + - - +
236G TRP* 4.5 7.1 + - - -
305G PHE 5.1 3.3 + - - -
308G PRO* 4.0 23.3 - - - +
309G ALA* 4.2 19.6 + - - +
312G LEU* 5.8 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 304 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234D THR* 6.5 0.2 - - + -
235D ALA* 3.8 23.3 - - - +
236D TRP* 5.4 0.9 - - - -
238D ILE* 4.2 23.6 - - + -
239D GLY* 3.9 21.3 - - - +
242D CYS* 5.0 2.9 - - + -
300D ILE* 3.0 44.9 + - + +
301D GLY* 2.9 5.4 + - - +
303D SER* 1.3 80.4 - - - +
305D PHE* 1.3 61.9 + - - +
306D ALA 3.3 0.8 + - - -
307D LEU* 3.9 32.3 + - + +
308D PRO* 4.2 4.3 - - - +
221G LEU* 3.5 44.6 - - + -
312G LEU* 5.5 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 305 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B LEU* 3.5 37.5 - - + +
302B VAL* 5.4 7.3 - - - +
303B SER* 5.1 3.1 + - - -
236D TRP* 5.1 12.9 + + - -
239D GLY* 3.2 36.8 - - - -
240D PHE* 4.4 3.6 - + + -
243D LEU* 4.1 18.8 - - + -
272D LEU* 5.0 6.3 - - + -
275D LEU* 3.3 55.4 - - + +
276D THR* 4.1 15.3 - - + +
301D GLY* 3.0 11.0 + - - +
304D PHE* 1.3 79.2 - - - +
306D ALA* 1.3 57.8 + - - +
307D LEU 3.5 1.1 + - - -
308D PRO* 4.1 11.9 - - - +
----------------------------------------------------------
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