Contacts of the helix formed by residues 251 - 272 (chain F) in PDB entry 4R8A
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 ASN 251 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217F ASP* 3.2 29.7 - - - +
249F TYR* 3.2 2.5 - - + +
250F ALA* 1.3 79.1 - - - +
252F PRO* 1.3 69.3 - - - +
253F TRP* 3.2 33.0 - - - +
254F LEU* 3.2 28.1 + - + +
255F GLU* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 252 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250F ALA 3.6 7.6 - - - +
251F ASN* 1.3 93.1 - - - +
253F TRP* 1.3 75.5 + - + +
255F GLU* 3.3 5.6 + - + +
256F GLY* 3.2 16.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 253 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181F GLY 5.0 2.2 - - - -
210F ARG* 3.5 17.9 - - - -
211F GLY 3.2 31.0 - - - -
212F PHE* 5.0 18.4 - + - -
221F TYR* 5.7 5.4 - + + -
251F ASN* 3.2 14.0 - - - +
252F PRO* 1.3 87.5 - - + +
254F LEU* 1.3 67.1 + - + +
256F GLY* 3.2 2.3 + - - -
257F ARG* 3.1 32.7 + - - +
408F GLY 4.9 3.4 - - - -
411F PHE* 4.2 6.5 - + - -
419F ALA* 4.2 26.1 + - + -
420F ASP* 5.4 4.2 - - + +
-1G C 3.2 48.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 254 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212F PHE* 5.5 3.1 - - + -
217F ASP* 3.5 46.7 - - + +
220F ALA* 3.7 17.3 - - + -
221F TYR* 3.6 42.8 - - + +
224F LEU* 3.6 14.5 - - + +
249F TYR* 3.6 21.0 - - + -
251F ASN* 3.2 19.1 - - + +
253F TRP* 1.3 81.6 - - + +
255F GLU* 1.3 58.1 + - - +
257F ARG* 3.4 5.7 + - - -
258F ARG* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 255 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248F PRO* 3.2 16.4 - - + +
249F TYR* 2.8 35.6 + - - +
251F ASN 2.9 18.0 + - - +
252F PRO* 3.8 6.1 - - + +
254F LEU* 1.3 75.2 - - - +
256F GLY* 1.3 60.8 + - - +
258F ARG* 2.9 35.6 + - - +
259F VAL* 2.9 41.9 + - + +
286F SER* 4.9 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 256 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252F PRO 3.2 7.4 + - - -
253F TRP 3.2 7.4 + - - -
255F GLU* 1.3 79.7 - - - +
257F ARG* 1.3 57.2 + - - +
259F VAL* 3.7 10.5 - - - +
260F LYS* 2.8 30.6 + - - +
287F HIS* 4.9 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 257 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221F TYR* 3.5 38.5 + - - -
224F LEU* 3.8 21.1 - - + +
225F PHE* 5.2 8.1 - - - +
253F TRP* 3.1 22.5 + - - +
254F LEU* 3.7 8.7 - - - +
255F GLU 3.1 0.6 - - - -
256F GLY* 1.3 75.8 - - - +
258F ARG* 1.3 60.1 + - - +
259F VAL 3.1 1.6 - - - -
260F LYS* 3.7 6.1 - - - +
261F LEU* 2.9 30.5 + - - +
-1G C 3.3 40.7 - - - +
0G C 3.3 41.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 258 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224F LEU* 3.7 13.4 - - + +
244F LEU* 4.5 7.2 - - + +
245F PRO* 3.7 36.2 + - + -
246F GLY 4.0 7.5 + - - -
247F GLU 4.6 0.9 - - - -
248F PRO* 3.7 21.6 - - - +
249F TYR* 3.5 31.4 - - + +
254F LEU 3.0 19.0 + - - +
255F GLU* 2.9 41.2 + - - +
257F ARG* 1.3 76.0 - - - +
259F VAL* 1.3 68.4 + - - +
261F LEU* 3.6 4.5 + - - +
262F LEU* 3.2 49.3 + - + +
284F GLN* 4.2 9.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 259 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255F GLU* 2.9 32.2 + - - +
256F GLY* 3.7 12.6 - - - +
258F ARG* 1.3 89.1 - - - +
260F LYS* 1.3 61.1 + - - +
261F LEU 3.2 0.4 - - - -
262F LEU* 3.6 4.2 + - + -
263F PHE* 3.1 15.6 + - - +
284F GLN 4.1 2.0 - - - +
285F SER* 3.1 28.5 + - - -
286F SER* 3.2 31.6 - - - +
287F HIS* 3.3 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 260 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256F GLY 2.8 21.0 + - - +
257F ARG* 3.7 6.7 - - - +
259F VAL* 1.3 75.3 - - - +
261F LEU* 1.3 64.0 + - - +
263F PHE* 3.4 5.1 + - + +
264F GLN* 3.2 46.1 + - + +
287F HIS* 3.5 33.9 - - + +
0G C 3.1 45.2 + - - +
1G A 4.1 5.3 + - - -
2G G 3.1 27.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 261 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224F LEU* 4.0 16.2 - - + +
227F CYS* 3.7 27.4 - - + -
228F ARG* 3.8 33.7 - - + -
244F LEU* 3.8 21.3 - - + -
257F ARG 2.9 16.6 + - - +
258F ARG 3.6 4.7 - - - +
260F LYS* 1.3 76.0 - - - +
262F LEU* 1.3 65.5 + - - +
264F GLN* 3.2 12.5 + - - +
265F PHE* 3.1 56.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 262 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241F LEU* 4.2 7.6 - - + -
244F LEU* 3.8 22.6 - - + +
258F ARG* 3.2 44.7 + - - +
259F VAL* 3.7 9.4 - - - +
261F LEU* 1.3 78.7 - - - +
263F PHE* 1.3 61.9 + - - +
265F PHE* 3.4 7.2 + - - +
266F ALA* 3.2 21.8 + - - +
281F LEU* 3.9 34.4 - - + +
284F GLN* 3.8 39.0 - - + +
285F SER* 4.2 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 263 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259F VAL 3.1 14.4 + - - +
260F LYS* 3.4 9.4 - - + +
262F LEU* 1.3 78.2 - - - +
264F GLN* 1.3 61.6 + - + +
266F ALA* 3.4 7.1 + - - +
267F GLN* 3.1 55.6 + - + +
282F TYR* 3.7 17.6 - + - -
285F SER* 3.9 5.1 - - - +
287F HIS* 3.5 33.2 - + + -
288F PRO 4.7 2.2 - - - -
289F GLY* 3.9 6.1 - - - -
290F ALA* 3.6 43.7 - - + -
293F ARG* 4.1 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 264 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228F ARG* 3.0 44.0 - - - +
231F PHE* 4.2 6.3 - - + -
260F LYS* 3.2 43.3 + - + +
261F LEU* 3.2 13.7 + - - +
263F PHE* 1.3 80.1 - - + +
265F PHE* 1.3 64.4 + - + +
266F ALA 3.2 0.4 - - - -
267F GLN* 3.1 21.1 + - - +
268F HIS* 3.0 28.2 + - - +
0G C 6.1 0.3 - - - +
1G A 5.4 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 265 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227F CYS* 4.5 4.9 - - + -
231F PHE* 3.4 46.2 - + + -
237F LEU* 3.6 26.2 - - + +
240F LEU* 4.4 15.0 - - + -
241F LEU* 3.6 23.3 - - + -
244F LEU* 3.7 27.4 - - + -
261F LEU* 3.1 41.4 + - + -
262F LEU* 3.4 9.8 + - - +
264F GLN* 1.3 77.8 - - + +
266F ALA* 1.3 58.5 + - - +
268F HIS* 3.4 3.1 + - - +
269F CYS* 2.9 32.4 + - - -
281F LEU* 3.9 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 266 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262F LEU 3.2 5.4 + - - +
263F PHE 3.6 2.9 - - - +
264F GLN 3.2 0.6 - - - -
265F PHE* 1.3 77.8 - - - +
267F GLN* 1.3 59.4 + - - +
269F CYS* 4.1 4.3 - - - -
270F GLU* 2.8 31.5 + - - +
278F ALA* 3.4 26.8 - - - +
281F LEU* 3.6 19.9 - - + +
282F TYR* 3.5 28.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 267 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263F PHE* 3.1 46.5 + - + +
264F GLN* 3.1 21.3 + - - +
266F ALA* 1.3 78.0 - - - +
268F HIS* 1.3 56.8 + - - +
270F GLU* 3.4 2.8 + - - +
271F LYS* 3.0 46.6 + - - +
282F TYR* 3.3 18.2 - - - +
293F ARG* 6.0 0.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 268 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231F PHE* 3.6 38.7 - + + -
237F LEU* 5.1 9.4 - - + -
264F GLN 3.0 6.7 + - - +
265F PHE 3.7 6.5 - - - +
267F GLN* 1.3 74.7 - - - +
269F CYS* 1.3 69.2 + - - +
271F LYS* 3.4 12.4 + - - +
272F GLN* 3.0 51.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 269 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237F LEU* 3.6 22.2 - - - -
265F PHE 2.9 24.8 + - - +
266F ALA 3.6 5.4 - - - +
268F HIS* 1.3 78.8 - - - +
270F GLU* 1.3 59.8 + - - +
272F GLN* 3.4 7.4 + - - -
274F ASP* 2.9 39.3 + - + +
277F LEU* 3.8 26.2 - - + -
278F ALA* 3.8 15.0 - - + -
281F LEU* 3.9 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 270 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266F ALA 2.8 15.5 + - - +
267F GLN* 3.7 4.2 - - - +
268F HIS 3.2 0.2 - - - -
269F CYS* 1.3 76.7 - - - +
271F LYS* 1.3 63.5 + - + +
273F ARG* 3.1 9.7 + - - -
275F PHE* 3.3 34.3 - - + -
278F ALA* 3.7 10.3 - - + +
282F TYR* 2.6 33.8 + - - -
293F ARG* 2.4 34.7 + - - -
297F SER* 3.3 23.6 + - - +
300F ARG* 3.8 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 271 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267F GLN* 3.0 35.8 + - - +
268F HIS* 3.8 9.6 - - - +
270F GLU* 1.3 72.9 - - + +
272F GLN* 1.3 61.4 + - + +
273F ARG* 3.1 11.2 + - - +
300F ARG* 6.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 272 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268F HIS* 3.0 45.1 + - + +
269F CYS* 4.0 5.4 - - - +
270F GLU 3.2 0.6 - - - -
271F LYS* 1.3 76.2 + - + +
273F ARG* 1.3 66.2 + - - +
274F ASP* 3.1 9.6 + - + +
----------------------------------------------------------
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