Contacts of the helix formed by residues 237 - 272 (chain p) in PDB entry 6FF7
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 ARG 237 (chain p).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235p ASN* 4.3 3.7 - - + +
236p PRO* 0.6 86.2 + - - +
238p GLU* 1.3 63.8 + - - +
240p LEU* 3.1 10.2 + - - +
241p ASP* 3.0 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 238 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235p ASN* 3.3 23.2 + - + +
236p PRO 2.4 9.5 + - - -
237p ARG* 1.3 70.1 - - - +
239p VAL* 1.3 62.5 + - - +
241p ASP* 3.1 9.9 + - - +
242p GLN* 3.0 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 239 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235p ASN 3.1 13.7 + - - +
236p PRO* 4.2 7.9 - - + -
238p GLU* 1.3 78.0 - - - +
240p LEU* 1.3 63.4 + - - +
242p GLN* 3.1 9.4 + - - +
243p VAL* 3.0 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 240 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236p PRO 4.1 3.7 - - - -
237p ARG* 3.1 17.1 + - - +
239p VAL* 1.3 78.2 - - - +
241p ASP* 1.3 63.5 + - - +
243p VAL* 3.1 9.8 + - - +
244p CYS* 3.0 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 241 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237p ARG 3.0 12.2 + - - +
238p GLU* 3.1 13.0 + - - +
240p LEU* 1.3 75.3 - - - +
242p GLN* 1.3 63.5 + - - +
244p CYS* 3.1 9.4 + - - +
245p TYR* 3.0 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 242 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238p GLU 3.0 12.2 + - - +
239p VAL* 3.4 12.3 - - - +
241p ASP* 1.3 74.7 - - - +
243p VAL* 1.3 63.9 + - - +
245p TYR* 3.1 10.0 + - - +
246p ARG* 3.0 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 243 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199 MET 5.7 0.7 - - - +
229 MET* 3.7 20.2 - - + +
239 ALA* 4.1 13.1 - - - +
269 MET* 3.5 24.7 - - + +
239p VAL 3.0 11.2 + - - +
240p LEU* 3.1 12.8 + - - +
242p GLN* 1.3 75.0 - - - +
244p CYS* 1.3 64.4 + - - +
246p ARG* 3.1 5.2 + - - +
247p VAL 3.0 18.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 244 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269 MET* 4.0 9.3 - - - +
439 THR* 4.7 1.9 - - - -
240p LEU 3.0 12.4 + - - +
241p ASP* 3.1 12.8 + - - +
243p VAL* 1.3 75.9 - - - +
245p TYR* 1.3 62.3 + - - +
247p VAL* 3.1 7.2 + - - +
248p GLU* 3.0 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 245 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738M VAL 4.9 11.8 - - - +
241p ASP 3.0 11.2 + - - +
242p GLN* 3.4 12.3 - - - +
244p CYS* 1.3 75.1 - - - +
246p ARG* 1.3 64.5 + - - +
248p GLU* 3.1 9.8 + - - +
249p TRP* 3.0 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 246 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239 ALA* 3.4 27.4 - - + +
279 LEU* 5.4 0.2 - - - -
242p GLN 3.0 12.2 + - - +
243p VAL 3.4 9.0 - - - +
245p TYR* 1.3 76.1 - - - +
247p VAL* 1.3 63.9 + - - +
249p TRP* 3.1 10.0 + - - +
250p ALA* 3.0 21.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 247 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239 ALA 4.3 0.8 + - - -
269 MET* 3.2 15.3 - - + +
279 LEU* 3.1 44.5 - - - +
309 LYS* 5.7 0.4 - - + -
439 THR* 3.8 10.7 - - - -
243p VAL 3.0 9.1 + - - +
244p CYS* 3.4 10.1 - - - +
246p ARG* 1.3 74.5 - - - +
248p GLU* 1.3 64.4 + - - +
250p ALA* 3.1 5.1 + - - +
251p LYS* 3.0 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 248 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439 THR* 3.1 35.2 - - - +
449 ARG* 3.2 10.9 - - + +
737M GLN 5.3 3.4 - - - +
738M VAL* 4.4 15.0 - - - +
244p CYS 3.0 11.7 + - - +
245p TYR* 3.3 12.1 - - - +
247p VAL* 1.3 74.7 - - - +
249p TRP* 1.3 62.9 + - - +
251p LYS 3.1 2.3 + - - -
252p PHE* 3.0 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 249 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738M VAL* 6.3 2.9 - - - -
245p TYR 3.0 12.0 + - - +
246p ARG* 3.4 12.1 - - - +
248p GLU* 1.3 75.7 - - - +
250p ALA* 1.3 64.5 + - - +
252p PHE* 3.1 9.6 + - - +
253p GLN* 3.0 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 250 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279 LEU* 4.5 12.1 - - + -
246p ARG 3.0 12.9 + - - +
247p VAL* 3.3 11.4 - - - +
249p TRP* 1.3 75.7 - - - +
251p LYS* 1.3 64.1 + - - +
253p GLN* 3.1 9.2 + - - +
254p GLU* 3.0 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 251 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439 THR* 4.4 4.7 - - - +
449 ARG* 3.5 24.5 - - + +
459 ALA* 4.1 6.8 - - - +
469 MET* 4.4 17.3 + - + +
247p VAL 3.0 11.2 + - - +
248p GLU* 3.1 9.2 + - - +
250p ALA* 1.3 75.1 - - - +
252p PHE* 1.3 64.7 + - - +
254p GLU* 3.1 9.6 + - - +
255p ARG* 3.0 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 252 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449 ARG* 3.5 13.4 - - + +
459 ALA* 5.1 0.7 - - - +
248p GLU 3.0 12.4 + - - +
249p TRP* 3.4 11.7 - - - +
251p LYS* 1.3 76.1 - - - +
253p GLN* 1.3 63.3 + - - +
255p ARG* 3.1 9.2 + - - +
256p GLU* 3.0 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 253 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249p TRP 3.0 12.2 + - - +
250p ALA* 3.4 11.9 - - - +
252p PHE* 1.3 75.5 - - - +
254p GLU* 1.3 63.8 + - - +
256p GLU* 3.1 9.9 + - - +
257p ARG* 3.0 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 254 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469 MET* 5.5 7.4 - - + -
250p ALA 3.0 12.4 + - - +
251p LYS* 3.4 12.1 - - - +
253p GLN* 1.3 76.3 - - - +
255p ARG* 1.3 63.7 + - - +
257p ARG* 3.1 9.6 + - - +
258p LYS* 3.0 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 255 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459 ALA* 3.5 32.3 - - + -
469 MET* 6.1 1.3 - - + +
251p LYS 3.0 8.2 + - - +
252p PHE* 3.4 10.8 - - - +
254p GLU* 1.3 76.4 - - - +
256p GLU* 1.3 62.7 + - - +
258p LYS* 3.1 9.3 + - - +
259p LYS* 3.0 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 256 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252p PHE 3.0 12.4 + - - +
253p GLN* 3.4 12.1 - - - +
255p ARG* 1.3 74.6 - - - +
257p ARG* 1.3 63.9 + - - +
259p LYS* 3.1 10.1 + - - +
260p GLU* 3.0 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 257 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253p GLN 3.0 12.6 + - - +
254p GLU* 3.1 12.1 + - - +
256p GLU* 1.3 73.9 - - - +
258p LYS* 1.3 64.7 + - - +
260p GLU* 3.1 9.4 + - - +
261p GLU* 3.0 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 258 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254p GLU 3.0 12.2 + - - +
255p ARG* 3.4 12.3 - - - +
257p ARG* 1.3 75.8 - - - +
259p LYS* 1.3 63.1 + - - +
261p GLU* 3.1 9.8 + - - +
262p GLU* 3.0 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 259 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255p ARG 3.0 12.0 + - - +
256p GLU* 3.1 13.0 + - - +
258p LYS* 1.3 76.5 - - - +
260p GLU* 1.3 62.1 + - - +
262p GLU* 3.1 9.6 + - - +
263p GLU* 3.0 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 260 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256p GLU 3.0 12.0 + - - +
257p ARG* 3.3 12.6 - - - +
259p LYS* 1.3 76.3 - - - +
261p GLU* 1.3 62.7 + - - +
263p GLU* 3.1 10.0 + - - +
264p LYS* 3.0 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 261 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257p ARG 3.0 11.2 + - - +
258p LYS* 3.1 12.8 + - - +
260p GLU* 1.3 75.5 - - - +
262p GLU* 1.3 64.1 + - - +
264p LYS* 3.1 9.5 + - - +
265p GLU* 3.0 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 262 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258p LYS 3.0 12.4 + - - +
259p LYS* 3.1 13.0 + - - +
261p GLU* 1.3 75.5 - - - +
263p GLU* 1.3 62.3 + - - +
265p GLU* 3.1 9.7 + - - +
266p LYS* 3.0 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 263 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259p LYS 3.0 11.4 + - - +
260p GLU* 3.4 12.1 - - - +
262p GLU* 1.3 75.5 - - - +
264p LYS* 1.3 63.9 + - - +
266p LYS* 3.1 9.8 + - - +
267p GLU* 3.0 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 264 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260p GLU 3.0 12.5 + - - +
261p GLU* 3.4 12.1 - - - +
263p GLU* 1.3 76.1 - - - +
265p GLU* 1.3 64.0 + - - +
267p GLU* 3.1 10.0 + - - +
268p ARG* 3.0 21.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 265 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261p GLU 3.0 12.5 + - - +
262p GLU* 3.4 11.7 - - - +
264p LYS* 1.3 75.1 - - - +
266p LYS* 1.3 64.2 + - - +
268p ARG* 3.1 10.0 + - - +
269p VAL* 3.0 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 266 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262p GLU 3.0 12.6 + - - +
263p GLU* 3.4 12.1 - - - +
265p GLU* 1.3 75.3 - - - +
267p GLU* 1.3 61.7 + - - +
269p VAL* 3.1 10.4 + - - +
270p ALA* 3.0 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 267 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263p GLU 3.0 12.0 + - - +
264p LYS* 3.3 12.3 - - - +
266p LYS* 1.3 75.5 - - - +
268p ARG* 1.3 64.3 + - - +
270p ALA* 3.1 9.8 + - - +
271p TYR* 3.0 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 268 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264p LYS 3.0 12.4 + - - +
265p GLU* 3.3 11.7 - - - +
267p GLU* 1.3 74.7 - - - +
269p VAL* 1.3 64.9 + - - +
271p TYR* 3.1 9.0 + - - +
272p ALA* 3.0 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 269 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265p GLU 3.0 11.4 + - - +
266p LYS* 3.1 12.5 + - - +
268p ARG* 1.3 76.9 - - - +
270p ALA* 1.3 63.6 + - - +
272p ALA* 3.1 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 270 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266p LYS 3.0 12.7 + - - +
267p GLU* 3.3 12.6 - - - +
269p VAL* 1.3 77.0 - - - +
271p TYR* 1.3 66.0 + - - +
272p ALA 3.9 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 271 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267p GLU 3.0 12.2 + - - +
268p ARG* 3.3 11.9 - - - +
270p ALA* 1.3 78.3 - - - +
272p ALA* 1.3 64.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 272 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268p ARG 3.0 12.5 + - - +
269p VAL* 3.1 20.8 + - - +
270p ALA 3.9 3.8 - - - -
271p TYR* 1.3 83.2 - - - +
----------------------------------------------------------
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