Contacts of the helix formed by residues 226 - 248 (chain T) 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 PHE 226 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222T ILE* 2.6 14.6 + - + +
223T ASN* 3.3 7.9 - - - -
225T LYS* 1.3 75.6 - - + +
227T PRO* 1.3 64.5 - - - +
228T GLN* 3.2 4.3 - - + -
229T ILE* 3.0 26.7 + - + +
230T GLY 3.4 7.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 227 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223T ASN* 3.0 19.9 - - + +
225T LYS 4.0 1.4 - - - -
226T PHE* 1.3 70.6 - - - +
228T GLN* 1.3 57.6 + - - +
230T GLY* 3.3 2.4 + - - -
231T GLU* 2.9 29.0 + - - +
366T PHE* 4.3 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 228 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226T PHE* 3.2 1.7 - - + -
227T PRO* 1.3 79.8 - - - +
229T ILE* 1.3 58.1 + - - +
231T GLU* 3.5 8.1 + - - +
232T LEU* 3.1 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 229 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190T ILE 5.3 3.1 - - - +
194T ARG* 4.7 21.8 - - + +
198T SER* 5.4 2.3 - - - -
222T ILE* 5.6 8.3 - - + -
226T PHE* 3.0 22.9 + - + +
228T GLN* 1.3 76.9 - - - +
230T GLY* 1.3 65.6 + - - +
232T LEU* 3.2 7.8 + - - +
233T ILE* 3.0 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 230 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219T VAL* 5.3 5.6 - - - -
222T ILE* 6.1 0.6 - - - +
223T ASN* 4.0 22.2 - - - +
226T PHE 3.4 4.9 + - - -
227T PRO 3.3 5.8 + - - -
229T ILE* 1.3 78.6 - - - +
231T GLU* 1.3 56.1 + - - +
233T ILE* 3.3 6.9 + - - +
234T LEU* 3.0 30.0 + - - +
268T VAL* 6.4 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 231 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227T PRO 2.9 17.4 + - - +
228T GLN* 3.6 10.5 - - - +
229T ILE 3.2 0.2 - - - -
230T GLY* 1.3 76.6 - - - +
232T LEU* 1.3 55.7 + - - +
234T LEU* 3.5 5.5 + - - +
235T LYS* 2.9 30.7 + - - +
368T HIS* 5.4 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 232 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194T ARG* 5.5 7.4 - - + +
195T GLY* 6.5 0.4 - - - -
198T SER* 4.9 11.8 - - - -
228T GLN 3.1 14.5 + - - +
229T ILE* 3.2 11.0 + - - +
231T GLU* 1.3 74.1 - - - +
233T ILE* 1.3 65.6 + - - +
235T LYS* 3.6 6.3 + - - +
236T ARG* 3.3 22.9 + - - +
378T PRO 5.1 7.9 - - - +
379T GLU* 6.3 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 233 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198T SER* 4.5 21.6 - - - +
201T VAL* 6.1 3.8 - - + -
219T VAL* 5.6 9.4 - - + -
229T ILE 3.0 13.1 + - - +
230T GLY* 3.7 9.6 - - - +
232T LEU* 1.3 76.5 - - - +
234T LEU* 1.3 57.7 + - - +
236T ARG* 3.3 5.0 + - - +
237T LEU* 2.9 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 234 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230T GLY 3.0 17.8 + - - +
231T GLU* 3.7 6.5 - - - +
233T ILE* 1.3 76.1 - - - +
235T LYS* 1.3 56.4 + - - +
237T LEU* 3.3 6.4 + - - +
238T ILE* 2.9 32.6 + - - +
263T LEU* 6.6 0.4 - - + -
268T VAL 6.0 0.9 - - - +
269T ALA* 5.4 12.3 - - + -
368T HIS* 5.6 7.2 - - + -
370T LEU* 5.4 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 235 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231T GLU 2.9 18.3 + - - +
232T LEU* 3.9 7.2 - - - +
234T LEU* 1.3 76.1 - - - +
236T ARG* 1.3 57.3 + - - +
238T ILE* 3.5 5.7 + - - +
239T LEU* 3.1 27.2 + - - +
376T TYR* 4.0 27.5 - - + +
377T ASN 4.5 12.8 - - - +
378T PRO* 5.2 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 236 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198T SER* 6.0 4.0 - - - -
202T LEU* 5.9 7.2 - - + -
232T LEU 3.3 15.3 + - - +
233T ILE* 3.8 4.5 - - - +
235T LYS* 1.3 77.8 - - - +
237T LEU* 1.3 54.8 - - - +
239T LEU* 3.3 6.8 + - - +
240T ASN* 2.7 35.8 + - - +
378T PRO* 4.9 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 237 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202T LEU* 6.2 5.3 - - + +
233T ILE 2.9 18.5 + - - +
234T LEU* 3.6 7.9 - - - +
236T ARG* 1.3 72.9 - - - +
238T ILE* 1.3 60.7 + - - +
240T ASN* 3.2 8.4 + - - +
241T PHE* 2.9 28.9 + - - +
256T ALA* 4.4 11.6 - - + +
259T PHE* 5.6 8.7 - - + -
260T VAL* 6.0 3.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 238 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234T LEU 2.9 16.7 + - - +
235T LYS* 3.8 6.5 - - - +
237T LEU* 1.3 75.9 - - - +
239T LEU* 1.3 63.3 + - - +
241T PHE* 3.2 8.4 + - - +
242T ARG* 3.0 22.7 + - - +
370T LEU* 6.2 3.8 - - + -
371T PRO 5.2 7.0 - - - +
372T LEU* 4.9 14.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 239 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235T LYS 3.1 17.4 + - - +
236T ARG* 3.3 7.4 + - - +
238T ILE* 1.3 76.6 - - - +
240T ASN* 1.3 56.6 + - - +
242T ARG* 3.2 7.6 + - - +
243T LYS* 2.9 29.9 + - - +
376T TYR* 5.8 6.3 - - + +
378T PRO* 5.4 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 240 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236T ARG 2.7 20.4 + - - +
237T LEU* 3.2 9.8 + - - +
239T LEU* 1.3 70.5 - - - +
241T PHE* 1.3 66.4 + - - +
243T LYS* 3.3 7.1 + - - +
244T GLY* 3.0 19.9 + - - -
252T LEU* 5.2 4.9 - - - +
256T ALA* 4.6 10.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 241 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237T LEU 2.9 12.8 + - - +
238T ILE* 3.5 10.5 - - - +
240T ASN* 1.3 75.4 - - - +
242T ARG* 1.3 57.5 + - - +
244T GLY* 3.2 3.4 + - - -
245T TYR* 2.9 29.1 + - - +
252T LEU 5.2 1.3 - - - -
253T CYS* 5.2 6.9 - - - +
256T ALA* 4.0 22.3 - - + +
257T SER* 5.2 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 242 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238T ILE 3.0 13.0 + - - +
239T LEU* 3.7 9.9 - - - +
241T PHE* 1.3 73.7 - - - +
243T LYS* 1.3 59.5 + - - +
245T TYR* 3.6 6.8 - - - +
246T ARG* 2.8 32.4 + - - +
372T LEU 5.7 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 243 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239T LEU 2.9 17.2 + - - +
240T ASN* 3.5 8.5 - - - +
242T ARG* 1.3 75.7 - - - +
244T GLY* 1.3 57.5 + - - +
246T ARG* 3.3 6.4 + - - +
247T ARG* 2.8 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 244 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240T ASN 3.0 14.0 + - - -
241T PHE 3.6 3.1 - - - -
243T LYS* 1.3 76.7 - - - +
245T TYR* 1.3 61.2 + - - +
247T ARG 3.3 0.5 + - - -
248T ASN* 2.9 4.0 + - - -
249T ASP* 2.8 50.9 + - - -
252T LEU* 4.5 9.2 - - - -
253T CYS* 4.9 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 245 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241T PHE 2.9 19.7 + - - +
242T ARG* 3.3 8.3 + - - +
244T GLY* 1.3 70.7 - - - +
246T ARG* 1.3 64.2 + - - +
248T ASN* 3.1 14.4 + - - +
253T CYS* 5.0 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 246 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242T ARG 2.8 18.9 + - - +
243T LYS* 3.5 6.1 - - - +
245T TYR* 1.3 77.6 - - - +
247T ARG* 1.3 58.6 + - - +
248T ASN* 3.2 2.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 247 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243T LYS 2.8 20.4 + - - +
244T GLY 4.1 2.0 - - - +
246T ARG* 1.3 72.9 - - + +
248T ASN* 1.3 70.3 - - - +
249T ASP* 3.2 11.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 248 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244T GLY 2.9 5.0 + - - -
245T TYR* 3.1 11.9 + - - +
246T ARG 3.2 1.7 - - - +
247T ARG* 1.3 81.2 - - - +
249T ASP* 1.3 59.1 + - - +
250T LYS* 3.5 6.4 + - - +
----------------------------------------------------------
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