Contacts of the helix formed by residues 226 - 244 (chain T) in PDB entry 6MZL
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 SER 226 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168T ILE* 3.6 11.1 - - - +
224T ALA* 3.5 8.1 - - - +
225T LYS* 1.3 79.4 - - - +
227T GLU* 1.3 65.1 + - - +
228T GLU* 4.1 5.2 + - - +
229T GLN* 3.3 32.6 + - - +
230T SER* 3.1 18.0 + - - -
318T ARG* 4.6 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 227 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168T ILE* 3.5 25.0 - - + +
226T SER* 1.3 71.4 - - - +
228T GLU* 1.3 59.9 + - - +
230T SER* 3.2 6.6 + - - -
231T ARG* 2.9 29.2 + - - +
253T PHE* 4.9 3.1 - - - -
255T ILE* 4.0 28.9 - - + -
258T MET* 3.8 16.3 - - - +
317T VAL* 5.6 0.3 - - - -
318T ARG* 3.1 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 228 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226T SER* 3.4 5.0 + - - +
227T GLU* 1.3 78.5 - - - +
229T GLN* 1.3 57.3 + - + +
231T ARG* 3.4 15.1 + - - +
232T LEU* 2.9 37.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 229 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLU* 5.8 0.2 - - - +
206T GLU* 5.6 3.6 + - - -
207T PRO* 3.6 32.5 - - + +
224T ALA* 3.8 7.6 - - + -
225T LYS* 3.6 22.4 + - - +
226T SER* 3.3 23.0 + - - +
227T GLU 3.3 0.4 - - - -
228T GLU* 1.3 81.0 - - + +
230T SER* 1.3 56.5 + - - +
232T LEU* 4.4 4.7 - - + -
233T ALA* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 230 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168T ILE* 4.1 21.1 + - - +
170T SER* 3.0 29.6 + - - -
221T CYS* 4.1 8.3 - - - -
224T ALA* 3.4 18.5 - - - +
226T SER 3.1 10.6 + - - -
227T GLU* 3.2 7.2 + - - -
229T GLN* 1.3 72.2 - - - +
231T ARG* 1.3 61.3 + - - +
233T ALA* 3.8 3.9 - - - +
234T ALA* 2.9 31.7 + - - +
253T PHE* 4.0 3.8 - - - -
255T ILE* 5.6 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 231 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ASP* 4.1 17.0 + - - +
227T GLU 2.9 17.6 + - - +
228T GLU* 3.8 18.2 - - - +
230T SER* 1.3 75.4 - - - +
232T LEU* 1.3 58.4 + - - +
234T ALA* 3.9 1.4 - - - +
235T ARG* 2.9 61.7 + - - +
250T PHE* 3.7 17.4 - - + -
253T PHE* 3.3 48.5 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
115A GLU 5.3 3.4 - - - +
116A VAL* 5.5 9.6 - - + -
206T GLU* 5.4 2.5 - - + -
207T PRO* 4.2 14.4 - - + -
228T GLU* 2.9 23.4 + - + +
229T GLN* 3.8 5.6 - - + +
231T ARG* 1.3 77.6 - - - +
233T ALA* 1.3 56.7 + - - +
235T ARG* 3.3 7.7 + - + +
236T LYS* 2.9 63.6 + - + +
239T ARG* 5.1 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 233 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204T ILE* 4.7 0.9 - - - -
207T PRO* 4.2 10.0 - - + +
209T THR* 3.3 38.1 - - + +
221T CYS* 4.4 6.7 - - - -
229T GLN 2.9 20.0 + - - +
230T SER* 3.8 3.4 - - - +
232T LEU* 1.3 76.4 - - - +
234T ALA* 1.3 57.0 + - - +
236T LYS* 3.0 9.1 + - - +
237T TYR* 2.9 37.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 234 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170T SER* 4.6 4.7 - - - +
172T VAL* 4.8 4.7 - - + -
219T MET* 3.4 17.7 - - + +
221T CYS* 4.6 10.0 - - + -
230T SER 2.9 19.5 + - - +
231T ARG 3.9 3.6 - - - +
233T ALA* 1.3 75.2 - - - +
235T ARG* 1.3 58.2 + - - +
237T TYR* 4.5 3.8 - - - -
238T ALA* 3.0 28.9 + - - +
250T PHE* 4.1 9.8 - - + -
253T PHE* 3.9 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 235 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A VAL* 4.8 6.2 - - + +
117A ALA* 2.8 45.7 + - + +
118A GLU 3.3 15.8 + - - -
119A ASP* 2.5 30.8 + - - -
231T ARG* 2.9 56.6 + - - +
232T LEU* 3.5 9.6 - - + +
233T ALA 3.2 0.2 - - - -
234T ALA* 1.3 76.1 - - - +
236T LYS* 1.3 57.3 + - - +
238T ALA* 3.4 5.6 + - - +
239T ARG* 2.9 47.9 + - - +
250T PHE* 3.3 34.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 236 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A TYR 6.1 0.4 - - - +
111A SER 5.7 3.4 + - - +
113A ILE* 3.6 28.8 + - + +
114A ASN* 5.2 5.6 + - - +
115A GLU 5.2 2.0 - - - -
204T ILE* 4.0 19.3 - - + -
206T GLU* 2.4 44.4 + - - +
232T LEU* 2.9 45.0 + - + +
233T ALA* 3.0 8.7 + - - +
235T ARG* 1.3 73.9 - - - +
237T TYR* 1.3 59.6 + - - +
239T ARG* 3.0 29.0 + - - +
240T VAL* 2.9 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 237 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202T MET* 3.2 53.1 + - + -
204T ILE* 2.8 31.8 + - + +
209T THR* 2.4 47.7 + - - -
210T THR 4.3 2.2 - - - -
211T ALA* 3.6 24.9 - - + -
213T ILE* 5.0 3.1 - - + +
219T MET* 3.7 24.0 - - + -
221T CYS* 5.0 3.8 - - + -
233T ALA* 2.9 28.4 + - + +
234T ALA* 4.5 2.7 - - - -
236T LYS* 1.3 72.8 - - - +
238T ALA* 1.3 61.0 + - - +
240T VAL* 3.2 7.5 + - + +
241T VAL* 3.0 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 238 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ALA* 5.7 2.2 - - + -
174T LEU* 3.7 29.6 - - + -
219T MET* 3.8 2.1 - - + +
234T ALA 3.0 18.3 + - - +
235T ARG* 3.5 11.2 - - - +
236T LYS 3.3 0.2 - - - -
237T TYR* 1.3 75.6 - - - +
239T ARG* 1.3 57.8 + - - +
241T VAL* 3.3 6.6 + - - +
242T GLN* 2.8 27.9 + - - +
248T ALA* 3.8 5.3 - - + +
249T LYS 4.5 7.4 - - - +
250T PHE* 4.6 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 239 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ILE* 3.4 29.1 + - + +
115A GLU* 3.0 41.9 + - - +
116A VAL* 3.5 3.8 - - - +
117A ALA* 3.0 34.8 - - + +
232T LEU* 4.8 4.8 + - - +
235T ARG* 2.9 35.2 + - - +
236T LYS* 3.0 37.5 + - - +
238T ALA* 1.3 73.7 - - - +
240T VAL* 1.3 61.0 + - - +
242T GLN* 3.9 19.1 - - + +
243T LYS* 2.8 48.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 240 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A TYR* 3.7 48.1 - - + +
113A ILE* 3.7 11.4 - - + +
183T ILE* 5.4 0.4 - - + -
187T ALA* 4.4 6.1 - - + -
202T MET* 3.7 36.3 - - + -
204T ILE* 5.1 3.1 - - + -
236T LYS* 2.9 20.5 + - + +
237T TYR* 3.2 15.2 + - + +
239T ARG* 1.3 77.5 - - - +
241T VAL* 1.3 62.7 + - + +
242T GLN 3.4 0.3 + - - -
243T LYS* 4.2 1.2 - - - +
244T LEU* 3.4 26.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 241 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174T LEU* 3.8 22.0 - - + -
178T LEU* 3.7 29.8 - - + -
183T ILE* 4.8 8.7 - - + -
213T ILE* 4.3 26.0 - - + -
219T MET* 5.0 0.7 - - - -
237T TYR 3.0 15.0 + - - +
238T ALA 3.4 7.9 - - - +
240T VAL* 1.3 77.3 - - + +
242T GLN* 1.3 63.0 + - - +
244T LEU* 3.6 11.8 + - - +
246T PHE* 3.4 26.0 + - + +
248T ALA* 3.8 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 242 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ALA* 4.0 22.2 - - - +
238T ALA 2.8 16.4 + - - +
239T ARG* 3.6 15.2 - - + +
240T VAL 3.2 0.8 - - - -
241T VAL* 1.3 76.9 - - - +
243T LYS* 1.3 63.7 + - + +
245T GLY* 3.2 13.0 + - - -
246T PHE 3.4 20.4 + - - +
247T PRO* 5.8 0.4 - - + -
248T ALA* 4.2 18.4 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
110A TYR* 3.9 31.7 + - + -
113A ILE* 3.5 32.9 - - + +
115A GLU* 3.5 32.2 + - - +
186T ARG* 5.2 3.5 + - - -
239T ARG* 2.8 34.4 + - + +
240T VAL 4.3 0.4 - - - +
241T VAL 3.5 0.2 - - - -
242T GLN* 1.3 75.0 - - + +
244T LEU* 1.3 60.4 + - - +
245T GLY 3.2 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 244 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A TYR* 3.3 29.8 - - + +
182T THR* 4.6 6.7 - - + +
183T ILE* 3.8 46.9 - - + +
186T ARG* 3.0 57.8 + - + +
187T ALA* 4.4 9.2 - - + +
240T VAL* 3.4 20.5 + - + +
241T VAL* 4.0 7.0 - - - +
242T GLN 3.2 1.4 - - - -
243T LYS* 1.3 77.2 - - - +
245T GLY* 1.3 56.8 + - - +
246T PHE* 3.6 13.5 - - + +
----------------------------------------------------------
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