Contacts of the helix formed by residues 150 - 168 (chain O) in PDB entry 3K9Q
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 150 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0O NAD 4.7 5.4 - - - -
122O PRO* 3.7 22.4 - - - +
149O ALA* 1.3 75.3 - - - +
151O GLY* 1.3 64.5 + - - +
152O THR* 3.7 6.0 + - - -
153O THR* 2.7 31.2 + - - -
154O ASN* 2.7 28.4 + - - -
211O THR* 4.9 2.7 + - - -
213O ALA* 4.2 8.5 + - - +
320O TYR* 3.4 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 151 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0O NAD 3.8 11.9 - - - -
150O SER* 1.3 72.1 - - - +
152O THR* 1.3 62.8 + - - +
154O ASN* 3.1 5.2 + - - +
155O SER 2.9 18.7 + - - -
178O HIS* 5.9 0.7 - - - -
289O GLY 4.9 0.3 - - - +
314O TYR* 3.4 22.8 - - - -
316O ASN* 4.6 5.2 - - - -
320O TYR* 3.5 26.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 152 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150O SER* 3.2 4.8 + - - -
151O GLY* 1.3 75.7 - - - +
153O THR* 1.3 62.3 + - - +
155O SER* 2.7 20.9 + - - -
156O LEU* 3.0 7.8 + - - +
174O MET* 3.9 13.7 - - + -
176O THR* 3.8 20.1 - - + +
178O HIS* 3.7 14.5 + - - -
211O THR* 4.4 7.0 + - - +
213O ALA* 3.5 23.8 - - + -
243O THR* 3.9 10.5 - - + +
314O TYR* 2.7 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 153 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122O PRO* 5.1 2.6 - - - +
129O THR* 5.5 0.7 - - + -
131O VAL* 3.9 8.1 - - + -
149O ALA* 3.9 11.6 - - + +
150O SER* 2.7 30.7 + - - -
151O GLY 3.4 0.2 - - - -
152O THR* 1.3 74.9 - - - +
154O ASN* 1.3 57.8 + - - +
156O LEU* 3.1 4.6 + - - -
157O ALA* 2.8 31.7 + - - +
213O ALA* 3.6 20.3 + - - +
216O ALA 5.6 1.6 - - - +
217O ILE* 3.8 17.7 - - + -
220O VAL* 3.8 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 154 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131O VAL* 3.4 21.1 - - + +
132O PHE 4.1 0.2 + - - -
148O GLY 3.3 22.7 + - - +
149O ALA* 3.9 6.5 - - - +
150O SER 2.7 24.0 + - - +
151O GLY* 3.1 9.0 + - - +
153O THR* 1.3 75.6 - - - +
155O SER* 1.3 60.5 + - - +
158O PRO* 3.3 18.2 - - - +
289O GLY 3.6 14.0 - - - +
290O SER* 3.7 3.1 - - - -
320O TYR* 3.5 12.8 - - + -
323O GLN* 3.0 48.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 155 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151O GLY 2.9 6.4 + - - -
152O THR 2.7 17.0 + - - -
154O ASN* 1.3 76.8 - - - +
156O LEU* 1.3 58.4 + - - +
158O PRO* 4.1 0.5 - - - +
159O VAL* 3.7 10.4 - - - +
243O THR* 2.7 26.4 + - - -
289O GLY 3.7 8.0 + - - -
290O SER* 2.7 24.3 + - - -
312O ALA* 4.0 5.8 - - - +
313O TRP 4.8 0.4 - - - -
314O TYR* 3.2 39.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 156 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152O THR 3.0 12.6 + - - +
153O THR* 3.8 2.7 - - - +
155O SER* 1.3 82.9 + - - +
157O ALA* 1.3 66.4 + - - +
158O PRO 3.4 0.9 - - - -
159O VAL* 3.1 6.9 + - + +
160O ALA* 2.8 27.1 + - + +
174O MET* 4.0 13.2 - - - -
213O ALA* 4.1 5.6 - - + +
214O ALA* 4.0 26.9 - - + -
217O ILE* 3.9 24.0 - - + -
228O LEU* 4.3 4.7 - - + -
243O THR* 4.5 17.0 - - + -
245O LEU* 3.8 37.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 157 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131O VAL* 4.0 8.1 - - + -
134O THR* 3.8 14.8 - - + +
153O THR 2.8 19.7 + - - +
156O LEU* 1.3 73.0 - - - +
158O PRO* 1.4 65.7 - - + +
160O ALA* 4.6 0.2 - - - -
161O LYS* 2.8 32.2 + - - +
217O ILE* 4.3 8.1 - - + -
220O VAL* 3.9 26.5 - - + -
221O ILE* 3.5 10.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 158 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131O VAL* 4.7 2.7 - - + -
133O ASN 5.9 1.1 - - - +
134O THR* 3.9 15.5 - - - +
154O ASN 3.3 15.3 - - - +
155O SER 4.1 0.2 - - - +
156O LEU 3.6 0.7 - - - -
157O ALA* 1.4 93.8 - - + +
159O VAL* 1.3 62.4 + - - +
161O LYS* 3.9 5.4 - - + +
162O VAL* 3.3 28.4 + - - +
270O SER* 5.4 3.6 - - - +
271O PHE* 3.6 32.7 - - + -
290O SER* 3.7 28.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 159 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155O SER 3.7 16.8 - - - +
156O LEU* 3.1 9.3 + - + +
158O PRO* 1.3 74.5 - - - +
160O ALA* 1.3 64.1 + - - +
162O VAL 3.4 1.7 + - - -
163O LEU* 3.1 24.1 + - + +
245O LEU* 4.3 7.6 - - + -
263O MET* 3.4 23.1 - - + +
271O PHE* 3.6 25.4 - - + -
292O PHE* 4.1 6.5 - - + -
310O VAL* 3.5 31.9 - - + -
311O ALA 6.1 0.4 - - - -
312O ALA* 3.8 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 160 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156O LEU* 2.8 27.3 + - + +
157O ALA* 3.9 2.9 - - - +
159O VAL* 1.3 72.1 - - - +
161O LYS* 1.3 59.0 + - - +
163O LEU* 3.3 11.1 + - - +
164O ASN* 2.9 31.6 + - - +
169O LEU* 5.1 3.9 - - + +
217O ILE* 4.9 0.9 - - + -
221O ILE* 4.2 4.9 - - + -
224O ILE* 4.0 23.6 - - + +
228O LEU* 4.0 18.2 - - + -
245O LEU* 4.7 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 161 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133O ASN 5.9 0.7 - - - +
134O THR* 4.4 26.3 + - + +
157O ALA 2.8 20.7 + - - +
158O PRO* 3.9 7.4 - - + +
160O ALA* 1.3 71.6 - - - +
162O VAL* 1.3 54.0 + - + +
164O ASN* 3.2 4.6 + - - +
165O ASP* 2.8 61.0 + - - +
221O ILE* 3.8 21.5 - - + +
223O GLU* 3.5 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 162 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158O PRO 3.3 14.0 + - - +
159O VAL 3.8 1.6 - - - +
161O LYS* 1.3 74.2 - - + +
163O LEU* 1.3 66.8 - - - +
165O ASP* 4.5 4.5 - - - +
166O ASP* 3.0 29.3 + - + +
167O PHE* 4.9 2.0 - - + -
262O ALA* 3.8 31.9 - - + +
263O MET* 3.7 31.6 - - + -
266O ALA* 3.4 32.3 - - + -
271O PHE* 4.6 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 163 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159O VAL* 3.1 17.8 + - + +
160O ALA* 3.6 8.1 - - - +
162O VAL* 1.3 74.6 - - - +
164O ASN* 1.3 59.5 + - - +
167O PHE* 3.0 46.9 + - + +
168O GLY 3.3 5.0 + - - -
169O LEU* 5.1 6.1 - - + -
245O LEU* 3.7 30.5 - - + -
247O VAL* 4.1 18.6 - - + -
249O LEU* 4.3 23.6 - - + +
259O VAL* 4.5 14.8 - - + -
263O MET* 3.7 15.9 - - + -
308O VAL* 4.9 1.6 - - + -
310O VAL* 4.1 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 164 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160O ALA 2.9 16.9 + - - +
161O LYS* 3.8 4.3 - - - +
163O LEU* 1.3 76.7 - - - +
165O ASP* 1.3 73.3 + - - +
168O GLY* 3.0 20.3 + - - -
169O LEU* 2.9 32.1 + - + +
221O ILE* 5.4 0.6 - - + +
223O GLU* 3.5 23.7 + - - +
224O ILE* 3.4 32.9 - - + +
227O LYS* 4.9 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 165 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161O LYS* 2.8 60.3 + - - +
162O VAL* 4.2 2.8 - - - +
164O ASN* 1.3 83.4 + - - +
166O ASP* 1.3 71.2 + - - +
168O GLY 5.0 0.2 + - - -
223O GLU* 4.4 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 166 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162O VAL* 3.0 20.4 + - - +
165O ASP* 1.3 91.4 - - - +
167O PHE* 1.3 77.0 + - + +
251O LYS* 3.0 26.5 + - - -
262O ALA* 3.2 25.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 167 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162O VAL* 4.4 3.6 - - + -
163O LEU* 3.0 32.9 + - + +
166O ASP* 1.3 98.5 - - + +
168O GLY* 1.3 64.2 + - - +
249O LEU* 3.7 23.3 - - + -
250O GLU* 3.3 2.8 + - - +
251O LYS* 2.9 48.5 + - + +
254O VAL* 4.0 29.6 - - + -
258O GLN* 3.8 34.3 - - + -
259O VAL* 4.0 18.4 - - + -
262O ALA* 4.1 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 168 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163O LEU 3.3 2.0 + - - -
164O ASN* 3.0 18.5 + - - -
165O ASP 4.8 0.2 - - - -
167O PHE* 1.3 74.7 - - - +
169O LEU* 1.3 61.8 + - - -
249O LEU* 3.2 7.8 - - - -
250O GLU* 2.8 50.3 + - - +
----------------------------------------------------------
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