Contacts of the helix formed by residues 150 - 170 (chain B) in PDB entry 3DAE
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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LYS 4.1 0.8 + - - -
149B MET* 1.3 78.7 - - - +
151B GLU* 1.3 64.2 + - - +
152B GLN* 3.1 12.8 + - - +
153B GLU* 3.2 32.0 + - - +
154B ALA* 3.3 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B MET 3.7 0.6 + - - -
150B SER* 1.3 73.0 - - - +
152B GLN* 1.3 57.4 + - + +
154B ALA* 3.9 0.5 - - - +
155B ARG* 3.0 35.8 + - - +
246B LEU* 3.9 17.8 - - + +
275B LEU* 5.0 1.0 - - - -
276B SER* 3.0 37.3 + - - -
279B ALA* 3.8 6.9 - - - +
305B TRP* 2.9 41.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B SER* 3.1 11.5 - - - +
151B GLU* 1.3 77.5 - - - +
153B GLU* 1.3 58.5 + - + +
155B ARG* 3.5 22.4 + - - +
156B ARG* 3.1 25.5 + - - +
309B ASP* 5.3 10.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B TYR* 2.6 37.0 + - - -
146B ARG* 4.8 8.3 + - - -
149B MET* 3.8 24.4 - - + +
150B SER* 3.2 18.8 + - - +
152B GLN* 1.3 76.5 - - - +
154B ALA* 1.3 61.5 + - - +
156B ARG* 2.9 14.8 + - - +
157B PHE* 2.9 42.4 + - + -
189B LEU* 5.1 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B MET* 3.7 13.4 - - + -
150B SER 3.3 5.2 + - - +
153B GLU* 1.3 79.0 - - - +
155B ARG* 1.3 56.3 + - - +
158B PHE* 3.0 29.1 + - - +
242B LEU* 4.0 4.8 - - + +
245B MET* 3.4 33.7 - - + +
246B LEU* 3.1 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B GLU* 3.0 20.9 + - - +
152B GLN* 4.0 24.0 + - - +
154B ALA* 1.3 78.4 - - - +
156B ARG* 1.3 59.7 + - - +
158B PHE* 4.0 2.9 - - + -
159B GLN* 2.8 51.8 + - + +
305B TRP* 2.6 92.2 + - + +
306B PHE* 3.6 2.5 - - + +
308B VAL* 3.3 40.6 + - - +
309B ASP* 4.9 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B GLN 3.1 14.1 + - - +
153B GLU* 2.9 19.1 + - - +
155B ARG* 1.3 75.2 - - - +
157B PHE* 1.3 86.0 + - - +
158B PHE 3.5 0.2 + - - -
159B GLN* 4.0 11.9 - - - +
160B GLN* 3.1 52.8 + - - +
188B HIS 3.5 14.7 + - - -
189B LEU* 2.4 34.9 + - - +
190B ASN* 3.7 10.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LEU* 4.2 9.0 - - + -
142B TYR* 3.5 40.8 - + - -
149B MET* 3.9 20.2 - - + -
153B GLU* 2.9 33.2 + - + +
154B ALA 4.1 0.2 - - - +
156B ARG* 1.3 103.3 - - - +
158B PHE* 1.3 58.0 + - - +
160B GLN* 3.3 5.3 - - - +
161B ILE* 2.9 34.4 + - + +
185B LEU* 3.8 15.7 - - + -
189B LEU* 3.6 13.2 - - + -
191B VAL* 3.4 22.8 - - + +
245B MET* 3.6 23.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ALA 3.0 21.9 + - - +
155B ARG* 4.0 4.9 - - - +
156B ARG 3.2 0.4 - - - -
157B PHE* 1.3 75.2 - - - +
159B GLN* 1.3 57.9 + - + +
161B ILE* 3.6 11.8 - - + +
162B ILE* 3.0 61.6 + - + +
238B CYS* 3.5 25.4 - - + -
241B ILE* 5.5 0.4 - - + -
242B LEU* 3.8 32.1 - - + -
245B MET* 4.1 4.3 - - + -
282B LEU* 4.4 6.1 - - + -
286B MET* 3.7 22.4 - - + -
300B ILE* 4.1 7.4 - - + -
305B TRP* 4.3 11.4 - + - -
306B PHE* 3.7 24.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ARG* 2.8 34.2 + - + +
156B ARG* 4.0 11.6 - - - +
158B PHE* 1.3 73.3 - - - +
160B GLN* 1.3 58.8 + - - +
162B ILE* 3.5 0.9 + - - +
163B SER* 2.9 35.7 + - - -
306B PHE* 2.9 43.2 + - + +
308B VAL 3.2 20.2 + - - -
309B ASP* 3.9 2.8 - - - +
310B LEU* 3.5 34.4 - - + +
311B PRO* 3.5 19.2 - - - +
314B LEU* 3.9 6.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B HIS* 3.4 39.9 - - + +
156B ARG* 3.1 58.8 + - - +
157B PHE 3.3 8.5 - - - +
159B GLN* 1.3 78.8 - - - +
161B ILE* 1.3 63.5 + - - +
163B SER* 3.6 3.4 + - - -
164B ALA* 3.3 19.1 + - - +
190B ASN* 3.7 6.0 + - - -
191B VAL* 2.9 39.1 + - + +
311B PRO* 6.5 0.2 - - + -
313B TYR* 4.2 9.1 + - - +
314B LEU* 4.1 9.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B HIS* 5.7 0.2 - - - -
139B LEU* 4.5 15.7 - - + -
157B PHE* 2.9 24.2 + - + +
158B PHE* 3.6 11.7 - - + +
160B GLN* 1.3 72.1 - - - +
162B ILE* 1.3 69.8 + - + +
164B ALA* 2.8 20.1 + - - +
165B VAL* 3.0 16.2 + - + +
178B LEU* 5.5 1.3 - - + -
183B LEU* 4.8 16.2 - - + -
191B VAL* 4.0 20.9 - - + -
193B ILE* 5.2 3.8 - - + -
238B CYS* 3.8 26.2 - - - -
241B ILE* 3.9 29.6 - - + -
245B MET* 4.6 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B PHE* 3.0 58.7 + - + +
159B GLN 3.9 0.2 - - - +
161B ILE* 1.3 77.5 - - - +
163B SER* 1.3 52.0 + - - +
165B VAL* 3.4 3.9 + - + +
166B GLU* 2.7 33.3 + - - +
238B CYS* 3.9 23.1 - - + -
297B ILE* 4.3 21.1 - - + -
300B ILE* 4.3 18.2 - - + -
301B MET* 4.2 19.3 - - + -
306B PHE* 3.9 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B HIS* 3.0 17.7 + - - -
159B GLN 2.9 18.6 + - - -
160B GLN 3.6 3.4 - - - -
161B ILE 2.9 0.2 + - - -
162B ILE* 1.3 77.1 - - - +
164B ALA* 1.3 63.2 + - - +
166B GLU* 3.0 12.5 + - - +
167B TYR* 2.9 22.5 + - - +
301B MET* 4.8 9.4 - - - +
314B LEU* 3.4 42.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B HIS* 3.4 25.0 - - + +
114B HIS* 4.2 7.9 - - + +
115B ILE* 4.0 11.5 - - + +
160B GLN 3.3 8.6 + - - +
161B ILE* 2.8 13.7 + - - +
163B SER* 1.3 73.1 - - - +
165B VAL* 1.3 63.8 + - - +
167B TYR* 2.9 14.2 + - - +
168B CYS* 2.9 19.2 + - - -
193B ILE* 3.5 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ILE* 3.0 12.0 + - + +
162B ILE* 3.5 9.2 - - - +
164B ALA* 1.3 76.1 - - - +
166B GLU* 1.3 62.3 + - - +
168B CYS* 3.2 7.3 + - - +
169B HIS* 3.0 54.0 + - + +
175B HIS* 6.2 0.7 - - + -
178B LEU* 4.1 14.1 - - + -
193B ILE* 4.2 13.4 - - + +
234B ASP* 4.1 10.8 - - + +
238B CYS* 4.0 24.7 - - - -
297B ILE* 3.5 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ILE 2.7 22.8 + - - +
163B SER* 3.5 7.1 + - - +
165B VAL* 1.3 73.5 - - - +
167B TYR* 1.3 62.7 + - - +
169B HIS* 3.7 5.7 + - + +
170B ARG* 3.2 52.9 + - - +
297B ILE* 3.5 28.3 - - + -
298B HIS* 3.9 24.3 + - + +
301B MET* 4.0 20.0 - - - +
314B LEU 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B LEU 3.5 9.7 + - - -
110B LEU* 3.8 19.7 - - + -
111B ARG* 3.1 47.6 + - - +
112B HIS* 3.6 32.8 - + + -
115B ILE* 3.9 7.9 - - + -
163B SER 2.9 11.2 + - - +
164B ALA 2.9 7.5 + - - +
166B GLU* 1.3 78.3 + - - +
168B CYS* 1.3 61.8 + - - +
170B ARG* 3.3 31.5 + - - +
171B HIS* 2.7 55.3 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU* 3.8 13.7 - - - -
115B ILE* 3.5 29.6 - - - -
164B ALA 2.9 11.8 + - - -
165B VAL* 3.6 10.5 - - - +
167B TYR* 1.3 74.7 - - - +
169B HIS* 1.3 58.1 + - + +
170B ARG 3.1 1.8 - - - -
171B HIS* 2.6 31.5 + - - +
173B ILE* 3.2 28.5 + - + +
175B HIS* 5.8 3.8 - - + +
193B ILE* 5.5 3.8 - - - -
196B PHE* 3.7 26.5 - - - -
234B ASP* 6.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B VAL* 3.0 35.6 + - + +
166B GLU* 3.8 7.2 - - + +
168B CYS* 1.3 76.5 - - + +
170B ARG* 1.3 59.2 + - - +
171B HIS 3.1 0.4 - - - -
172B LYS* 3.3 16.0 + - - +
173B ILE 3.8 16.8 - - - +
174B VAL* 4.2 6.9 - - + +
231B PRO* 3.3 47.9 - - + +
234B ASP* 3.1 27.4 + - + +
297B ILE* 3.7 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B GLU* 3.2 52.5 + - - +
167B TYR* 3.3 42.8 - - - +
168B CYS 3.0 0.8 + - - -
169B HIS* 1.3 75.1 - - - +
171B HIS* 1.3 68.4 + - + +
172B LYS* 3.3 4.8 + - - +
315B LEU 5.8 1.6 + - - -
----------------------------------------------------------
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