Contacts of the helix formed by residues 153 - 174 (chain B) in PDB entry 4I93
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 LYS 153 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B GLN* 3.8 27.7 - - - +
151B PRO 3.3 5.4 + - - +
152B MSE 1.3 77.4 - - - +
154B TRP* 1.3 65.1 + - - +
155B ALA* 4.2 6.7 - - + +
156B MSE 3.0 11.5 + - + +
157B ARG* 3.0 19.8 + - - +
276B GLN* 3.6 13.7 - - - +
323B GLN 3.9 10.7 + - - -
324B LEU* 2.9 49.2 + - + +
325B LEU 5.0 0.8 - - - -
326B GLY* 4.8 5.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B MSE 3.6 1.8 + - - -
153B LYS* 1.3 70.3 - - - +
155B ALA* 1.3 63.2 + - + +
157B ARG* 3.1 13.8 + - + +
158B LEU* 3.0 60.6 + - + +
245B LEU 5.1 4.7 - - - -
246B LEU* 4.2 3.8 - - + -
269B MSE 3.9 26.2 - - + -
273B LEU* 3.8 30.9 - - + +
276B GLN* 3.1 43.9 + - + +
277B PHE* 3.3 25.4 - - + +
278B SER 5.1 0.2 - - - +
281B ASP* 4.3 23.5 + - + +
282B GLY* 4.3 7.0 - - - -
285B LEU* 3.8 29.2 - - + -
315B LYS* 4.9 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LYS* 3.2 3.9 - - + +
154B TRP* 1.3 79.8 - - - +
156B MSE 1.3 58.4 + - - +
158B LEU* 3.5 5.6 + - - +
159B ARG* 3.1 27.2 + - - +
314B GLN* 4.9 0.7 - - - +
315B LYS* 4.0 33.1 + - + +
316B ASP* 3.7 22.9 - - - +
324B LEU* 4.1 19.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B MSE 4.0 14.8 - - + -
153B LYS* 3.0 15.4 + - + +
155B ALA* 1.3 76.6 - - - +
157B ARG* 1.3 60.6 + - - +
159B ARG* 3.2 15.1 + - + +
160B VAL* 2.8 49.6 + - + +
189B PHE* 4.0 15.9 - - + -
193B ALA 4.3 4.7 - - - +
195B PRO* 4.1 14.6 - - + -
321B SER* 4.0 19.3 - - - +
324B LEU* 3.6 39.2 - - + +
325B LEU* 4.1 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LEU* 3.7 19.7 + - - +
151B PRO* 3.9 9.9 - - - +
152B MSE 2.9 54.9 + - - +
153B LYS 3.0 12.7 + - - +
154B TRP* 3.1 15.0 + - + +
156B MSE 1.3 76.6 - - - +
158B LEU* 1.3 61.6 + - + +
160B VAL* 3.4 4.3 + - - +
161B ALA* 3.1 18.5 + - - +
245B LEU* 2.8 65.3 + - + +
248B GLY 4.0 2.0 - - - +
270B ASP* 2.9 32.3 + - - +
272B GLY 4.7 0.4 + - - -
273B LEU* 3.6 32.7 - - - +
285B LEU* 6.2 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B TRP* 3.0 67.9 + - + +
155B ALA* 3.9 4.5 - - - +
157B ARG* 1.3 73.7 - - - +
159B ARG* 1.3 64.9 + - - +
161B ALA* 3.4 1.0 + - - -
162B LEU 3.0 18.4 + - - -
281B ASP* 5.8 1.3 - - + -
285B LEU* 4.0 17.7 - - + -
310B MSE 3.6 22.7 - - + +
313B LEU* 3.2 33.2 - - + +
314B GLN* 3.0 24.7 + - - +
315B LYS* 4.2 9.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ALA 3.1 15.8 + - - +
156B MSE 3.2 17.9 + - + +
158B LEU* 1.3 75.6 - - - +
160B VAL* 1.3 66.5 + - - +
162B LEU* 3.3 1.0 + - - +
163B HIS* 2.9 54.5 + - + +
195B PRO* 4.5 2.2 - - + -
314B GLN* 3.3 15.0 + - - +
315B LYS 4.2 3.6 + - - -
316B ASP 2.9 32.5 + - - -
317B LEU* 3.8 15.4 + - - +
319B ILE 2.9 22.0 + - - -
320B ALA* 3.8 0.6 - - - +
321B SER* 2.9 39.7 + - - +
324B LEU* 3.6 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LEU* 4.2 22.9 - - + -
152B MSE 4.6 3.8 - - - -
156B MSE 2.8 36.1 + - + +
157B ARG* 3.5 8.7 - - - +
159B ARG* 1.3 76.8 - - - +
161B ALA* 1.3 64.3 + - - +
163B HIS* 3.3 1.0 + - - +
164B ILE* 2.9 31.4 + - + +
187B VAL* 4.0 23.8 - - + -
189B PHE* 3.9 22.0 - - + -
195B PRO* 3.9 9.6 - - + -
241B LEU* 5.2 1.8 - - + -
245B LEU* 4.4 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ARG 3.1 11.4 + - - +
158B LEU* 3.7 2.5 - - - +
160B VAL* 1.3 79.0 - - - +
162B LEU* 1.3 63.0 + - - +
164B ILE* 4.9 0.9 - - - -
165B ALA* 3.0 24.6 + - - +
238B PHE* 3.4 13.3 - - + -
241B LEU* 5.7 1.1 - - - -
242B LEU* 3.8 25.8 - - + -
245B LEU* 4.0 8.1 - - + -
285B LEU* 5.2 1.8 - - + -
310B MSE 3.6 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B LEU 3.0 16.7 + - - +
159B ARG* 3.8 3.6 - - + +
161B ALA* 1.3 75.6 - - - +
163B HIS* 1.3 67.4 + - + +
165B ALA* 3.2 4.0 + - - +
166B GLN* 2.9 57.7 + - + +
307B VAL* 4.0 17.5 - - + +
310B MSE 3.8 23.9 - - + +
311B ILE* 4.1 15.7 - - + -
314B GLN* 3.6 33.9 - - + +
317B LEU* 6.2 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ARG* 4.7 14.4 + - + +
159B ARG* 2.9 48.6 + - + +
160B VAL 3.9 0.4 - - - +
162B LEU* 1.3 87.8 - - + +
164B ILE* 1.3 59.2 + - - +
166B GLN* 3.3 20.4 + - - +
167B ALA* 2.9 28.1 + - - +
194B ASN* 5.1 11.1 - - + +
195B PRO* 3.8 44.5 + - + +
321B SER* 5.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B VAL* 2.9 24.6 + - + +
161B ALA 4.2 2.0 - - - +
163B HIS* 1.3 75.9 - - - +
165B ALA* 1.3 66.8 + - - +
167B ALA* 3.2 3.2 + - + +
168B LEU* 2.9 24.8 + - + +
182B LEU* 4.4 17.9 - - + -
187B VAL* 3.9 32.3 - - + -
195B PRO* 4.7 2.7 - - + -
196B ARG* 3.9 32.3 - - - +
197B LEU* 3.9 15.7 - - + +
238B PHE* 4.1 12.8 - - + -
241B LEU* 4.0 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ALA 3.0 18.9 + - - +
162B LEU* 3.2 6.0 + - - +
164B ILE* 1.3 77.6 - - - +
166B GLN* 1.3 56.4 + - - +
168B LEU* 3.3 9.2 + - - +
169B GLU* 2.9 28.6 + - - +
238B PHE* 3.8 12.9 - - + -
303B PRO* 4.7 2.4 - - - +
306B LEU* 3.9 25.8 - - + +
307B VAL* 3.7 20.6 - - + +
310B MSE 4.8 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ARG* 3.4 45.7 + - - +
162B LEU* 2.9 42.9 + - + +
163B HIS* 3.6 18.4 + - - +
165B ALA* 1.3 75.1 - - - +
167B ALA* 1.3 57.4 - - - +
169B GLU* 3.4 4.5 + - - +
170B TYR* 2.8 29.8 + - - +
307B VAL* 3.9 23.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ARG* 3.8 23.9 - - + +
115B MSE 4.5 3.4 - - - -
163B HIS 2.9 17.2 + - - +
164B ILE* 3.2 7.2 + - + +
166B GLN* 1.3 77.0 - - - +
168B LEU* 1.3 55.3 + - - +
170B TYR* 3.3 7.6 + - - +
171B CYS* 2.9 33.1 + - - -
197B LEU* 3.8 32.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ILE* 2.9 19.6 + - + +
165B ALA* 3.6 8.7 - - - +
167B ALA* 1.3 71.7 - - - +
169B GLU* 1.3 60.9 - - - +
171B CYS* 3.3 7.4 + - + +
172B THR* 3.0 33.1 + - - -
179B TYR* 4.3 14.6 - - + -
182B LEU* 4.1 16.2 - - + -
197B LEU* 3.9 20.0 - - + -
234B VAL* 3.8 29.4 - - + +
235B ILE* 5.3 3.1 - - + -
238B PHE* 4.0 29.2 - - + -
303B PRO* 4.4 9.6 - - + -
306B LEU* 4.8 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ALA 2.9 16.8 + - - +
166B GLN* 3.7 8.8 - - - +
168B LEU* 1.3 72.7 - - - +
170B TYR* 1.3 71.2 + - - +
172B THR* 3.3 6.5 + - - +
173B SER* 2.9 34.7 + - - -
303B PRO* 3.8 14.1 - - + +
304B LYS* 3.5 53.8 + - + +
307B VAL* 4.3 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU* 3.7 21.2 - - + -
111B ARG 3.3 28.5 + - - -
112B ASN* 3.5 38.4 - - + -
114B ARG* 4.5 9.4 - - + +
115B MSE 4.1 18.8 - - + -
166B GLN 2.8 17.8 + - - +
167B ALA* 3.4 9.9 - - - +
169B GLU* 1.3 80.6 + - - +
171B CYS* 1.3 67.8 + - - +
173B SER* 2.7 25.2 + - - -
174B LYS* 3.1 43.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU* 4.0 14.6 - - + -
115B MSE 3.4 30.1 - - - -
167B ALA 2.9 20.6 + - - +
168B LEU* 3.6 8.7 - - + +
169B GLU 3.3 0.4 - - - -
170B TYR* 1.3 77.9 - - - +
172B THR* 1.3 62.8 + - - +
174B LYS* 3.1 10.2 + - - +
175B GLY 3.4 0.2 + - - -
176B ARG* 3.0 34.6 + - - +
179B TYR* 5.4 0.7 - - + -
197B LEU* 4.6 7.0 - - - -
202B LEU* 3.9 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LEU* 3.0 14.9 + - - +
169B GLU* 3.6 11.9 - - - +
171B CYS* 1.3 75.3 - - - +
173B SER* 1.3 63.6 + - - +
175B GLY* 3.1 14.2 + - - -
176B ARG 3.5 10.5 + - - -
177B ALA* 4.1 23.1 + - + +
231B PRO* 6.4 0.7 - - + -
303B PRO* 4.0 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B GLU* 2.9 29.0 + - - -
170B TYR* 2.7 25.1 + - - -
172B THR* 1.3 77.4 - - - +
174B LYS* 1.3 64.6 + - - +
175B GLY 3.3 1.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B GLN* 4.9 12.0 + - - -
110B LEU* 4.1 26.0 - - + +
170B TYR* 3.1 50.9 + - + +
171B CYS 3.1 6.4 + - - +
173B SER* 1.3 82.4 - - - +
175B GLY* 1.3 59.9 + - - +
176B ARG* 3.5 2.3 + - - +
----------------------------------------------------------
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