Contacts of the helix formed by residues 178 - 195 (chain B) in PDB entry 2B4M
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 TRP 178 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ILE* 3.6 17.5 - - + -
22B ASP* 2.9 39.5 - - - -
25B SER* 4.2 4.5 - - - -
50B SER* 3.9 24.5 - - - -
72B TRP* 4.7 3.8 - + - +
176B VAL* 2.9 43.2 + - + +
177B ALA* 1.3 78.0 - - - +
179B ASP* 1.3 62.0 + - - +
180B SER* 3.2 5.6 - - - +
181B GLU* 3.0 36.1 + - + +
182B ILE* 3.0 11.2 + - - +
206B ALA* 5.6 3.4 - - - +
230B HIS* 5.9 1.2 + - - -
310B PBE 3.4 63.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B SER* 5.5 4.7 + - - -
75B HIS* 4.0 16.3 + - + +
76B TRP* 3.0 38.6 + - + +
132B MET* 3.7 20.0 - - + +
135B VAL* 5.4 8.0 - - + +
136B GLU* 4.2 8.7 - - - +
177B ALA 4.0 2.0 + - - +
178B TRP* 1.3 72.4 - - - +
180B SER* 1.3 61.6 + - - +
182B ILE* 3.5 20.6 + - - +
183B ALA* 3.2 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TRP* 5.2 1.9 + - - -
74B PRO 3.8 17.0 + - - -
75B HIS* 5.8 1.6 - - - -
128B MET* 3.4 30.9 - - - +
132B MET* 3.8 5.6 - - - -
178B TRP* 3.9 7.4 - - - +
179B ASP* 1.3 76.2 - - - +
181B GLU* 1.3 85.4 + - - +
183B ALA* 3.0 23.7 + - - +
184B SER* 3.1 7.4 + - - -
225B TRP* 4.0 12.8 - - - -
310B PBE 4.5 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ILE* 3.9 10.6 - - - +
128B MET* 4.5 1.2 - - - +
175B TYR* 4.4 2.2 - - + +
176B VAL 3.4 24.5 - - - +
178B TRP* 3.0 16.4 + - + +
180B SER* 1.3 100.0 + - - +
182B ILE* 1.3 61.6 + - - +
183B ALA 3.2 0.4 - - - -
184B SER* 3.3 7.5 + - - +
185B THR* 2.5 35.7 + - - +
222B LEU 3.6 10.2 - - - +
223B SER* 3.2 36.3 - - - +
225B TRP* 3.1 30.0 + - - -
310B PBE 3.9 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ILE* 5.3 0.4 - - - +
135B VAL* 4.9 12.8 - - + -
141B PRO* 4.0 31.2 - - + +
175B TYR* 4.6 13.5 - - + -
177B ALA* 4.2 27.1 - - + +
178B TRP 3.0 16.3 + - - +
179B ASP* 3.7 25.4 - - - +
181B GLU* 1.3 75.4 - - - +
183B ALA* 1.3 67.7 + - - +
185B THR* 5.0 0.4 - - - -
186B ASN* 2.9 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B TRP* 4.1 5.8 - - + -
128B MET* 3.8 21.5 - - + -
131B ILE* 3.8 33.6 - - + +
132B MET* 4.1 4.5 - - + -
179B ASP 3.2 12.6 + - - +
180B SER 3.0 12.2 + - - +
182B ILE* 1.3 81.3 - - - +
184B SER* 1.3 62.8 + - - +
186B ASN* 3.8 1.7 - - - +
187B VAL* 3.1 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ILE* 6.3 1.3 - - - -
121B PHE* 4.0 17.9 - - - -
123B TRP* 3.8 16.8 - - - -
128B MET* 4.4 5.2 - - - -
180B SER 3.1 2.9 + - - -
181B GLU* 3.3 22.0 + - - +
183B ALA* 1.3 76.7 - - - +
185B THR* 1.3 72.7 + - - +
187B VAL* 3.1 12.0 - - - +
188B ILE* 3.0 27.2 + - - +
222B LEU* 3.7 18.6 + - - +
247B SER* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B LEU* 4.1 17.4 - - + +
174B ALA 4.8 2.6 + - - +
175B TYR* 3.3 33.4 - - + +
181B GLU* 2.5 26.9 + - - +
184B SER* 1.3 79.5 + - - +
186B ASN* 1.3 60.9 + - - +
188B ILE* 4.1 0.3 - - - +
189B GLY* 2.8 26.3 + - - -
201B LEU* 3.6 25.7 - - + +
221B SER* 6.4 0.2 - - - -
222B LEU* 3.7 16.9 + - + +
223B SER* 4.5 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ILE* 6.2 1.6 - - + -
141B PRO* 3.3 29.6 - - + +
142B ALA* 3.6 15.9 - - - +
145B ALA* 3.6 15.0 - - + +
175B TYR* 5.7 4.7 - - - -
182B ILE* 2.9 32.3 + - - +
183B ALA* 3.4 2.6 + - - +
184B SER 3.2 0.8 - - - -
185B THR* 1.3 78.1 - - - +
187B VAL* 1.3 59.7 + - - +
189B GLY* 3.6 1.9 - - - -
190B LYS* 2.8 31.4 + - - +
201B LEU* 4.3 20.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B PHE* 4.3 12.6 - - + -
123B TRP* 3.7 16.2 - - + -
131B ILE* 4.0 10.3 - - + -
145B ALA* 3.9 8.7 - - + +
148B TYR* 3.7 33.0 - - + -
149B VAL* 3.9 13.4 - - + +
159B TRP* 4.1 13.7 - - + -
183B ALA 3.1 15.0 + - - +
184B SER* 3.1 24.2 - - - +
186B ASN* 1.3 75.1 - - - +
188B ILE* 1.3 57.5 + - - +
190B LYS* 3.2 4.9 + - - +
191B VAL* 3.0 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 4.8 14.6 - - + +
118B LEU* 4.0 15.0 - - + -
121B PHE* 3.5 53.4 - - + -
159B TRP* 4.1 16.8 - - + -
173B LEU* 4.0 5.6 - - + -
184B SER 3.0 15.1 + - - +
187B VAL* 1.3 75.3 - - - +
189B GLY* 1.3 64.8 + - - +
191B VAL* 3.1 10.7 + - + +
192B LEU* 3.0 41.1 + - + +
222B LEU* 3.8 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B LEU* 4.1 14.4 - - - -
185B THR 2.8 20.9 + - - -
186B ASN* 3.6 2.2 - - - -
188B ILE* 1.3 77.5 - - - +
190B LYS* 1.3 56.3 + - - +
192B LEU* 3.4 4.4 + - - +
193B GLU* 3.1 35.5 + - - +
199B VAL* 3.8 10.8 - - - +
201B LEU* 4.7 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ALA* 4.5 5.2 - - + +
145B ALA* 4.1 10.8 - - + -
146B ALA* 3.7 42.2 - - + +
149B VAL* 4.4 6.9 - - + +
150B ASN* 5.6 3.0 - - - +
186B ASN 2.8 19.3 + - - +
187B VAL* 3.5 6.1 - - - +
188B ILE 3.2 0.2 - - - -
189B GLY* 1.3 70.0 - - - +
191B VAL* 1.3 60.7 + - - +
193B GLU* 3.0 20.0 + - + +
194B ASP* 2.8 58.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 3.8 29.6 - - + -
149B VAL* 4.0 18.4 - - + -
156B ILE* 4.2 17.7 - - + -
159B TRP* 4.2 14.8 - - + -
160B THR* 3.8 17.5 - - + -
187B VAL 3.0 19.8 + - - +
188B ILE* 3.1 11.6 + - + +
190B LYS* 1.3 76.3 - - - +
192B LEU* 1.3 56.3 + - - +
194B ASP* 3.3 9.7 + - + +
195B LEU* 3.0 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ALA* 4.7 11.9 - - + +
117B LEU* 3.5 24.7 - - + -
118B LEU* 4.8 4.0 - - + -
171B ILE* 4.6 14.6 - - + -
173B LEU* 4.0 23.8 - - + -
188B ILE* 3.0 34.8 + - + +
189B GLY* 3.6 6.5 - - - +
191B VAL* 1.3 76.4 - - - +
193B GLU* 1.3 56.8 + - - +
195B LEU* 3.1 14.9 + - + +
196B GLY 3.2 0.7 + - - -
197B TYR* 3.0 59.4 + - + +
199B VAL* 3.7 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B GLY 3.1 19.4 + - - +
190B LYS* 3.0 26.8 + - + +
192B LEU* 1.3 71.4 - - - +
194B ASP* 1.3 64.9 + - - +
195B LEU 3.0 4.5 - - - -
196B GLY* 3.1 14.0 + - - -
197B TYR 3.9 11.9 - - - +
199B VAL* 3.6 27.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B VAL* 3.9 16.1 - - - +
150B ASN* 5.0 3.6 + - - +
165B LYS* 4.4 15.2 + - - +
190B LYS* 2.8 48.6 + - - +
191B VAL* 3.3 12.5 + - + +
193B GLU* 1.3 77.5 - - - +
195B LEU* 1.3 61.9 + - + +
196B GLY 3.3 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 4.1 26.2 - - + -
160B THR* 4.7 14.4 - - + -
163B VAL* 3.9 28.7 - - + +
164B GLN 4.0 13.2 - - - +
165B LYS* 3.7 31.3 - - + +
166B VAL* 3.3 24.8 + - - +
191B VAL* 3.0 15.9 + - + +
192B LEU* 3.3 11.9 - - - +
193B GLU 3.0 1.0 - - - -
194B ASP* 1.3 82.4 - - + +
196B GLY* 1.3 55.8 + - - +
197B TYR* 3.6 16.6 - - + -
----------------------------------------------------------
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