Contacts of the helix formed by residues 178 - 195 (chain B) in PDB entry 2PKG
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 THR 178 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B PHE* 4.1 12.1 - - + +
144B ARG* 3.4 10.9 + - - -
176B ASP* 2.8 25.1 + - - +
177B ASP* 1.3 80.1 - - - +
179B PRO* 1.3 66.5 - - + +
180B MET* 3.0 48.7 - - + -
181B VAL* 3.5 6.9 + - - -
182B ARG* 3.2 17.8 + - - +
134D VAL* 5.1 2.6 - - + +
147D TRP* 3.6 15.7 - - + -
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Residues in contact with PRO 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ASP 3.7 1.8 - - - +
178B THR* 1.3 90.3 - - + +
180B MET* 1.3 72.9 + - + +
182B ARG* 2.8 30.3 + - + +
183B ARG* 2.6 34.9 + - + +
217B GLN* 3.1 26.5 - - - +
220B VAL* 4.8 3.1 - - + -
147D TRP* 3.4 41.1 - - + +
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Residues in contact with MET 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B PHE* 3.7 37.9 - - + -
145B THR* 4.6 6.7 - - + +
178B THR* 3.0 35.9 - - + -
179B PRO* 1.3 87.6 - - + +
181B VAL* 1.3 50.9 + - - +
183B ARG* 2.9 19.6 + - - +
184B ALA* 2.7 32.5 + - - +
134D VAL* 5.5 1.8 - - - -
146D MET* 4.0 26.9 - - + +
147D TRP* 3.4 39.7 - - + +
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Residues in contact with VAL 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B PHE* 3.9 15.3 - - + +
144B ARG* 3.8 21.1 - - + +
145B THR* 4.1 5.3 + - - +
148B CYS* 4.4 4.3 - - - -
173B LEU* 3.5 29.4 - - + +
176B ASP* 3.3 47.3 - - + +
178B THR* 3.5 9.6 + - - +
179B PRO 3.2 0.6 - - - -
180B MET* 1.3 76.4 - - - +
182B ARG* 1.3 52.5 + - - +
184B ALA* 3.0 7.9 + - - +
185B ALA* 2.7 33.1 + - - +
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Residues in contact with ARG 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B LEU 4.1 4.5 - - - -
174B CYS 3.5 23.8 - - - +
175B SER* 4.5 2.7 - - - +
176B ASP 2.5 45.8 + - - +
177B ASP* 3.3 9.1 + - - +
178B THR 3.2 14.7 + - - +
179B PRO* 2.8 39.2 + - + +
181B VAL* 1.3 73.7 - - - +
183B ARG* 1.3 60.2 + - - +
185B ALA* 3.0 4.6 + - - +
186B ALA* 2.7 30.3 + - - +
212B LEU* 4.3 5.9 - - + +
215B ASP* 2.4 37.7 + - - -
216B GLU* 5.5 5.5 + - - +
217B GLN* 4.4 6.7 + - - +
220B VAL* 4.1 11.8 - - + +
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Residues in contact with ARG 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B PRO* 2.6 25.9 + - - +
180B MET* 3.4 30.3 - - - +
182B ARG* 1.3 71.6 - - - +
184B ALA* 1.3 62.4 + - - +
186B ALA* 3.2 7.9 - - - +
187B SER* 3.0 23.6 + - - -
217B GLN* 3.8 4.0 + - - -
219B SER* 3.6 28.0 + - - +
220B VAL* 3.5 17.9 - - + -
223B LEU* 3.6 17.1 - - + +
146D MET* 2.8 24.4 + - - +
147D TRP 3.2 21.0 + - - -
148D PHE 3.5 4.6 - - - -
149D GLY* 3.4 22.0 - - - +
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Residues in contact with ALA 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B THR* 3.7 27.4 - - + +
148B CYS* 3.7 20.0 - - + -
180B MET 2.7 11.7 + - - +
181B VAL* 3.0 11.2 + - - +
183B ARG* 1.3 74.9 - - - +
185B ALA* 1.3 67.9 + - - +
187B SER* 3.0 20.0 + - - -
188B LYS* 3.2 14.7 + - - +
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Residues in contact with ALA 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B CYS* 3.7 14.1 - - - -
170B PHE* 3.4 17.0 - - + -
173B LEU* 3.9 5.4 - - + +
174B CYS* 3.7 40.4 - - - +
181B VAL 2.7 18.3 + - - +
182B ARG 3.6 3.4 - - - +
184B ALA* 1.3 72.9 - - - +
186B ALA* 1.3 58.8 + - - +
188B LYS 3.3 0.3 + - - -
189B LEU* 2.8 28.3 + - - +
212B LEU* 4.7 1.8 - - + -
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Residues in contact with ALA 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ARG 2.7 12.9 + - - +
183B ARG* 3.2 13.5 - - - +
184B ALA 3.0 0.2 - - - -
185B ALA* 1.3 76.5 - - - +
187B SER* 1.3 56.2 + - - +
188B LYS 2.7 1.2 + - - -
189B LEU* 2.6 33.2 + - - +
190B GLY 3.9 1.6 + - - -
212B LEU* 3.9 23.9 - - + +
220B VAL* 4.7 5.8 - - + +
223B LEU* 3.6 28.3 - - + -
224B ALA* 4.9 1.8 - - - +
227B ALA* 5.0 4.2 - - - +
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Residues in contact with SER 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B ARG 3.0 9.4 + - - -
184B ALA* 3.0 15.4 + - - -
186B ALA* 1.3 77.3 - - - +
188B LYS* 1.3 76.9 + - - +
190B GLY* 4.5 4.0 + - - -
191B GLU* 5.2 2.9 + - - +
223B LEU* 4.3 17.2 - - - +
226B GLU* 5.9 6.7 - - - +
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Residues in contact with LYS 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ARG* 4.8 10.1 - - - +
148B CYS* 3.3 31.9 - - + +
149B GLY* 4.1 15.0 - - - +
152B SER* 6.1 0.2 - - - -
170B PHE* 4.2 8.7 - - + -
184B ALA* 3.2 16.0 + - + +
185B ALA 3.6 3.6 - - - +
186B ALA 2.7 2.6 + - - -
187B SER* 1.3 92.4 + - - +
189B LEU* 1.3 65.9 + - - +
190B GLY 3.2 2.9 + - - -
191B GLU* 3.3 32.8 + - + +
192B PHE* 3.2 22.7 + - - +
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Residues in contact with LEU 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B PHE* 3.4 28.7 - - + -
174B CYS* 4.5 0.2 - - - -
185B ALA 2.8 9.4 + - - +
186B ALA* 2.6 23.7 + - - +
188B LYS* 1.3 71.1 - - - +
190B GLY* 1.3 64.2 + - - +
192B PHE* 3.4 1.4 + - - +
193B ALA* 3.2 18.9 + - - +
205B ILE* 4.5 17.4 - - + +
208B MET* 4.2 20.2 - - + -
209B PHE* 3.6 38.6 - - + -
212B LEU* 3.7 17.5 - - + -
224B ALA* 6.0 1.1 - - - -
227B ALA* 4.2 15.5 - - + -
231B ILE* 4.4 2.2 - - + -
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Residues in contact with GLY 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B ALA 3.9 2.4 + - - -
187B SER 4.5 3.7 + - - -
188B LYS 3.2 1.0 - - - -
189B LEU* 1.3 81.9 - - - +
191B GLU* 1.3 60.7 + - - +
193B ALA* 3.1 17.7 + - - +
194B LYS* 3.4 9.2 + - - +
226B GLU* 6.4 0.2 - - - -
227B ALA* 4.1 14.4 - - - +
230B ASN* 4.2 29.6 - - - +
231B ILE* 5.2 1.6 - - - -
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Residues in contact with GLU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ARG* 3.0 32.9 + - - -
149B GLY 4.7 1.0 - - - +
152B SER* 3.7 22.9 + - - +
187B SER 5.2 1.9 + - - +
188B LYS* 3.3 39.6 + - + +
190B GLY* 1.3 74.1 - - - +
192B PHE* 1.3 65.3 + - - +
193B ALA 3.1 0.7 + - - -
194B LYS* 3.2 29.5 + - + +
195B VAL* 3.7 10.4 + - - +
230B ASN* 4.9 2.4 - - - +
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Residues in contact with PHE 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B PHE* 3.9 24.5 - + + -
152B SER* 4.0 13.0 - - - +
155B TYR* 3.7 26.0 - + + -
166B LEU 4.8 0.9 - - - -
167B ARG* 4.1 21.3 - - + -
170B PHE* 3.9 44.2 - + + -
188B LYS* 3.2 17.9 + - + +
189B LEU 3.9 2.9 - - - +
190B GLY 3.3 0.2 - - - -
191B GLU* 1.3 79.0 - - - +
193B ALA* 1.3 58.4 + - - +
195B VAL* 2.8 32.2 - - + +
196B LEU* 3.3 37.7 - - + +
205B ILE* 4.1 14.4 - - + -
208B MET* 4.8 2.7 - - + -
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Residues in contact with ALA 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B LEU 3.2 11.6 + - - +
190B GLY 3.1 11.1 + - - +
191B GLU 3.1 0.2 - - - -
192B PHE* 1.3 73.9 - - - +
194B LYS* 1.3 55.4 + - - +
195B VAL 2.7 16.6 + - - -
196B LEU* 2.8 21.0 + - - +
201B VAL* 3.8 9.3 - - + +
205B ILE* 4.1 34.5 - - + -
231B ILE* 4.6 8.5 - - + -
234B LEU* 3.9 17.6 - - + +
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Residues in contact with LYS 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B GLY 3.4 7.6 + - - +
191B GLU* 3.2 21.5 + - + +
193B ALA* 1.3 77.5 - - - +
195B VAL* 1.3 61.2 + - + +
196B LEU 4.4 3.3 - - - +
230B ASN* 3.7 32.4 - - + +
233B GLN* 4.6 12.3 + - - -
234B LEU* 3.9 29.4 - - + +
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Residues in contact with VAL 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B SER* 3.8 16.4 - - - +
155B TYR* 3.6 27.6 - - + -
156B PRO* 3.8 26.9 - - + +
191B GLU 3.9 9.2 - - - +
192B PHE* 2.8 36.1 - - + +
193B ALA 2.7 6.9 + - - -
194B LYS* 1.3 78.8 - - + +
196B LEU* 1.3 64.0 + - + +
197B GLU* 4.4 4.3 - - - +
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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) + - + + + + + -
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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