Contacts of the helix formed by residues 169 - 187 (chain B) in PDB entry 4BLV
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 MET 169 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B GLU* 1.3 92.1 - - + +
170B LYS* 1.3 67.7 + - + +
171B THR* 3.2 5.8 - - + +
172B ASP* 3.0 22.2 + - - +
173B TYR* 3.7 10.6 - - - -
1282B PEG 3.3 33.7 - - - +
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Residues in contact with LYS 170 (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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169B MET* 1.3 74.7 - - + +
171B THR* 1.3 65.2 + - + +
172B ASP 3.2 0.9 + - - -
173B TYR* 3.2 18.5 + - - +
174B GLN* 3.7 11.7 - - - +
200B LEU* 6.3 0.4 - - - +
203B GLN* 3.0 44.1 - - - +
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Residues in contact with THR 171 (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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169B MET* 4.3 2.8 - - + +
170B LYS* 1.3 78.7 - - + +
172B ASP* 1.3 64.2 + - - +
173B TYR 3.3 0.2 - - - -
174B GLN* 3.2 23.9 + - - +
175B ALA* 3.0 23.2 + - - +
1282B PEG 3.6 26.9 + - - -
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Residues in contact with ASP 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B PRO* 3.3 17.6 - - - +
167B TYR* 3.7 7.6 - - - -
168B GLU* 2.9 27.9 + - - +
169B MET 3.0 21.9 + - - +
171B THR* 1.3 78.2 + - - +
173B TYR* 1.3 60.2 + - - +
174B GLN 3.3 0.7 + - - -
175B ALA* 3.4 0.7 + - - -
176B VAL* 3.4 12.7 + - - +
1282B PEG 3.1 41.1 + - - +
1286B EDO 3.0 40.9 + - - +
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Residues in contact with TYR 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B TYR* 3.4 59.4 + + + +
168B GLU 5.6 0.2 - - - -
169B MET 3.7 14.8 - - - -
170B LYS 3.2 9.1 + - - +
172B ASP* 1.3 77.6 - - + +
174B GLN* 1.3 60.9 + - + +
176B VAL* 3.8 7.1 - - - +
177B VAL* 3.8 18.2 - - - +
197B PRO* 4.4 11.8 + - - +
199B VAL* 5.1 11.3 + - - +
200B LEU 5.5 1.2 + - - -
203B GLN* 3.6 49.6 - - + +
204B ILE* 3.6 22.9 - - + +
207B MET* 3.8 21.7 - - + +
210B ASP* 5.7 0.2 - - - +
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Residues in contact with GLN 174 (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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170B LYS* 3.7 13.5 - - - +
171B THR* 3.2 29.4 + - - +
172B ASP 3.2 0.6 - - - -
173B TYR* 1.3 77.9 - - + +
175B ALA* 1.3 65.9 + - - +
176B VAL 3.1 1.6 - - - -
177B VAL* 3.1 8.3 + - - +
178B SER* 3.1 27.8 + - - +
206B ARG* 6.0 6.1 - - - +
210B ASP* 5.3 11.9 + - - +
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Residues in contact with ALA 175 (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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145B PHE* 3.9 13.5 - - + -
171B THR 3.0 15.8 + - - +
172B ASP 3.4 4.2 + - - +
174B GLN* 1.3 76.0 - - - +
176B VAL* 1.3 57.0 - - - +
178B SER* 3.8 6.1 - - - -
179B GLY* 2.8 28.2 + - - -
1286B EDO 3.7 24.9 - - - +
1293B EDO 4.2 2.2 + - - -
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Residues in contact with VAL 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B PHE* 3.9 13.1 - - + -
163B ILE* 5.3 1.1 - - + -
165B PRO* 3.7 29.6 - - + -
167B TYR* 3.8 12.1 - - + +
172B ASP 3.4 12.9 + - - +
173B TYR 3.8 8.5 - - - +
174B GLN 3.1 0.8 - - - -
175B ALA* 1.3 77.5 - - - +
177B VAL* 1.3 59.4 + - + +
179B GLY* 3.3 1.2 + - - -
180B ILE* 3.0 36.3 + - + +
194B LEU* 3.5 37.0 - - + -
207B MET* 4.3 8.7 - - - -
1286B EDO 3.8 5.4 - - - +
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Residues in contact with VAL 177 (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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173B TYR 3.8 15.3 - - - +
174B GLN* 3.1 8.3 + - - +
176B VAL* 1.3 78.6 - - + +
178B SER* 1.3 64.2 + - - +
180B ILE* 3.4 5.9 + - - +
181B ALA* 3.0 23.4 + - - +
207B MET* 3.8 30.7 - - + +
210B ASP* 3.8 35.4 - - + +
211B LEU* 3.9 14.1 - - + +
214B THR* 3.8 16.5 - - + +
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Residues in contact with SER 178 (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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174B GLN* 3.1 18.9 + - - +
175B ALA* 3.9 5.8 - - - -
177B VAL* 1.3 77.4 - - - +
179B GLY* 1.3 63.5 + - - +
181B ALA* 3.4 6.6 + - - +
182B GLU* 3.1 24.2 + - - +
1293B EDO 3.0 14.3 + - - -
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Residues in contact with GLY 179 (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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145B PHE* 4.1 4.7 - - - -
148B LEU* 3.2 21.2 - - - +
175B ALA 2.8 16.7 + - - -
176B VAL 3.7 1.3 - - - -
177B VAL 3.2 0.2 - - - -
178B SER* 1.3 74.5 - - - +
180B ILE* 1.3 63.0 + - - +
182B GLU* 3.2 4.2 + - - +
183B GLY 3.0 18.7 + - - -
1293B EDO 2.9 22.6 + - - -
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Residues in contact with ILE 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B PHE* 5.4 0.2 - - - -
148B LEU* 4.2 4.0 - - - +
163B ILE* 3.7 23.1 - - + -
176B VAL* 3.0 34.5 + - + +
177B VAL* 3.8 4.7 - - - +
179B GLY* 1.3 74.2 - - - +
181B ALA* 1.3 53.8 + - - +
183B GLY* 3.2 1.8 + - - -
184B TYR* 2.8 34.4 + - + +
192B TYR* 4.8 13.7 - - + -
194B LEU* 4.1 23.8 - - + -
211B LEU* 4.3 20.0 - - + -
216B ILE* 4.1 12.3 - - + -
241B ILE* 5.9 0.9 - - + -
243B ILE* 3.6 30.5 - - + -
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Residues in contact with ALA 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B VAL 3.0 17.1 + - - +
178B SER* 3.6 7.6 - - - +
179B GLY 3.2 0.2 - - - -
180B ILE* 1.3 79.9 - - - +
182B GLU* 1.3 62.4 + - + +
184B TYR* 3.9 5.2 - - - +
185B LYS* 3.0 25.2 + - - +
214B THR* 4.4 6.3 - - + -
216B ILE* 4.7 3.8 - - - -
1294B EDO 3.5 41.8 - - - +
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Residues in contact with GLU 182 (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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148B LEU* 4.4 1.3 - - + -
149B LYS* 3.6 24.0 + - + -
178B SER* 3.1 20.6 + - - +
179B GLY 3.2 2.9 + - - +
181B ALA* 1.3 77.5 - - + +
183B GLY* 1.3 65.4 - - - +
185B LYS* 3.4 20.7 + - - +
186B ARG* 2.9 52.1 + - - +
1293B EDO 3.3 32.7 - - - +
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Residues in contact with GLY 183 (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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148B LEU* 3.7 10.7 + - - +
152B LEU* 3.6 22.8 - - - +
179B GLY 3.0 14.0 + - - -
180B ILE 3.6 2.9 - - - -
182B GLU* 1.3 77.1 - - - +
184B TYR* 1.3 56.3 + - - +
186B ARG* 2.9 8.0 + - - +
187B PHE 2.9 23.6 + - - -
192B TYR* 3.1 14.5 + - - -
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Residues in contact with TYR 184 (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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180B ILE* 2.8 20.8 + - + +
181B ALA* 3.9 3.6 - - - +
183B GLY* 1.3 68.2 - - - +
185B LYS* 1.3 68.7 + - - +
186B ARG 3.2 0.3 + - - -
187B PHE 3.9 0.4 - - - -
188B ALA* 3.1 67.8 + - + +
192B TYR* 3.5 22.2 + + + -
216B ILE* 3.7 41.5 - - + -
217B ARG* 4.5 13.2 + - - +
243B ILE* 4.0 15.3 - - + -
244B ASN* 3.9 12.6 + - - -
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Residues in contact with LYS 185 (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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181B ALA 3.0 16.0 + - - +
182B GLU* 3.4 23.5 + - - +
184B TYR* 1.3 80.2 - - - +
186B ARG* 1.3 89.3 + - + +
188B ALA* 5.1 1.9 + - - +
1294B EDO 6.0 2.9 - - - -
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Residues in contact with ARG 186 (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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148B LEU 3.5 20.4 - - - -
149B LYS* 3.5 45.1 + - - +
152B LEU* 3.7 20.9 - - + +
153B PRO* 3.4 23.9 - - + +
182B GLU* 2.9 45.8 + - - +
183B GLY 2.9 7.4 + - - +
185B LYS* 1.3 96.1 - - + +
187B PHE* 1.3 58.6 + - - +
188B ALA 4.1 0.4 - - - -
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Residues in contact with PHE 187 (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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152B LEU* 4.0 14.1 - - + -
153B PRO* 3.6 23.6 - - + -
154B PRO* 3.6 22.7 - - + -
157B ARG* 3.6 37.7 - - + -
158B ARG* 3.7 7.2 - - - -
159B GLY* 4.1 10.1 - - - -
161B ILE* 4.1 9.2 - - + -
183B GLY 2.9 5.0 + - - +
184B TYR 3.4 2.7 - - - +
186B ARG* 1.3 80.1 - - - +
188B ALA* 1.3 65.0 + - - +
189B THR* 3.2 21.5 - - - -
190B GLY* 3.3 33.3 + - - -
192B TYR* 2.7 35.1 + - - +
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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
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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