Contacts of the helix formed by residues 173 - 188 (chain B) in PDB entry 3BRS
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 ASN 173 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B LYS* 5.2 9.7 - - - +
49B GLU* 5.9 1.3 - - - +
170B CYS* 3.2 18.0 + - - +
171B ASP* 4.3 4.3 - - + +
172B SER* 1.3 76.9 - - - +
174B TYR* 1.3 63.9 + - - +
175B ASP* 3.2 14.3 + - - +
176B LYS* 2.9 38.7 + - + +
177B ALA* 3.1 21.0 + - - +
200B TYR* 4.8 1.3 - - - -
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Residues in contact with TYR 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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16B ASP* 4.8 1.1 - - - -
18B SER* 3.4 26.6 + - - -
172B SER 4.3 0.6 - - - -
173B ASN* 1.3 74.4 - - - +
175B ASP* 1.3 60.3 + - - +
177B ALA* 3.3 4.0 - - - +
178B TYR* 3.0 26.7 + - - +
199B GLN* 3.1 23.7 + - - -
200B TYR* 3.4 53.0 - + - -
203B THR* 3.5 43.7 - - + -
204B GLY* 3.8 4.7 - - - +
207B ARG* 3.9 23.4 + - - +
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Residues in contact with ASP 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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173B ASN* 3.2 11.9 + - - +
174B TYR* 1.3 79.5 - - - +
176B LYS* 1.3 63.2 + - + +
178B TYR* 3.5 7.8 - - - +
179B ASP* 2.9 34.9 + - - +
207B ARG* 5.3 3.8 + - - -
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Residues in contact with LYS 176 (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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77A GLU 5.6 1.0 + - - -
78A LYS* 3.8 22.2 - - - +
81A ASP* 2.8 40.5 + - - +
84A LYS* 6.3 0.9 - - - +
168B TYR* 3.1 34.3 + - - +
169B TYR 4.1 10.4 + - - -
170B CYS* 3.7 24.9 - - - +
171B ASP* 3.8 5.4 + - + -
173B ASN* 2.9 21.5 + - + +
175B ASP* 1.3 77.6 - - + +
177B ALA* 1.4 55.9 + - - +
179B ASP* 4.2 7.0 - - - +
180B GLY 2.8 29.5 + - - -
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Residues in contact with ALA 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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137B ILE* 4.0 7.2 - - - +
170B CYS* 3.4 12.4 - - + +
173B ASN 3.1 10.9 + - - +
174B TYR 3.3 10.1 - - - +
176B LYS* 1.4 73.8 - - - +
178B TYR* 1.3 61.2 + - - +
180B GLY* 4.1 0.2 - - - -
181B THR* 2.8 31.6 + - - -
200B TYR 3.4 24.0 - - - +
201B SER* 3.9 15.7 - - - +
204B GLY* 3.7 10.8 - - - -
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Residues in contact with TYR 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 TYR 3.0 10.9 + - - +
175B ASP* 3.5 11.7 - - - +
177B ALA* 1.3 81.5 - - - +
179B ASP* 1.4 71.4 + - - +
181B THR* 3.3 4.3 + - - -
182B VAL* 3.0 46.5 + - + +
204B GLY* 3.6 12.7 - - - +
207B ARG* 3.9 14.8 - - + +
208B ALA* 3.5 34.6 - - + +
211B ASP* 2.4 40.3 + - + +
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Residues in contact with ASP 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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84A LYS* 4.8 11.3 + - - -
168B TYR* 4.5 6.7 - - + +
175B ASP* 2.9 26.1 + - - +
176B LYS* 3.8 9.4 - - - +
178B TYR* 1.4 84.4 - - - +
180B GLY* 1.3 62.0 + - - +
182B VAL* 3.5 6.3 + - - +
183B GLU* 2.9 28.8 + - - +
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Residues in contact with GLY 180 (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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137B ILE* 3.9 6.1 - - - -
168B TYR* 3.7 31.8 - - - -
176B LYS 2.8 15.1 + - - -
177B ALA 4.1 0.2 - - - -
179B ASP* 1.3 78.8 - - - +
181B THR* 1.3 58.4 + - - +
183B GLU* 3.6 3.3 - - - +
184B LEU* 2.8 35.0 + - - +
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Residues in contact with THR 181 (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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137B ILE* 3.3 20.4 - - - +
177B ALA 2.8 22.4 + - - -
178B TYR 3.4 4.5 - - - -
180B GLY* 1.3 72.8 - - - +
182B VAL* 1.3 60.3 + - - -
184B LEU* 4.5 3.4 - - - -
185B LEU* 2.8 51.1 + - + +
194B MET* 4.6 7.6 - - + -
205B ALA* 3.3 28.0 - - + +
208B ALA* 3.6 20.6 - - + -
209B ILE* 4.5 3.4 - - + -
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Residues in contact with VAL 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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178B TYR* 3.0 38.5 + - + +
179B ASP* 3.7 9.4 - - - +
180B GLY 3.4 0.2 - - - -
181B THR* 1.3 75.7 - - - +
183B GLU* 1.3 59.3 + - - +
185B LEU* 4.3 0.3 - - - +
186B THR* 2.5 43.1 + - - +
208B ALA* 4.1 13.0 - - + -
212B MET* 3.9 25.5 - - + +
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Residues in contact with GLU 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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168B TYR* 3.5 29.4 - - - -
179B ASP 2.9 17.3 + - - +
180B GLY* 3.6 2.6 - - - +
181B THR 3.2 0.4 - - - -
182B VAL* 1.3 80.0 - - - +
184B LEU* 1.3 63.9 + - + +
186B THR* 3.3 4.9 + - - -
187B LYS* 2.8 42.6 + - + +
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Residues in contact with LEU 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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135B GLY* 4.2 2.7 - - - -
136B VAL 3.9 20.9 - - - +
137B ILE* 3.8 26.9 - - + -
166B ALA* 4.1 26.5 - - + +
168B TYR* 4.1 19.5 - - + +
180B GLY 2.8 18.1 + - - +
181B THR* 3.9 3.1 - - - +
183B GLU* 1.3 80.8 - - + +
185B LEU* 1.3 57.0 + - - +
187B LYS* 4.7 0.9 - - - -
188B TYR* 2.8 43.0 + - + +
191B ILE* 3.9 12.4 - - + +
194B MET* 4.0 18.6 - - + -
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Residues in contact with LEU 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 THR* 2.8 31.7 + - + +
184B LEU* 1.3 73.0 - - - +
186B THR* 1.3 60.2 + - - +
188B TYR 3.8 13.8 - - - +
189B PRO* 3.9 7.2 - - + +
191B ILE* 3.5 38.1 - - + +
194B MET* 4.1 10.3 - - + -
209B ILE* 4.0 25.1 - - + -
212B MET* 3.7 23.7 - - + +
214B LEU* 3.7 24.5 - - + +
218B VAL* 4.2 16.6 - - + -
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Residues in contact with THR 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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182B VAL* 2.5 32.7 + - - +
183B GLU* 3.7 4.9 - - - -
185B LEU* 1.3 78.2 - - - +
187B LYS* 1.3 64.1 + - - +
188B TYR 3.6 0.2 + - - -
189B PRO* 3.9 8.1 - - - +
212B MET* 4.0 9.4 - - - +
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Residues in contact with LYS 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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183B GLU* 2.8 29.8 + - + +
184B LEU* 4.7 0.4 - - - -
186B THR* 1.3 77.2 - - - +
188B TYR* 1.3 101.4 + - + +
189B PRO* 3.2 8.4 - - - +
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Residues in contact with TYR 188 (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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165B GLU* 3.1 41.6 + - + -
166B ALA* 3.7 22.7 - - + +
184B LEU* 2.8 25.7 + - + +
185B LEU* 3.8 8.7 - - - +
187B LYS* 1.3 116.1 - - + +
189B PRO* 1.4 65.2 - - - +
190B ASP* 3.2 13.0 - - - +
191B ILE* 3.1 37.0 + - + +
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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
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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