Contacts of the helix formed by residues 180 - 192 (chain B) in PDB entry 2FBW
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 GLY 180 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165B SER* 3.9 2.0 - - - -
171B TYR* 3.7 15.7 - - - -
178B TYR* 3.2 17.9 - - - -
179B LEU* 1.3 80.1 - - - +
181B PRO* 1.3 77.5 - - - +
182B ALA 3.3 2.8 + - - -
183B VAL 3.3 0.9 + - - -
184B LEU* 3.0 27.7 + - - +
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Residues in contact with PRO 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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164B CYS* 3.6 9.9 - - - +
165B SER* 3.4 36.6 - - - +
168B CYS* 4.3 9.2 - - + -
171B TYR* 5.0 0.4 - - + -
178B TYR* 4.1 14.4 - - + +
180B GLY* 1.3 83.5 - - - +
182B ALA* 1.3 61.3 + - - +
184B LEU* 4.1 0.2 - - - +
185B MET* 2.9 27.4 + - - +
221B CYS* 3.7 27.4 - - + -
231B PRO* 3.8 15.6 - - + +
235B ILE* 3.9 17.2 - - + +
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Residues in contact with ALA 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B PHE* 3.7 25.6 - - + -
158B CYS* 4.8 17.3 - - - -
160B LEU* 4.9 4.0 - - + -
162B ALA* 5.2 1.8 - - - +
164B CYS* 3.6 17.8 - - - -
165B SER* 3.3 16.9 + - - +
180B GLY 3.3 0.2 + - - -
181B PRO* 1.3 78.8 - - - +
183B VAL* 1.3 65.0 + - + +
185B MET* 4.0 4.6 - - - +
186B GLN* 3.2 26.4 + - - +
231B PRO* 5.4 0.9 - - - -
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Residues in contact with VAL 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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118B PHE* 4.2 17.5 - - + +
121B GLN* 3.7 15.9 - - + +
122B TYR* 3.6 33.2 - - + +
125B ILE* 3.6 32.8 - - + +
160B LEU* 5.8 0.7 - - + -
165B SER* 4.8 0.4 + - - -
179B LEU* 3.7 32.5 - - + +
180B GLY 3.3 2.6 + - - -
182B ALA* 1.3 76.0 - - + +
184B LEU* 1.3 60.6 + - - +
186B GLN* 3.1 8.0 + - - +
187B ALA* 2.8 25.5 + - - +
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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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178B TYR* 3.7 30.1 - - + -
179B LEU* 4.0 20.2 - - + -
180B GLY 3.0 18.9 + - - +
181B PRO 4.1 0.7 - - - +
183B VAL* 1.3 76.9 - - - +
185B MET* 1.3 57.3 + - - +
187B ALA* 3.1 9.0 + - + +
188B TYR 2.9 23.0 + - - -
206B LEU* 4.2 24.2 - - + -
211B SER 3.8 16.2 - - - +
212B LEU* 3.9 22.9 - - + +
235B ILE* 4.0 25.1 - - + -
238B ILE* 3.4 13.6 - - + +
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Residues in contact with MET 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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154B GLY 4.0 8.5 - - - +
155B LEU* 3.7 25.9 - - + +
158B CYS* 4.2 20.6 - - + -
181B PRO 2.9 18.6 + - - +
182B ALA* 4.0 4.5 - - - +
184B LEU* 1.3 76.8 - - - +
186B GLN* 1.3 61.5 + - - +
188B TYR* 3.1 3.9 + - - +
189B ARG* 2.9 25.3 + - - +
229B LEU* 4.0 30.5 - - + -
230B ASN 4.2 5.8 - - - +
231B PRO* 3.7 33.7 - - + +
234B ALA* 3.7 23.1 - - + -
235B ILE* 5.1 0.6 - - - +
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Residues in contact with GLN 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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122B TYR* 3.9 35.8 + - + -
125B ILE* 4.1 5.2 - - + -
155B LEU 3.0 28.5 + - - +
156B TYR* 4.9 3.1 - - - +
158B CYS* 3.6 19.2 - - - +
160B LEU* 4.6 10.1 - - + -
182B ALA 3.2 14.0 + - - +
183B VAL 3.1 9.4 + - - +
185B MET* 1.3 81.9 + - - +
187B ALA* 1.3 65.0 - - - +
189B ARG* 3.1 32.8 + - - +
190B TRP* 3.1 22.2 + - + -
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Residues in contact with ALA 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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125B ILE* 3.7 27.2 - - + +
183B VAL 2.8 13.2 + - - +
184B LEU* 3.1 18.4 + - + +
186B GLN* 1.3 76.2 - - - +
188B TYR* 1.3 61.1 + - - +
190B TRP* 3.2 6.2 + - - +
191B MET* 3.0 42.1 + - + +
202B ARG* 4.7 5.5 - - + +
205B GLN* 6.1 0.2 - - - +
206B LEU* 5.3 4.0 - - + -
238B ILE* 4.7 1.6 - - + -
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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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155B LEU* 3.7 30.1 - - + -
184B LEU 2.9 12.0 + - - +
185B MET* 3.1 11.2 + - - +
187B ALA* 1.3 76.5 - - - +
189B ARG* 1.3 61.7 + - - +
191B MET* 3.0 19.5 + - - +
192B ILE* 3.0 52.8 + - + +
234B ALA* 4.0 15.7 - - + +
237B GLU* 3.4 38.2 + - + +
238B ILE* 3.8 23.7 - - + +
241B MET* 3.8 18.6 - - - -
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Residues in contact with ARG 189 (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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114A GLY 3.2 25.3 + - - -
116A PRO* 4.0 21.5 - - - +
160A THR* 5.8 0.4 + - - -
152B LEU* 3.6 17.6 - - + +
155B LEU* 3.9 33.7 - - + -
156B TYR* 4.5 14.7 - - + +
185B MET 2.9 12.9 + - - +
186B GLN* 3.1 27.2 + - - +
188B TYR* 1.3 76.8 - - - +
190B TRP* 1.3 101.9 + - - +
192B ILE 3.9 0.2 + - - -
193B ASP* 2.7 40.5 + - - +
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Residues in contact with TRP 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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113A TYR 4.2 7.4 - - - -
114A GLY* 4.1 9.6 - - - -
160A THR* 5.8 6.7 - - + -
122B TYR* 5.1 1.2 + - - -
125B ILE* 4.9 2.0 - - + -
126B GLU 4.7 0.4 - - - -
127B PRO* 3.4 48.2 + - + +
128B TYR* 3.8 12.1 - - - -
129B LEU* 3.4 36.6 - - + -
186B GLN* 3.1 29.4 + - - -
187B ALA 4.0 4.0 - - - +
188B TYR 3.2 0.2 - - - -
189B ARG* 1.3 124.1 - - - +
191B MET* 1.3 65.4 + - - +
192B ILE 3.5 0.2 + - - -
193B ASP* 3.5 16.5 + - + -
196B ASP* 3.5 28.1 - - - +
202B ARG* 3.5 28.7 - - - +
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Residues in contact with MET 191 (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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187B ALA* 3.0 32.1 + - + +
188B TYR* 3.0 16.7 + - - +
190B TRP* 1.3 78.3 - - - +
192B ILE* 1.3 63.0 + - + +
193B ASP 3.6 3.6 + - - +
196B ASP 5.5 0.2 - - - +
199B THR* 3.3 38.9 + - + +
202B ARG* 3.9 33.6 - - + +
203B LEU* 3.7 31.0 - - + -
206B LEU* 3.9 23.3 - - + -
238B ILE* 4.1 15.0 - - + -
241B MET* 4.3 13.1 - - + +
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Residues in contact with ILE 192 (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 ASP 5.1 1.7 - - - +
151B LYS* 3.2 51.3 - - + +
152B LEU* 4.2 6.6 - - + +
155B LEU* 3.3 22.4 - - + -
188B TYR* 3.0 54.2 + - + +
189B ARG 4.1 3.6 - - - +
191B MET* 1.3 78.1 - - + +
193B ASP* 1.3 66.3 + - - +
194B SER* 3.2 5.2 + - - -
241B MET* 4.6 7.9 - - + -
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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