Contacts of the helix formed by residues 166 - 181 (chain A) in PDB entry 2BEW
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 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A PRO* 3.0 29.9 + - + +
164A LEU 3.1 4.2 - - - +
165A ALA* 1.3 77.1 - - - +
167A GLN* 1.3 60.0 + - - +
168A ILE 3.3 0.9 + - - -
169A PRO* 3.5 3.3 - - - +
170A GLN* 3.3 14.3 + - - +
200A ASP* 3.6 9.9 - - - +
601A THW 6.4 0.2 - - + -
1401A K 3.1 9.7 - - - -
108B ASP* 3.5 24.9 - - - +
109B GLN* 3.0 27.0 + - - +
113B GLU* 3.2 31.1 + - + -
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Residues in contact with GLN 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A PHE* 3.9 22.4 - - + -
111A GLY 3.3 25.3 + - - +
112A GLN* 4.2 7.7 + - - +
165A ALA* 3.4 12.2 + - - +
166A THR* 1.3 83.6 + - - +
168A ILE* 1.3 63.9 + - - +
169A PRO 3.6 0.2 - - - -
170A GLN* 3.6 13.2 - - - +
171A ALA* 2.8 30.8 + - - +
189A CYS* 4.0 11.2 - - - -
190A TYR 3.1 22.0 + - - -
191A PHE* 3.9 14.5 - - - +
1401A K 2.8 22.5 - - - -
113B GLU* 5.5 0.9 - - - +
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Residues in contact with ILE 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A ALA* 3.0 34.9 + - + +
167A GLN* 1.3 83.1 - - - +
169A PRO* 1.3 69.3 - - + +
171A ALA* 3.2 3.1 + - - +
172A VAL* 3.2 21.7 + - - +
189A CYS* 3.7 17.5 - - - -
191A PHE* 3.8 31.2 - - + -
195A ALA 5.0 1.3 - - - +
200A ASP 4.0 4.5 - - - +
201A ALA* 3.9 22.4 - - + -
204A GLY* 4.0 12.6 - - - -
205A PHE* 4.4 4.5 - - + -
217A PHE* 3.7 28.8 - - + -
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Residues in contact with PRO 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A ALA 3.5 5.8 - - - +
166A THR 3.5 4.9 - - - +
168A ILE* 1.3 96.9 - - + +
170A GLN* 1.3 60.7 + - - +
172A VAL* 3.2 5.9 + - + +
173A GLY 3.1 16.8 + - - -
200A ASP* 3.5 23.6 - - + +
203A ALA* 4.7 1.6 - - + -
204A GLY* 4.0 18.8 - - - +
207A PHE* 6.1 2.0 - - + -
77B GLN 4.4 2.9 - - - +
78B GLY* 4.2 12.1 - - - +
81B GLY* 3.8 7.2 - - - -
82B PHE* 3.4 22.1 - - + +
109B GLN* 3.6 23.3 - - - +
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Residues in contact with GLN 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A PHE* 4.0 11.8 - - + -
166A THR 3.3 15.3 + - - +
167A GLN* 3.5 14.3 + - - +
168A ILE 3.2 0.8 - - - -
169A PRO* 1.3 75.3 - - - +
171A ALA* 1.3 66.0 + - - +
173A GLY 3.1 1.9 + - - -
174A ALA* 3.0 19.8 + - - +
81B GLY 3.2 20.2 - - - +
84B ILE* 3.8 16.8 - - + +
85B GLY* 3.2 14.1 - - - -
109B GLN* 3.0 23.5 + - - +
113B GLU* 2.9 33.3 + - - +
117B TYR* 2.8 24.5 + - - +
120B ARG* 4.7 0.3 + - - -
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Residues in contact with ALA 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A PHE* 3.6 30.2 - - + -
167A GLN 2.8 22.5 + - - +
168A ILE 3.2 5.4 + - - +
170A GLN* 1.3 73.3 - - - +
172A VAL* 1.3 57.6 + - - +
174A ALA* 3.3 1.0 + - - +
175A ALA* 2.9 28.2 + - - +
187A VAL* 3.7 8.6 - - + +
189A CYS* 3.7 15.5 - - + -
215A ILE* 3.7 16.4 - - + -
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Residues in contact with VAL 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ILE 3.2 14.5 + - - +
169A PRO* 3.4 8.1 - - + +
170A GLN 3.1 0.4 - - - -
171A ALA* 1.3 77.5 - - - +
173A GLY* 1.3 57.2 + - - +
175A ALA* 3.2 6.1 + - - +
176A TYR* 2.9 25.8 + - - +
204A GLY* 3.4 26.5 - - - +
207A PHE* 4.0 6.7 - - + -
208A ALA* 3.7 28.7 - - + +
213A CYS* 3.8 12.2 - - - -
215A ILE* 3.9 8.5 - - + -
217A PHE* 3.7 18.8 - - + -
82B PHE* 3.9 13.2 - - + -
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Residues in contact with GLY 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A PRO 3.1 11.5 + - - -
170A GLN 3.1 1.3 + - - -
172A VAL* 1.3 77.7 - - - +
174A ALA* 1.3 61.9 + - - +
176A TYR* 3.3 1.0 + - - +
177A ALA* 3.0 19.6 + - - +
82B PHE* 3.4 39.8 - - - -
86B ILE* 3.3 19.1 - - - +
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Residues in contact with ALA 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A LEU* 3.9 10.7 - - + +
110A PHE* 3.8 23.6 - - + -
170A GLN 3.0 11.6 + - - +
171A ALA 3.3 7.6 + - - +
173A GLY* 1.3 75.7 - - - +
175A ALA* 1.3 57.8 + - - +
177A ALA* 3.3 3.3 + - - +
178A ALA* 2.9 27.9 + - - +
185A ARG* 6.0 0.2 + - - -
187A VAL* 4.0 4.6 - - + +
85B GLY 3.5 18.7 - - - +
88B VAL* 5.4 0.4 - - + -
89B THR* 3.7 18.0 - - + +
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Residues in contact with ALA 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A ALA 2.9 13.8 + - - +
172A VAL 3.2 8.7 + - - +
174A ALA* 1.3 75.4 - - - +
176A TYR* 1.3 64.4 + - - +
178A ALA* 3.2 4.5 + - - +
179A LYS 2.9 18.5 + - - -
187A VAL* 3.6 13.4 - - + +
213A CYS* 3.9 15.0 - - + -
214A PRO* 3.5 36.8 - - - +
215A ILE* 4.0 9.0 - - + -
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Residues in contact with TYR 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A VAL 2.9 6.8 + - - +
173A GLY 3.3 7.8 + - - +
175A ALA* 1.3 75.4 - - - +
177A ALA* 1.3 64.2 + - - +
179A LYS* 3.2 24.3 + - - +
180A ARG* 3.0 40.7 + - + +
211A LEU* 3.8 37.0 - - + -
213A CYS* 3.9 12.7 - - - -
42B VAL* 4.8 3.1 - - + -
66B LYS 4.6 0.2 + - - -
67B ASP* 2.6 38.1 + - + +
70B PHE* 3.5 30.5 - + - -
82B PHE* 3.7 28.5 - + + -
86B ILE* 4.5 8.7 - - + -
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Residues in contact with ALA 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A GLY 3.0 13.7 + - - +
174A ALA 3.6 8.1 - - - +
176A TYR* 1.3 79.4 - - - +
178A ALA* 1.3 58.6 + - - +
180A ARG* 3.2 9.3 + - - +
181A ALA* 2.9 29.8 + - - +
86B ILE* 4.4 14.1 - - + -
89B THR* 3.4 29.8 - - + +
91B ALA* 4.7 5.8 - - + -
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Residues in contact with ALA 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A ALA 2.9 17.1 + - - +
175A ALA* 3.2 9.2 + - - +
177A ALA* 1.3 78.3 - - - +
179A LYS* 1.3 61.5 + - - +
181A ALA* 3.2 7.1 + - - +
183A ALA* 3.1 43.4 + - + +
185A ARG* 4.4 30.1 - - + +
187A VAL* 5.3 3.6 - - + -
214A PRO* 5.0 1.3 - - + -
89B THR* 5.3 1.0 - - + +
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Residues in contact with LYS 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ALA 2.9 13.1 + - - +
176A TYR* 3.2 32.1 + - - +
178A ALA* 1.3 77.6 - - - +
180A ARG* 1.3 65.1 + - - +
182A ASN* 3.1 21.0 + - - +
211A LEU 2.8 27.2 + - - -
212A GLU* 2.9 32.5 + - - +
214A PRO* 4.1 5.7 - - + +
276A ASN* 3.6 34.5 - - + +
67B ASP* 6.4 0.9 - - - -
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Residues in contact with ARG 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A TYR* 3.0 35.2 + - + +
177A ALA* 3.2 9.8 + - - +
179A LYS* 1.3 80.8 - - + +
181A ALA* 1.3 57.6 + - - +
182A ASN* 3.1 13.5 + - - +
39B PRO 3.5 23.0 + - - -
40B THR* 4.0 16.2 + - - +
42B VAL* 3.9 11.8 - - - +
67B ASP* 2.9 49.4 + - + +
68B ARG* 3.6 23.0 - - - +
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Residues in contact with ALA 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A ALA 2.9 15.5 + - - +
178A ALA* 3.2 7.4 + - - +
179A LYS 3.2 0.4 - - - -
180A ARG* 1.3 76.4 - - - +
182A ASN* 1.3 71.4 + - - +
183A ALA* 4.2 7.5 - - + +
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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