Contacts of the helix formed by residues 167 - 185 (chain B) in PDB entry 2B2T
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 ASP 167 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B TYR* 5.6 2.4 - - - +
150B ASP* 3.6 13.2 + - - +
166B GLU* 1.3 73.9 + - - +
168B GLY* 1.3 66.1 + - - +
169B ALA* 3.5 13.7 + - - +
170B LEU* 3.3 33.0 + - + +
171B ILE* 3.2 21.5 + - - +
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Residues in contact with GLY 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B TYR* 4.0 10.5 + - - +
149B PRO 3.2 26.7 + - - -
150B ASP* 3.7 3.6 + - - -
151B TYR* 4.0 16.9 - - - -
166B GLU 3.2 3.0 + - - -
167B ASP* 1.3 73.7 + - - +
169B ALA* 1.3 67.1 + - - +
171B ILE* 4.0 0.7 - - - +
172B SER* 3.0 28.2 + - - -
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Residues in contact with ALA 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B TYR* 3.7 34.3 - - + +
167B ASP* 3.4 13.8 + - - +
168B GLY* 1.3 75.8 - - - +
170B LEU* 1.3 58.2 - - - +
172B SER* 2.8 19.7 + - - -
173B LYS* 3.2 29.6 - - - +
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Residues in contact with LEU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B TYR* 3.5 64.2 - - + +
70B ILE* 4.2 16.4 - - + -
71B HIS* 4.6 6.1 - - + -
166B GLU* 5.5 2.2 - - + +
167B ASP* 3.3 24.5 + - + +
168B GLY 3.2 0.4 - - - -
169B ALA* 1.3 78.4 - - - +
171B ILE* 1.3 66.4 + - + +
173B LYS* 3.6 24.7 + - + +
174B LYS* 4.2 4.9 + - - +
175B PHE* 5.4 0.9 - - - -
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Residues in contact with ILE 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ILE* 5.6 3.8 - - + -
133B VAL* 3.2 26.2 - - + -
136B ILE* 4.0 20.6 - - + -
151B TYR* 4.1 10.5 - - + -
153B CYS* 2.9 37.9 - - + -
155B TRP* 4.5 4.7 - - + -
166B GLU* 4.0 18.6 - - + +
167B ASP 3.2 11.4 + - - +
168B GLY 4.2 1.3 - - - +
170B LEU* 1.3 82.0 - - + +
172B SER* 1.3 55.6 + - - +
174B LYS 3.4 1.2 + - - -
175B PHE* 2.7 45.5 + - + +
179B ILE* 4.1 9.4 - - + -
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Residues in contact with SER 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B TYR* 3.8 19.8 + - - -
151B TYR* 5.5 3.6 - - - -
168B GLY 3.0 14.5 + - - -
169B ALA* 2.8 24.8 + - - -
171B ILE* 1.3 77.7 - - - +
173B LYS* 1.3 61.9 + - - +
174B LYS 2.9 6.8 + - - -
175B PHE 4.6 0.2 - - - -
176B GLN* 3.4 50.4 + - - +
179B ILE* 5.0 4.7 - - - -
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Residues in contact with LYS 173 (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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41B ALA* 6.1 4.1 - - + +
169B ALA* 3.2 28.5 + - - +
170B LEU* 3.8 18.5 - - + +
171B ILE 3.3 0.8 - - - -
172B SER* 1.3 82.4 + - - +
174B LYS* 1.3 58.9 + - + +
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Residues in contact with LYS 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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36B ILE* 3.8 14.5 - - + +
40B GLU* 2.9 38.7 + - - +
131B GLN* 5.1 3.6 + - - +
132B ILE* 5.6 6.5 - - - +
170B LEU 4.2 4.0 + - - +
171B ILE 3.4 2.0 + - - -
172B SER 4.1 0.2 - - - -
173B LYS* 1.3 82.2 - - + +
175B PHE* 1.3 98.6 + - + +
176B GLN* 3.5 3.8 + - - -
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Residues in contact with PHE 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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70B ILE* 5.4 4.5 - - + -
131B GLN 3.5 24.7 - - - -
132B ILE* 4.0 14.1 - - + -
133B VAL* 3.4 48.9 - - + -
155B TRP* 4.9 2.5 - + - -
170B LEU 5.6 0.4 - - - -
171B ILE* 2.7 39.1 + - + +
174B LYS* 1.3 111.8 - - + +
176B GLN* 1.3 65.7 + - - +
177B ALA* 3.2 3.6 - - - +
178B MSE 3.0 26.7 + - + +
179B ILE* 3.1 14.7 - - - +
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Residues in contact with GLN 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B TYR* 5.9 0.2 - - - -
172B SER* 3.4 35.7 + - - +
174B LYS 3.5 3.2 + - - -
175B PHE* 1.3 75.2 - - - +
177B ALA* 1.3 63.8 + - - +
179B ILE* 2.9 49.0 + - - +
180B ASP* 3.0 34.1 + - - +
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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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175B PHE* 3.2 1.5 - - - -
176B GLN* 1.3 78.8 - - - +
178B MSE 1.3 60.8 + - + +
180B ASP* 3.2 9.4 + - - +
181B GLU* 3.0 44.7 + - + +
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Residues in contact with MSE 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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133B VAL* 3.6 31.4 - - + +
134B GLY 2.8 33.7 - - - +
135B ARG* 2.9 26.9 - - + +
136B ILE* 3.6 19.9 + - + +
175B PHE* 3.0 22.7 + - + +
177B ALA* 1.3 80.4 - - + +
179B ILE* 1.3 59.1 + - - +
181B GLU* 4.1 24.3 - - + +
182B TYR* 3.6 11.3 + - - +
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Residues in contact with ILE 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ILE* 3.2 28.3 - - + -
151B TYR* 3.8 21.5 - - + +
171B ILE* 4.1 10.5 - - + -
172B SER* 5.0 4.5 - - - -
175B PHE 3.1 19.7 - - - +
176B GLN* 2.9 31.5 + - - +
178B MSE 1.3 75.2 - - - +
180B ASP* 1.3 75.3 + - - +
181B GLU 3.2 1.6 - - - -
182B TYR* 3.3 7.8 + - - +
183B PHE* 3.3 46.4 + - + -
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Residues in contact with ASP 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B GLN* 3.0 46.3 + - - +
177B ALA* 3.2 7.4 + - - +
179B ILE* 1.3 81.5 - - - +
181B GLU* 1.3 65.6 + - + +
183B PHE* 3.4 7.7 + - - +
184B SER* 3.1 21.8 + - - -
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Residues in contact with GLU 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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177B ALA* 3.0 30.2 + - - +
178B MSE 4.2 24.5 - - + +
180B ASP* 1.3 76.4 - - + +
182B TYR* 1.3 64.5 + - - +
184B SER* 3.1 25.5 + - - +
185B ARG* 3.2 8.7 + - - +
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Residues in contact with TYR 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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136B ILE* 3.1 34.3 - - + +
137B ILE* 3.6 22.2 + - - -
138B ALA* 3.3 16.6 - - - -
139B HIS* 3.2 32.1 + + + -
151B TYR* 4.8 2.0 - + - -
178B MSE 3.6 14.4 + - - +
179B ILE 3.3 9.4 + - - +
181B GLU* 1.3 80.4 - - - +
183B PHE* 1.3 95.7 + + - +
185B ARG* 3.1 26.6 - - + +
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Residues in contact with PHE 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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139B HIS* 3.7 33.0 - + - -
149B PRO* 5.4 1.1 - - + -
151B TYR* 3.8 13.2 - + - -
179B ILE* 3.3 40.1 + - + -
180B ASP* 4.0 7.4 - - - +
181B GLU 3.2 0.4 - - - -
182B TYR* 1.3 99.7 - + - +
184B SER* 1.3 61.8 - - - +
185B ARG 2.9 6.7 + - - -
186B LYS* 3.4 16.7 + - - +
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Residues in contact with SER 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 ASP 3.1 14.5 + - - -
181B GLU* 3.1 19.2 + - - +
183B PHE* 1.3 77.3 - - - +
185B ARG* 1.3 56.6 + - - +
186B LYS* 2.8 10.9 + - - +
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Residues in contact with ARG 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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109A SER* 4.5 18.2 + - - +
111A GLU* 5.5 7.4 - - + +
112A ASP* 5.0 11.9 - - - +
135B ARG* 6.2 0.7 - - - +
181B GLU 3.2 9.6 + - - +
182B TYR* 3.1 20.5 - - + +
183B PHE 2.9 2.4 - - - -
184B SER* 1.3 75.2 - - - +
186B LYS* 1.3 63.1 + - - +
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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
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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