Contacts of the helix formed by residues 158 - 174 (chain B) in PDB entry 2JB2
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 SER 158 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A GLN* 4.2 5.5 + - - -
213A ARG* 3.8 5.0 + - - -
157B LEU* 1.3 76.2 - - - +
159B ARG* 1.3 59.2 + - - +
160B GLU* 3.4 14.8 + - - -
161B ASP* 3.0 35.7 + - - -
162B LYS* 2.8 29.9 + - - +
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Residues in contact with ARG 159 (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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158B SER* 1.3 74.4 - - - +
160B GLU* 1.3 70.9 + - + +
162B LYS* 3.3 19.9 + - - +
163B ASP* 3.0 53.3 + - - +
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Residues in contact with GLU 160 (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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213A ARG* 3.4 36.4 + - - +
158B SER* 3.4 14.9 + - - -
159B ARG* 1.3 86.8 + - + +
161B ASP* 1.3 65.2 + - - +
163B ASP* 3.4 8.2 + - - +
164B ALA* 3.0 24.6 + - - +
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Residues in contact with ASP 161 (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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209A GLN* 3.1 30.5 + - - +
212A ILE* 3.6 11.1 - - + +
213A ARG* 3.0 37.1 + - - +
156B VAL 4.3 2.8 - - - +
157B LEU* 3.7 24.5 - - + +
158B SER* 3.0 32.9 + - - +
160B GLU* 1.3 76.2 - - - +
162B LYS* 1.3 56.7 + - - +
164B ALA 3.3 0.9 + - - -
165B LEU* 2.9 31.7 + - - +
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Residues in contact with LYS 162 (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 THR* 3.6 41.8 + - + +
149B ASP* 5.3 4.6 + - - +
151B GLY* 4.6 2.4 - - - -
153B LEU 5.4 0.7 - - - -
154B ASP* 2.8 35.5 + - - +
157B LEU* 3.8 24.5 - - + +
158B SER 2.8 24.1 + - - +
159B ARG* 3.5 17.3 - - - +
161B ASP* 1.3 76.9 - - - +
163B ASP* 1.3 59.2 + - - +
165B LEU* 3.4 4.3 + - - +
166B SER* 2.9 35.1 + - - -
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Residues in contact with ASP 163 (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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159B ARG* 3.0 43.3 + - - +
160B GLU* 3.8 7.9 - - - +
161B ASP 3.3 0.2 - - - -
162B LYS* 1.3 79.0 - - - +
164B ALA* 1.3 63.1 + - - +
166B SER* 3.4 6.8 + - - -
167B GLU* 3.1 23.2 + - - +
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Residues in contact with ALA 164 (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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212A ILE* 3.9 26.3 - - + +
213A ARG* 4.3 11.4 - - - +
160B GLU 3.0 17.9 + - - +
161B ASP 3.7 4.0 - - - +
163B ASP* 1.3 73.9 - - - +
165B LEU* 1.3 64.1 + - - +
167B GLU* 3.4 12.7 + - - +
168B PHE* 3.2 22.2 + - - +
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Residues in contact with LEU 165 (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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140A MET* 5.5 5.8 - - + -
143A LEU* 4.2 16.6 - - + -
212A ILE* 3.9 22.4 - - + +
144B LEU* 4.4 12.8 - - + -
148B THR* 3.8 18.6 - - + +
157B LEU* 3.8 25.6 - - + -
161B ASP 2.9 17.9 + - - +
162B LYS 3.7 4.5 - - - +
164B ALA* 1.3 74.9 - - - +
166B SER* 1.3 57.9 + - - +
168B PHE* 3.2 15.0 + - + +
169B LEU* 2.9 57.2 + - + +
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Residues in contact with SER 166 (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 LYS* 4.5 20.2 - - - +
148B THR* 4.3 9.4 - - - +
149B ASP* 4.2 14.2 + - - -
162B LYS* 2.9 23.3 + - - +
163B ASP* 3.6 8.2 - - - -
164B ALA 3.3 0.2 - - - -
165B LEU* 1.3 77.6 - - - +
167B GLU* 1.3 56.7 + - - +
169B LEU* 3.2 10.1 + - - +
170B SER* 2.9 35.0 + - - -
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Residues in contact with GLU 167 (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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163B ASP 3.1 11.5 + - - +
164B ALA* 3.6 13.8 - - - +
166B SER* 1.3 79.4 - - - +
168B PHE* 1.3 62.7 + - - +
170B SER* 3.5 5.9 + - - -
171B ASP* 3.3 21.9 + - + +
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Residues in contact with PHE 168 (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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136A THR* 3.8 22.7 - - + -
137A PHE* 4.3 7.0 - + - -
140A MET* 4.1 21.8 - - + -
217A GLY* 3.3 39.7 - - - -
218A ARG* 4.7 3.1 - - - +
220A PHE* 4.1 5.2 - + + -
164B ALA 3.2 10.3 + - - +
165B LEU* 3.5 16.8 - - + +
167B GLU* 1.3 81.1 - - - +
169B LEU* 1.3 65.1 + - + +
171B ASP* 3.2 9.0 + - - +
172B PHE* 2.7 69.2 + + + +
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Residues in contact with LEU 169 (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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140A MET* 3.5 31.9 - - + -
141B SER* 3.5 28.3 - - - +
144B LEU* 3.8 19.1 - - + -
145B LYS* 3.8 34.3 - - + +
148B THR* 4.9 1.1 - - - +
165B LEU* 2.9 42.3 + - + +
166B SER* 3.2 6.5 + - - +
168B PHE* 1.3 87.3 - - + +
170B SER* 1.3 57.5 + - - +
172B PHE* 4.4 0.7 - - - -
173B GLY* 2.9 25.8 + - - -
175B LEU* 3.8 3.3 - - + +
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Residues in contact with SER 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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145B LYS* 3.6 20.6 - - - +
166B SER 2.9 19.3 + - - -
167B GLU* 3.8 6.3 - - - -
168B PHE 3.3 0.2 - - - -
169B LEU* 1.3 76.9 - - - +
171B ASP* 1.3 57.5 + - - +
174B ASP* 3.0 8.3 + - - -
175B LEU* 3.0 44.2 + - - +
176B SER 5.2 2.8 + - - -
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Residues in contact with ASP 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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217A GLY 4.9 1.2 - - - +
218A ARG* 3.3 23.7 - - - +
221A SER* 2.6 30.4 + - - -
167B GLU 3.3 10.6 + - - +
168B PHE* 3.2 11.7 + - - +
170B SER* 1.3 76.7 - - - +
172B PHE* 1.3 61.2 + - - +
174B ASP* 3.2 3.9 + - - +
186B ARG* 2.9 36.6 + - - +
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Residues in contact with PHE 172 (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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137A PHE* 3.4 36.6 - + - -
140A MET* 4.1 9.6 - - + -
220A PHE* 4.4 12.3 - - + -
221A SER* 4.3 7.2 - - - -
224A PHE* 3.5 44.6 - + - -
137B PHE* 3.7 24.8 - + + +
140B MET* 3.5 26.5 - - + -
141B SER* 3.6 15.0 - - - +
168B PHE* 2.7 48.0 + + + +
169B LEU 4.2 1.8 - - - +
171B ASP* 1.3 75.1 - - - +
173B GLY* 1.3 55.8 + - - +
186B ARG* 3.0 15.0 + - - +
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Residues in contact with GLY 173 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134B ALA 4.9 0.3 - - - +
137B PHE 3.8 8.7 - - - -
138B GLY* 3.6 7.2 - - - -
141B SER* 3.5 21.2 + - - -
169B LEU 2.9 13.3 + - - -
172B PHE* 1.3 77.3 - - - +
174B ASP* 1.3 70.2 + - - +
175B LEU* 3.3 5.1 + - - +
181B TYR* 3.6 20.8 - - - -
186B ARG* 4.1 0.7 - - - -
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Residues in contact with ASP 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 SER 3.0 10.2 + - - -
171B ASP* 3.2 7.7 + - - +
172B PHE 3.5 0.2 - - - -
173B GLY* 1.3 80.5 - - - +
175B LEU* 1.3 64.7 + - - +
176B SER 3.9 0.3 + - - -
180B ARG 4.7 0.5 - - - +
181B TYR* 4.3 3.5 - - - -
182B LEU 5.2 0.9 + - - -
183B GLY 4.1 12.1 - - - +
184B SER* 2.6 37.7 + - - +
185B SER* 4.5 4.3 + - - -
186B ARG* 3.7 26.3 + - - +
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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