Contacts of the helix formed by residues 153 - 173 (chain B) in PDB entry 2PXA
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 153 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B SER* 3.0 13.9 + - - -
152B PRO* 1.3 78.5 - - - +
154B ALA* 1.3 63.9 + - - +
155B GLU* 3.4 15.9 + - - +
156B ILE* 3.2 33.4 + - - +
157B GLU* 3.0 23.7 + - - +
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Residues in contact with ALA 154 (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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10B GLU* 5.0 5.4 - - + -
13B LYS* 4.5 13.0 - - + +
152B PRO 3.7 5.3 + - - -
153B SER* 1.3 71.4 - - - +
155B GLU* 1.3 71.1 + - - +
157B GLU* 3.5 7.2 + - - +
158B GLU* 2.9 27.9 + - - +
185B CYS* 4.1 0.3 - - - -
187B TYR* 3.8 23.8 - - + +
188B MET* 4.1 21.5 - - - +
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Residues in contact with GLU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLU* 4.6 5.5 - - - +
153B SER* 3.4 14.9 + - - +
154B ALA* 1.3 90.5 + - - +
156B ILE* 1.3 64.4 + - + +
158B GLU* 3.3 16.7 - - - +
159B GLN* 3.1 24.6 + - - +
188B MET* 4.2 15.5 - - + +
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Residues in contact with ILE 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B SER* 3.6 11.7 - - - +
153B SER* 3.1 28.9 + - - +
155B GLU* 1.3 79.2 - - + +
157B GLU* 1.3 56.9 + - - +
159B GLN* 3.4 6.4 + - - +
160B ARG* 2.9 63.7 + - + +
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Residues in contact with GLU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TRP* 5.9 0.9 - - - -
13B LYS* 3.3 20.3 + - - +
149B GLU 4.5 0.2 - - - +
150B SER* 3.3 12.0 - - - -
151B SER* 2.9 41.3 + - - +
153B SER 3.0 15.5 + - - +
154B ALA* 3.8 6.2 - - - +
156B ILE* 1.3 72.7 - - - +
158B GLU* 1.3 54.5 + - - +
160B ARG* 3.6 4.5 - - - +
161B THR* 2.7 42.4 + - - -
184B LEU* 3.9 27.3 - - + +
185B CYS* 3.8 21.2 - - + +
187B TYR* 4.1 8.5 + - - -
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Residues in contact with GLU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ALA 2.9 15.6 + - - +
155B GLU* 3.3 18.2 - - - +
157B GLU* 1.3 75.7 - - - +
159B GLN* 1.3 62.8 + - - +
161B THR* 3.0 4.4 + - - -
162B LEU* 2.8 40.3 + - + +
185B CYS* 4.2 3.5 - - - +
188B MET* 3.3 37.0 - - + +
189B PRO* 4.2 2.1 - - - +
190B LYS* 3.4 41.8 + - - +
191B VAL* 3.6 24.5 - - + -
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Residues in contact with GLN 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B GLU 3.1 13.5 + - - +
156B ILE* 3.8 6.1 - - - +
158B GLU* 1.3 86.4 - - - +
160B ARG* 1.3 62.3 + - + +
162B LEU* 3.4 25.0 + - - +
163B ARG* 3.0 24.8 + - - +
190B LYS* 4.8 9.6 + - - +
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Residues in contact with ARG 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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45A ARG* 5.6 8.3 + - - +
133B PHE* 5.3 0.3 - - - -
148B GLY* 6.0 1.1 - - - -
149B GLU* 2.9 67.3 + - - +
150B SER 3.0 17.4 + - - -
151B SER* 3.5 10.7 - - - -
156B ILE* 2.9 41.6 + - + +
157B GLU* 3.6 6.7 - - - +
159B GLN* 1.3 78.4 - - + +
161B THR* 1.3 62.0 + - - +
163B ARG* 3.4 10.2 + - - +
164B ILE* 3.1 28.7 + - + +
184B LEU* 4.5 6.5 - - + -
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Residues in contact with THR 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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157B GLU 2.7 26.5 + - - -
158B GLU 3.0 4.2 + - - -
160B ARG* 1.3 74.3 - - - +
162B LEU* 1.3 60.9 + - - +
164B ILE* 3.2 10.1 + - + +
165B LEU* 3.0 28.4 + - + +
183B ILE* 3.8 20.4 - - + -
184B LEU* 3.4 13.5 - - - +
185B CYS* 3.2 20.2 + - - +
191B VAL* 3.6 34.8 - - + -
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Residues in contact with LEU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B GLU* 2.8 30.0 + - + +
159B GLN* 3.9 27.8 - - - +
161B THR* 1.3 72.1 - - - +
163B ARG* 1.3 57.3 + - - +
165B LEU* 3.2 8.8 + - + +
166B GLU* 3.0 35.0 + - + +
190B LYS* 3.5 50.5 - - + +
191B VAL* 4.0 9.0 - - + -
194B LYS* 3.8 31.5 - - + -
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Residues in contact with ARG 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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131B ASP* 5.0 0.8 + - - -
133B PHE* 3.3 55.8 - - + +
134B TYR* 2.8 36.8 + - - -
159B GLN 3.0 18.9 + - - +
160B ARG* 3.5 9.4 - - - +
162B LEU* 1.3 78.1 - - - +
164B ILE* 1.3 60.8 + - - +
166B GLU* 3.4 25.3 + - - +
167B MET* 3.4 10.0 + - - +
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Residues in contact with ILE 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B PHE* 3.4 24.5 - - + -
145B CYS* 4.6 5.8 - - - -
147B ILE* 3.3 51.6 - - + +
148B GLY* 5.2 3.8 - - - -
160B ARG* 3.1 19.1 + - + +
161B THR* 3.2 12.5 + - + +
163B ARG* 1.3 75.2 - - - +
165B LEU* 1.3 61.9 + - + +
167B MET* 3.4 11.9 - - + +
168B VAL* 3.0 40.9 + - + +
181B ILE* 4.6 3.8 - - + -
182B LYS 4.6 11.4 - - - +
183B ILE* 6.0 0.2 - - + -
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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
----------------------------------------------------------
161B THR* 3.0 34.2 + - + +
162B LEU* 3.2 12.8 + - + +
164B ILE* 1.3 76.8 - - + +
166B GLU* 1.3 65.1 + - - +
168B VAL* 3.4 14.4 - - + +
169B SER* 3.1 23.7 + - - -
181B ILE* 5.2 1.6 - - + -
183B ILE* 3.8 26.2 - - + -
191B VAL* 4.4 13.9 - - + +
194B LYS* 4.0 28.7 - - + -
195B LEU* 4.4 11.2 - - + -
198B LEU* 4.1 24.0 - - + +
221B TRP* 4.8 4.3 - - + -
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Residues in contact with GLU 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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162B LEU* 3.0 18.6 + - - +
163B ARG* 3.4 23.4 + - - +
165B LEU* 1.3 77.3 - - - +
167B MET* 1.3 61.8 + - - +
169B SER* 3.4 16.2 - - - -
170B ASP* 3.5 14.0 + - - +
194B LYS* 5.3 13.6 - - - +
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Residues in contact with MET 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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80B LEU* 3.9 28.5 - - + -
132B VAL* 3.2 42.2 - - + +
133B PHE* 4.0 27.4 - - + +
145B CYS* 3.9 19.3 - - - -
147B ILE* 4.1 4.7 - - + -
163B ARG 3.4 5.5 + - - +
164B ILE* 3.4 17.2 + - + +
165B LEU 3.2 0.4 - - - -
166B GLU* 1.3 78.4 - - - +
168B VAL* 1.3 68.6 + - + +
170B ASP* 3.1 17.2 + - - +
171B TRP* 3.1 30.9 - - + -
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Residues in contact with VAL 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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80B LEU* 5.1 1.8 - - + -
143B LEU* 4.0 3.2 - - + +
145B CYS* 4.1 15.9 - - + -
164B ILE* 3.0 25.0 + - + +
165B LEU* 3.4 28.3 - - + +
167B MET* 1.3 77.6 - - + +
169B SER* 1.3 60.7 + - - +
171B TRP* 3.0 10.1 + - - +
172B LEU* 2.8 36.5 + - - +
181B ILE* 3.5 44.4 - - + -
198B LEU* 5.2 1.1 - - + -
221B TRP* 4.3 10.1 - - + -
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Residues in contact with SER 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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165B LEU 3.1 13.8 + - - -
166B GLU* 3.4 13.2 - - - -
168B VAL* 1.3 78.8 - - - +
170B ASP* 1.3 58.7 + - - +
172B LEU* 3.3 8.4 + - - +
173B SER* 2.9 31.4 + - - -
198B LEU* 3.9 23.5 - - - +
201B ARG* 4.0 15.6 + - - -
202B PHE* 4.0 6.0 - - - -
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Residues in contact with ASP 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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137B SER* 4.0 11.7 + - - +
166B GLU 3.5 13.4 + - - +
167B MET* 3.1 14.2 + - - +
168B VAL 3.1 0.8 - - - -
169B SER* 1.3 81.6 + - - +
171B TRP* 1.3 64.7 + - + +
173B SER* 2.5 27.0 + - - -
174B ARG* 3.4 10.6 - - - +
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Residues in contact with TRP 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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78B VAL* 3.7 20.0 - - + -
80B LEU* 3.9 26.2 - - + -
103B TYR* 4.3 8.3 - + - -
132B VAL* 4.6 3.0 + - + -
135B LYS* 4.1 22.7 + - + -
136B PRO 4.0 7.4 - - - -
137B SER* 3.6 26.3 - - - +
138B GLU* 3.4 56.4 - - + +
140B SER* 5.2 2.0 + - - -
143B LEU* 3.3 36.8 - - + -
167B MET* 3.1 44.1 - - - +
168B VAL 3.0 3.4 + - - +
170B ASP* 1.3 76.8 - - + +
172B LEU* 1.3 65.9 + - - +
174B ARG* 3.2 15.3 + - - +
176B PRO* 3.4 13.9 - - - +
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Residues in contact with LEU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LEU* 3.6 20.4 - - + -
168B VAL* 2.8 20.4 + - + +
169B SER* 3.8 1.8 - - - +
171B TRP* 1.3 68.8 - - - +
173B SER* 1.3 62.7 + - - +
174B ARG 3.0 6.5 + - - -
175B GLY* 3.0 14.2 + - - -
176B PRO* 3.6 19.6 - - + +
179B PHE* 3.8 33.0 - - + -
181B ILE* 3.9 11.4 - - + -
202B PHE* 3.6 40.4 - - + -
221B TRP* 3.4 40.2 - - + -
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Residues in contact with SER 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B SER 2.9 15.9 + - - -
170B ASP* 2.5 23.2 + - - -
172B LEU* 1.3 75.3 - - - +
174B ARG* 1.3 66.1 + - - +
175B GLY 3.3 2.1 + - - -
201B ARG* 3.9 22.2 - - - +
202B PHE* 3.8 8.9 - - - -
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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
------------------------------------------------------------
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