Contacts of the helix formed by residues 191 - 205 (chain B) in PDB entry 2PQG
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 GLN 191 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124B LEU 4.1 9.4 + - - +
126B PHE* 3.6 30.7 - - + -
159B LYS* 2.9 29.7 + - - +
160B LYS 5.4 0.2 + - - -
162B MET* 5.3 10.3 - - - +
189B ASP* 3.2 1.7 - - - +
190B PRO* 1.3 89.7 - - + +
192B ALA* 1.3 63.5 + - - +
193B ASP 3.3 2.2 - - - -
194B THR* 2.9 29.8 + - - +
195B LYS* 3.0 34.1 + - - +
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Residues in contact with ALA 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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189B ASP* 3.2 36.5 + - + +
190B PRO 3.1 3.6 - - - +
191B GLN* 1.3 78.0 - - - +
193B ASP* 1.3 63.8 + - - +
195B LYS* 3.7 4.8 - - - +
196B SER* 3.1 24.5 + - - -
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Residues in contact with ASP 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ASP* 2.5 36.2 - - - +
190B PRO 4.4 5.0 + - - +
191B GLN 3.3 0.4 - - - -
192B ALA* 1.3 76.3 - - - +
194B THR* 1.3 68.1 + - - +
196B SER* 3.0 8.5 + - - -
197B LYS* 2.9 42.2 + - - +
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Residues in contact with THR 194 (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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98B PHE* 4.8 0.9 - - + -
124B LEU* 4.2 4.3 - - + -
126B PHE* 4.0 8.7 - - + -
155B ASP* 5.6 0.6 + - - -
156B LEU* 3.8 23.3 - - + +
159B LYS* 3.5 24.6 - - + +
191B GLN* 2.9 30.1 + - - +
192B ALA 3.5 0.2 - - - -
193B ASP* 1.3 80.7 + - - +
195B LYS* 1.3 64.8 + - - +
197B LYS* 3.0 3.7 + - - +
198B LEU* 2.8 44.2 + - + +
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Residues in contact with LYS 195 (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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126B PHE* 3.8 48.1 - - + +
132B ASP 3.5 23.5 + - - +
133B LEU* 3.9 28.1 - - + +
134B ILE* 6.2 0.2 - - - -
188B ALA 5.5 0.4 + - - -
189B ASP* 2.9 30.4 + - - +
191B GLN* 3.0 32.7 + - - +
192B ALA* 3.7 3.8 - - - +
194B THR* 1.3 75.3 - - - +
196B SER* 1.3 58.0 + - - +
198B LEU* 3.3 2.8 + - - +
199B VAL* 3.0 32.7 + - - +
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Residues in contact with SER 196 (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 LEU 5.9 0.4 - - - -
134B ILE* 6.0 1.1 - - - -
192B ALA 3.1 11.5 + - - -
193B ASP* 3.0 12.9 + - - -
195B LYS* 1.3 80.5 - - - +
197B LYS* 1.3 70.2 + - - +
199B VAL* 3.3 21.2 - - - +
200B LYS* 3.4 23.9 + - - +
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Residues in contact with LYS 197 (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 GLU* 5.4 2.0 - - - -
151B ARG* 4.1 20.0 - - - +
152B ALA* 3.4 36.8 - - + +
155B ASP* 4.1 24.5 + - + +
156B LEU* 3.9 18.4 - - + -
193B ASP* 2.9 31.0 + - - +
194B THR 3.7 4.7 - - - +
196B SER* 1.3 85.5 + - - +
198B LEU* 1.3 66.1 + - - +
200B LYS* 3.4 27.6 + - + +
201B LEU* 3.4 17.8 + - - +
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Residues in contact with LEU 198 (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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86B LEU* 5.7 0.7 - - + -
95B LEU* 4.0 21.3 - - + -
98B PHE* 3.7 27.6 - - + -
108B PHE* 3.5 32.5 - - + -
124B LEU* 3.9 8.7 - - + -
126B PHE* 3.9 11.4 - - + -
133B LEU* 4.6 3.6 - - + -
156B LEU* 3.9 13.5 - - + -
194B THR* 2.8 42.9 + - + +
195B LYS* 3.7 4.0 - - - +
197B LYS* 1.3 71.8 - - - +
199B VAL* 1.3 59.8 + - - +
201B LEU* 3.1 9.9 + - + +
202B VAL* 2.8 32.1 + - - +
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Residues in contact with VAL 199 (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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130B TYR* 4.0 22.4 - - + -
133B LEU* 3.4 31.1 - - + +
134B ILE* 4.0 24.0 - - + -
142B VAL* 4.0 28.7 - - + -
195B LYS 3.0 13.5 + - - +
196B SER* 3.3 18.2 - - - +
198B LEU* 1.3 76.0 - - - +
200B LYS* 1.3 66.2 + - - +
202B VAL* 3.6 2.2 - - + +
203B VAL* 3.0 24.5 + - + +
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Residues in contact with LYS 200 (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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141B THR 5.6 0.2 + - - -
142B VAL* 3.7 16.4 - - + +
143B THR* 2.7 46.2 + - - +
144B MET* 4.3 1.1 - - - +
148B GLU* 3.3 31.2 + - + +
152B ALA* 4.8 3.6 - - + -
196B SER* 3.4 28.1 + - - +
197B LYS* 3.4 28.9 + - + +
198B LEU 3.2 0.8 - - - -
199B VAL* 1.3 78.3 - - - +
201B LEU* 1.3 57.2 + - - +
203B VAL* 4.2 1.7 - - - +
204B MET* 3.1 46.1 + - + +
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Residues in contact with LEU 201 (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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77B LEU* 4.1 13.7 - - + -
84B ILE* 3.8 29.6 - - + -
86B LEU* 4.4 17.7 - - + +
95B LEU* 5.6 1.3 - - + -
149B MET* 3.6 35.4 - - + +
152B ALA* 4.1 15.0 - - + -
153B VAL* 4.6 2.2 - - + -
156B LEU* 3.8 19.1 - - + -
197B LYS 3.4 9.8 + - - +
198B LEU* 3.1 10.4 + - + +
200B LYS* 1.3 75.0 - - - +
202B VAL* 1.3 61.4 + - + +
203B VAL 3.3 0.2 - - - -
204B MET* 4.3 8.5 - - + +
205B VAL* 2.9 34.5 + - + +
206B CYS* 3.9 0.5 + - - -
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Residues in contact with VAL 202 (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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94B TYR* 3.4 38.6 - - + +
95B LEU* 3.9 29.2 - - + -
108B PHE* 4.7 6.7 - - + -
130B TYR* 3.9 16.8 - - + +
133B LEU* 4.4 9.9 - - + -
198B LEU 2.8 22.6 + - - +
199B VAL* 3.2 9.4 + - - +
201B LEU* 1.3 76.4 - - - +
203B VAL* 1.3 59.1 + - + +
206B CYS* 3.1 19.2 + - + +
207B GLU* 3.0 23.5 + - + +
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Residues in contact with VAL 203 (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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130B TYR* 3.6 30.3 - - + +
139B LEU* 4.4 11.2 - - + +
142B VAL* 4.9 8.1 - - + -
144B MET* 3.5 26.7 - - + -
199B VAL* 3.0 19.5 + - + +
202B VAL* 1.3 75.1 - - - +
204B MET* 1.3 64.7 + - - +
207B GLU* 3.3 14.4 - - + +
208B GLY 3.0 19.2 + - - -
214B VAL* 3.6 9.2 - - + +
230B LEU* 3.9 24.2 - - + -
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Residues in contact with MET 204 (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 TYR* 2.5 35.7 + - + -
40B ILE* 4.3 1.0 - - - +
144B MET* 3.6 27.1 - - + -
145B GLY 3.5 29.6 - - - +
148B GLU* 4.6 0.2 - - + -
149B MET* 3.8 49.1 - - + +
200B LYS* 3.1 46.8 + - + +
201B LEU* 4.3 6.1 - - + +
203B VAL* 1.3 77.8 - - - +
205B VAL* 1.3 61.8 + - + +
208B GLY* 3.5 4.3 - - - -
218B VAL* 4.0 12.8 - - + -
222B PHE* 4.2 7.0 - - - -
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Residues in contact with VAL 205 (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 TYR* 5.8 1.3 - - + -
39B PHE* 5.1 12.8 - - + -
40B ILE* 4.8 3.5 - - + +
75B THR* 4.3 15.9 - - + +
77B LEU* 4.7 13.2 - - + -
86B LEU* 4.5 14.4 - - + -
88B ILE* 3.9 23.6 - - + -
149B MET* 4.3 20.0 - - + -
201B LEU* 2.9 19.0 + - - +
204B MET* 1.3 79.6 - - + +
206B CYS* 1.3 65.6 + - - +
207B GLU 3.5 0.2 - - - -
208B GLY* 3.8 0.2 - - - -
209B LEU* 3.0 38.9 + - + +
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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