Contacts of the helix formed by residues 178 - 197 (chain F) in PDB entry 2POZ
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 178 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163F GLN* 5.4 0.8 + - - -
177F MSE 1.3 76.5 - - - +
179F ALA* 1.3 64.4 + - - +
180F GLU* 3.6 10.3 + - - +
181F ALA* 2.9 33.7 + - - +
182F ILE* 3.0 12.0 + - - +
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Residues in contact with ALA 179 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199E GLU 5.9 3.1 - - - +
201E GLU* 3.9 23.9 + - + +
177F MSE 3.9 0.8 + - - -
178F SER* 1.3 72.7 - - - +
180F GLU* 1.3 61.5 + - - +
182F ILE* 3.4 11.7 + - - +
183F GLU* 3.0 24.4 + - - +
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Residues in contact with GLU 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178F SER* 3.0 9.3 + - - +
179F ALA* 1.3 79.4 - - - +
181F ALA* 1.3 57.7 + - - +
183F GLU* 3.4 7.3 + - + +
184F LEU* 2.9 29.8 + - + +
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Residues in contact with ALA 181 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163F GLN* 3.3 32.6 + - - +
177F MSE 3.9 10.9 - - + +
178F SER* 2.9 30.4 + - - +
180F GLU* 1.3 77.9 - - - +
182F ILE* 1.3 57.1 + - - +
184F LEU* 3.3 12.5 + - + +
185F ALA* 2.9 26.9 + - - +
188F ARG* 5.7 1.0 + - - -
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Residues in contact with ILE 182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177F MSE 3.3 45.1 - - + +
178F SER 3.0 13.1 + - - +
179F ALA* 3.8 10.3 - - - +
180F GLU 3.3 0.2 - - - -
181F ALA* 1.3 73.2 - - - +
183F GLU* 1.3 66.5 + - - +
185F ALA* 3.1 4.8 + - - +
186F TYR* 3.0 20.6 + - - +
210F LEU* 4.2 9.6 - - + -
214F GLU* 3.8 28.3 - - + +
217F ARG* 6.2 4.0 - - + -
218F PHE* 4.1 24.1 - - + -
221F LYS* 6.2 3.1 - - + -
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Residues in contact with GLU 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179F ALA 3.0 18.3 + - - +
180F GLU* 3.6 7.4 - - - +
182F ILE* 1.3 73.1 - - - +
184F LEU* 1.3 67.0 + - - +
186F TYR* 3.1 9.2 + - - +
187F ARG* 2.5 72.3 + - + +
221F LYS* 4.1 18.5 + - - +
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Residues in contact with LEU 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F ASP* 3.8 11.2 - - - +
137F THR* 5.8 0.7 - - - -
138F PRO* 4.5 13.2 - - + -
163F GLN* 5.4 6.1 - - - +
180F GLU* 2.9 18.9 + - + +
181F ALA* 3.3 16.4 - - - +
183F GLU* 1.3 76.8 - - - +
185F ALA* 1.3 60.8 + - - +
187F ARG* 3.2 9.3 + - - +
188F ARG* 2.8 69.9 + - + +
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Residues in contact with ALA 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160F PRO* 3.4 25.1 - - - +
161F LEU* 3.7 20.6 - - + -
177F MSE 4.8 0.9 - - + -
181F ALA 2.9 14.4 + - - +
182F ILE* 3.1 13.2 + - - +
184F LEU* 1.3 76.5 - - - +
186F TYR* 1.3 61.9 + - - +
188F ARG* 3.2 14.1 + - - +
189F VAL* 3.2 18.0 + - - +
218F PHE* 3.8 11.7 - - + -
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Residues in contact with TYR 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182F ILE 3.0 11.3 + - - +
183F GLU* 3.4 9.9 - - - +
185F ALA* 1.3 76.6 - - - +
187F ARG* 1.3 97.2 + - - +
189F VAL* 3.2 3.1 + - - +
190F LYS* 2.9 48.1 + - + +
218F PHE* 3.6 14.0 - - + -
221F LYS* 3.4 61.2 - - + -
222F ILE* 3.9 14.1 - - + -
224F GLU* 4.1 14.6 + - - -
225F LEU* 3.9 21.5 - - + +
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Residues in contact with ARG 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138F PRO* 3.6 21.7 - - + +
183F GLU* 2.5 51.3 + - + +
184F LEU* 3.6 9.9 - - - +
186F TYR* 1.3 100.9 - - - +
188F ARG* 1.3 57.0 + - - +
190F LYS* 3.7 24.7 - - - +
191F ALA* 2.8 31.5 + - - +
221F LYS* 5.6 2.4 - - - +
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Residues in contact with ARG 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F ALA 4.9 0.8 + - - -
136F ASP* 2.9 41.0 + - - +
138F PRO* 4.3 10.1 - - + -
141F PHE* 3.5 38.5 - - + +
158F PHE* 4.6 0.7 - - + -
160F PRO* 3.0 34.9 + - + +
161F LEU* 3.8 1.2 - - - +
162F ALA* 2.8 39.4 + - - +
163F GLN* 5.3 2.0 - - - +
164F ARG 5.4 0.4 - - - +
169F LEU* 6.0 1.0 - - - +
181F ALA 5.7 1.0 + - - -
184F LEU* 2.8 45.9 + - + +
185F ALA* 3.3 7.2 - - - +
186F TYR 3.1 0.2 - - - -
187F ARG* 1.3 76.6 - - - +
189F VAL* 1.3 63.2 + - - +
191F ALA* 3.2 6.9 + - - +
192F VAL* 3.0 28.9 + - - +
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Residues in contact with VAL 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158F PHE* 3.9 22.2 - - + -
160F PRO* 3.7 26.7 - - + -
185F ALA 3.5 12.6 - - - +
186F TYR 3.2 6.6 + - - +
188F ARG* 1.3 75.4 - - - +
190F LYS* 1.3 62.7 + - - +
192F VAL* 3.1 4.9 + - - +
193F ARG* 3.0 20.8 + - - +
202F LEU* 4.7 1.9 - - + +
204F VAL* 4.4 6.7 - - + -
218F PHE* 4.2 11.7 - - + -
222F ILE* 4.2 10.3 - - + -
225F LEU* 3.7 17.7 - - + -
227F ILE* 4.0 23.6 - - + -
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Residues in contact with LYS 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186F TYR* 2.9 34.2 + - + +
187F ARG* 3.7 33.7 - - - +
189F VAL* 1.3 76.0 - - - +
191F ALA* 1.3 58.3 + - - +
193F ARG* 3.2 2.8 + - - +
194F ASP* 2.9 58.1 + - - +
225F LEU* 3.6 28.9 - - + +
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Residues in contact with ALA 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138F PRO* 3.3 33.7 - - + +
139F ASP* 5.3 0.2 - - - -
141F PHE* 4.8 0.2 - - + -
142F ALA* 3.8 11.3 - - + +
187F ARG 2.8 20.5 + - - +
188F ARG 3.4 5.2 - - - +
189F VAL 3.2 0.2 - - - -
190F LYS* 1.3 77.4 - - - +
192F VAL* 1.3 57.5 + - - +
194F ASP* 3.5 7.0 + - - +
195F ALA* 3.0 31.2 + - - +
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Residues in contact with VAL 192 (chain F).
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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131F TRP* 4.1 10.3 - - + -
141F PHE* 4.0 27.8 - - + +
142F ALA* 5.0 0.4 - - - +
145F VAL* 3.8 21.7 - - + +
156F LEU* 4.6 1.6 - - + -
158F PHE* 3.7 28.7 - - + -
188F ARG 3.0 15.9 + - - +
189F VAL 3.6 6.3 - - - +
191F ALA* 1.3 74.8 - - - +
193F ARG* 1.3 59.8 + - - +
195F ALA* 3.8 0.6 - - - +
196F ALA* 2.8 34.7 + - + +
202F LEU* 3.8 26.2 - - + -
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Residues in contact with ARG 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189F VAL 3.0 12.7 + - - +
190F LYS* 3.2 10.5 + - - +
192F VAL* 1.3 77.3 - - - +
194F ASP* 1.3 69.5 + - - +
196F ALA* 5.1 0.6 - - - +
197F GLY* 2.8 46.2 + - - +
198F PRO* 3.8 11.2 + - - -
200F ILE* 2.7 32.1 + - - +
201F GLU* 4.9 0.4 - - - +
202F LEU* 3.6 33.3 - - + +
225F LEU* 2.8 37.4 + - + +
226F ASP* 2.8 40.1 + - - +
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Residues in contact with ASP 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190F LYS* 2.9 53.2 + - - +
191F ALA* 3.9 6.7 - - - +
193F ARG* 1.3 84.6 - - - +
195F ALA* 1.3 61.7 + - - +
196F ALA 3.6 0.2 + - - -
197F GLY* 3.6 7.3 + - - -
225F LEU* 5.8 0.5 - - - +
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Residues in contact with ALA 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142F ALA* 3.6 36.3 - - + +
145F VAL* 3.8 11.8 - - + +
149F LEU* 4.8 2.1 - - - +
191F ALA 3.0 18.7 + - - +
192F VAL 4.0 1.6 - - - +
194F ASP* 1.3 77.9 - - - +
196F ALA* 1.3 61.3 + - - +
197F GLY 3.6 0.2 + - - -
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Residues in contact with ALA 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F VAL* 4.6 2.0 - - + -
149F LEU* 3.7 25.6 - - + +
156F LEU* 4.6 8.5 - - + -
192F VAL* 2.8 24.0 + - + +
193F ARG* 4.2 1.3 - - - +
195F ALA* 1.3 74.9 - - - +
197F GLY* 1.3 62.3 + - - +
199F GLU* 5.2 0.3 + - - +
200F ILE* 3.3 38.1 - - + +
202F LEU* 4.7 5.6 - - + -
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Residues in contact with GLY 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193F ARG* 2.8 38.1 + - - +
194F ASP 3.6 5.8 + - - -
195F ALA 3.3 3.0 - - - -
196F ALA* 1.3 81.9 - - - +
198F PRO* 1.3 72.4 - - - +
199F GLU 3.4 3.8 + - - -
200F ILE 3.7 2.4 + - - -
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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