Contacts of the helix formed by residues 179 - 196 (chain B) in PDB entry 3EUP
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 ASN 179 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B HIS* 4.0 5.8 + - - -
177B THR* 3.1 11.1 + - - +
178B LYS* 1.3 77.5 - - - +
180B ARG* 1.3 63.4 + - - +
181B ALA* 2.8 38.5 + - - +
182B TYR* 3.2 59.9 + - + +
183B SER* 3.8 4.0 + - - -
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Residues in contact with ARG 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B TYR* 3.5 28.3 + - - -
94B ASN* 2.9 43.1 + - - +
97B ASP* 3.0 52.1 + - - +
98B GLY* 3.6 3.8 - - - +
174B HIS* 3.5 28.5 + - + +
178B LYS 4.1 1.2 + - - -
179B ASN* 1.3 71.7 + - - +
181B ALA* 1.3 57.0 + - - +
182B TYR 3.2 0.4 - - - -
183B SER* 3.2 9.3 + - - +
184B ASP* 2.9 41.0 + - - +
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Residues in contact with ALA 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ASN* 2.8 20.0 + - - +
180B ARG* 1.3 77.8 - - - +
182B TYR* 1.3 67.3 + - + +
184B ASP* 3.4 20.2 + - - +
185B TYR* 3.2 22.7 - - + +
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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
----------------------------------------------------------
131A LEU* 3.8 33.5 - - + +
134A LYS* 6.4 0.2 - - - -
157A THR* 6.1 0.2 - - + -
161A PHE* 3.4 36.8 - + + +
173B ILE* 3.7 18.4 - - + -
177B THR* 3.5 27.8 - - + -
179B ASN* 3.2 36.8 + - + +
181B ALA* 1.3 80.8 - - + +
183B SER* 1.3 63.4 + - - +
185B TYR* 3.3 30.6 + + - +
186B VAL* 3.9 2.6 + - - +
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Residues in contact with SER 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B TYR* 5.3 0.6 - - - -
94B ASN* 4.7 5.6 + - - -
170B ALA* 3.4 30.5 - - - -
173B ILE* 4.0 5.6 - - - +
174B HIS* 3.6 19.8 - - - +
179B ASN 3.8 1.2 + - - -
180B ARG* 3.2 24.3 + - - +
182B TYR* 1.3 74.8 - - - +
184B ASP* 1.3 64.1 + - - +
186B VAL* 2.9 19.7 + - - +
187B PHE* 3.1 23.9 + - - -
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Residues in contact with ASP 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B SER* 5.0 2.4 + - - -
94B ASN* 4.0 21.8 + - - +
180B ARG* 2.9 32.8 + - - +
181B ALA* 3.5 12.3 - - - +
182B TYR 3.2 0.4 - - - -
183B SER* 1.3 75.9 - - - +
185B TYR* 1.3 57.1 + - - +
187B PHE* 3.3 8.8 + - - +
188B GLU* 2.9 29.4 + - - +
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Residues in contact with TYR 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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155A ASP* 4.6 9.4 - - - -
157A THR* 3.5 29.1 - - + +
158A LYS* 3.9 36.3 - - + +
161A PHE* 3.5 25.1 - + + -
162A SER* 3.9 1.8 + - - -
181B ALA* 3.2 27.9 + - + +
182B TYR* 3.3 16.5 + + - +
183B SER 3.2 1.0 - - - -
184B ASP* 1.3 78.8 - - + +
186B VAL* 1.3 57.2 + - - +
188B GLU* 3.4 17.1 + - - +
189B SER* 3.0 27.4 + - - -
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Residues in contact with VAL 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A PHE* 3.7 29.6 - - + +
162A SER* 4.2 6.1 - - - -
165A ALA* 3.4 15.9 - - + -
166B LEU* 3.3 40.2 - - + +
170B ALA* 3.6 9.9 - - + -
173B ILE* 3.8 19.5 - - + -
182B TYR 4.1 8.7 - - - +
183B SER* 2.9 10.6 + - - +
185B TYR* 1.3 75.7 - - - +
187B PHE* 1.3 60.8 + - + +
189B SER* 3.0 4.5 + - - -
190B LEU* 2.9 26.0 + - - +
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Residues in contact with PHE 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU* 5.6 0.3 - - - +
89B TYR* 3.9 11.9 - - + -
90B SER* 3.7 44.0 - - - +
93B TYR* 4.2 27.8 - + + -
94B ASN* 3.6 22.7 - - - -
166B LEU 5.7 0.2 - - - -
167B VAL* 4.6 17.9 - - + -
170B ALA* 3.7 24.0 - - + -
171B ILE* 5.0 0.7 - - + -
183B SER* 3.1 28.4 + - - -
184B ASP* 3.3 9.6 + - - +
186B VAL* 1.3 75.6 - - + +
188B GLU* 1.3 61.7 + - - +
190B LEU* 3.3 19.5 + - + +
191B GLU* 3.2 19.8 + - - +
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Residues in contact with GLU 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ASP* 4.9 4.7 - - - +
158A LYS* 3.3 33.3 + - + +
184B ASP 2.9 14.6 + - - +
185B TYR* 3.4 20.6 - - - +
187B PHE* 1.3 76.9 - - - +
189B SER* 1.3 56.9 + - - +
191B GLU* 3.2 12.9 + - + +
192B ASP* 3.0 28.4 + - - +
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Residues in contact with SER 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LYS* 3.7 13.3 - - - +
159A ILE* 5.6 0.2 - - - -
162A SER* 2.5 36.2 + - - -
193A LEU* 4.8 11.2 - - - +
166B LEU* 4.2 10.6 - - - +
185B TYR 3.0 9.8 + - - -
186B VAL* 3.0 8.2 + - - -
188B GLU* 1.3 72.7 - - - +
190B LEU* 1.3 60.4 + - - +
192B ASP* 3.3 12.7 + - - +
193B LEU* 2.8 27.7 + - - +
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Residues in contact with LEU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU 4.2 7.6 - - - +
87B LEU* 3.8 19.7 - - + -
89B TYR* 4.2 11.9 - - + -
90B SER 5.6 0.7 - - - +
163B MET* 3.8 45.3 - - + +
166B LEU* 3.7 20.6 - - + +
167B VAL* 3.9 24.0 - - + -
186B VAL 2.9 15.5 + - - +
187B PHE* 3.5 20.6 - - + +
188B GLU 3.2 0.2 - - - -
189B SER* 1.3 72.9 - - - +
191B GLU* 1.3 62.4 + - - +
193B LEU* 3.1 6.6 + - + +
194B ILE* 3.1 22.5 + - + +
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Residues in contact with GLU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LYS* 4.5 14.8 + - - +
87B LEU* 3.8 31.7 - - + +
187B PHE 3.2 10.0 + - - +
188B GLU* 3.2 14.0 + - + +
190B LEU* 1.3 76.8 - - - +
192B ASP* 1.3 60.5 + - - +
194B ILE* 3.3 1.6 + - - +
195B ALA* 2.9 31.8 + - + +
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Residues in contact with ASP 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LYS* 2.6 36.4 + - - -
188B GLU* 3.0 21.8 + - - +
189B SER* 3.5 12.4 + - - +
191B GLU* 1.3 76.0 - - - +
193B LEU* 1.3 63.6 + - - +
195B ALA* 3.3 6.9 + - - +
196B GLY* 3.0 21.1 + - - -
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Residues in contact with LEU 193 (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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189A SER* 4.9 13.2 - - - +
159B ILE* 3.6 36.1 - - + +
162B SER* 3.9 24.2 - - - -
163B MET* 4.0 19.1 - - + +
166B LEU* 3.9 18.8 - - + -
189B SER 2.8 17.8 + - - +
190B LEU* 3.1 9.8 + - + +
192B ASP* 1.3 74.6 - - - +
194B ILE* 1.3 62.8 + - + +
196B GLY* 3.3 8.2 + - - -
197B ILE* 3.6 13.0 + - - +
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Residues in contact with ILE 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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83B LYS* 4.2 23.6 - - + +
86B LEU* 3.9 22.0 - - + -
87B LEU* 3.8 21.1 - - + -
150B PHE* 4.1 22.0 - - + -
159B ILE* 3.9 18.6 - - + -
163B MET* 3.8 30.3 - - + -
190B LEU* 3.1 19.0 + - + +
191B GLU 4.0 2.9 - - - +
193B LEU* 1.3 75.0 - - + +
195B ALA* 1.3 66.4 + - - +
197B ILE* 2.9 27.0 + - + +
198B GLU* 3.5 5.4 + - - +
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Residues in contact with ALA 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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83B LYS* 4.8 7.7 - - - +
191B GLU* 2.9 24.1 + - + +
192B ASP* 3.7 7.2 - - - +
194B ILE* 1.3 72.2 - - - +
196B GLY* 1.3 61.1 + - - +
198B GLU* 3.1 39.2 + - - +
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Residues in contact with GLY 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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151B ARG* 2.9 27.7 + - - -
192B ASP 3.0 14.3 + - - -
193B LEU 3.8 5.4 - - - -
194B ILE 3.1 0.8 - - - -
195B ALA* 1.3 76.8 - - - +
197B ILE* 1.3 59.2 + - - +
198B GLU 3.4 0.2 - - - -
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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