Contacts of the helix formed by residues 179 - 193 (chain B) in PDB entry 4EOZ
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 ASP 179 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168B MSE 3.3 26.6 - - + +
178B VAL* 1.3 71.8 - - - +
180B ARG* 1.3 61.3 + - - +
181B GLY* 3.3 7.4 + - - -
182B ALA* 3.3 33.6 + - + +
183B ILE* 3.5 7.3 + - - +
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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
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172B GLU* 2.9 43.7 + - - +
178B VAL* 3.0 12.9 + - + +
179B ASP* 1.3 71.8 + - - +
181B GLY* 1.3 65.2 + - - +
183B ILE* 3.4 6.8 + - - +
184B ARG* 3.1 23.8 + - - +
243B GLU* 5.3 2.4 + - - +
246B GLU* 4.1 6.1 + - - +
247B ARG* 4.0 24.5 - - - +
250B HIS* 3.6 37.9 + - + +
251B CYS* 3.3 29.7 - - - -
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Residues in contact with GLY 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ASP* 3.3 7.2 + - - -
180B ARG* 1.3 79.6 - - - +
182B ALA* 1.3 56.4 + - - +
184B ARG* 3.2 22.5 + - - +
185B ASN* 2.9 37.8 + - - +
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Residues in contact with ALA 182 (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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102B LEU* 4.1 31.3 - - + +
168B MSE 4.6 1.6 - - + -
179B ASP* 3.3 34.4 + - + +
180B ARG 3.3 1.0 - - - -
181B GLY* 1.3 76.2 - - - +
183B ILE* 1.3 60.5 + - - +
185B ASN* 3.3 9.6 + - - +
186B ALA* 3.1 23.2 + - - +
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Residues in contact with ILE 183 (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* 4.0 20.6 - - + +
168B MSE 4.1 35.9 - - + -
169B ILE* 4.4 19.1 - - + -
172B GLU* 6.1 0.9 - - - +
178B VAL* 4.2 11.9 - - + -
179B ASP 3.5 14.8 - - - +
180B ARG* 3.4 11.2 + - - +
181B GLY 3.2 0.2 - - - -
182B ALA* 1.3 72.1 - - - +
184B ARG* 1.3 60.6 + - - +
186B ALA* 3.1 3.3 + - - +
187B CYS* 2.8 37.8 + - - -
205B PHE* 5.4 0.2 - - + -
251B CYS* 3.8 24.5 - - + +
252B LEU* 3.8 20.0 - - + -
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Residues in contact with ARG 184 (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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180B ARG 3.1 12.7 + - - +
181B GLY* 3.5 18.9 - - - +
183B ILE* 1.3 81.4 - - - +
185B ASN* 1.3 81.8 + - - +
187B CYS* 3.5 2.1 + - - +
188B GLN* 3.1 37.1 + - + +
250B HIS 4.0 16.6 - - - +
251B CYS 3.2 19.0 + - - +
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Residues in contact with ASN 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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106B ASN* 3.4 41.5 - - + +
109B TRP* 5.0 1.6 + - - -
181B GLY 2.9 21.5 + - - +
182B ALA* 3.7 8.2 - - - +
184B ARG* 1.3 100.9 + - - +
186B ALA* 1.3 60.4 + - - +
188B GLN* 3.6 11.7 + - - +
189B MSE 3.2 23.7 + - - +
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Residues in contact with ALA 186 (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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102B LEU* 5.2 4.3 - - + -
105B LEU* 6.1 0.4 - - + -
106B ASN* 5.5 0.7 - - - -
161B LEU* 4.3 12.8 - - + -
165B LEU* 3.7 27.8 - - + -
182B ALA 3.1 14.2 + - - +
183B ILE 3.1 7.6 + - - +
185B ASN* 1.3 75.2 - - - +
187B CYS* 1.3 66.4 + - - +
189B MSE 3.3 14.2 - - + +
190B LEU* 3.1 28.7 + - - +
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Residues in contact with CYS 187 (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* 4.9 4.3 - - - -
183B ILE* 2.8 27.5 + - - +
184B ARG 3.9 4.0 - - - +
185B ASN 3.4 0.2 - - - -
186B ALA* 1.3 73.4 - - - +
188B GLN* 1.3 56.6 + - - +
190B LEU* 3.2 6.2 + - - +
191B MSE 2.9 32.7 + - - +
201B TYR* 3.7 29.3 - - + -
205B PHE* 4.2 13.7 - - - -
251B CYS 4.0 7.4 - - - +
252B LEU* 4.0 26.2 - - - -
253B ASP* 4.5 8.5 - - + +
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Residues in contact with GLN 188 (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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109B TRP* 5.6 2.7 - - - +
184B ARG* 3.1 30.7 + - + +
185B ASN* 3.9 14.3 - - - +
186B ALA 3.3 0.2 - - - -
187B CYS* 1.3 72.9 - - - +
189B MSE 1.3 62.8 + - - +
191B MSE 3.2 12.9 - - - +
192B ILE* 3.0 45.2 + - + +
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Residues in contact with MSE 189 (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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105B LEU* 4.2 17.9 - - + -
106B ASN* 5.6 2.0 - - - +
109B TRP* 3.5 56.5 - - + +
147B PHE* 4.2 3.6 - - - -
152B VAL* 4.0 21.3 - - + -
161B LEU* 4.0 18.4 - - + -
185B ASN 3.2 11.4 + - - +
186B ALA* 3.3 28.9 - - + +
188B GLN* 1.3 79.8 - - - +
190B LEU* 1.3 79.7 + - + +
192B ILE* 3.1 4.2 + - - +
193B LEU* 3.0 33.5 + - + +
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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
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152B VAL* 3.9 27.4 - - + -
161B LEU* 4.1 13.0 - - + -
165B LEU* 4.9 5.8 - - + -
186B ALA 3.1 15.1 + - - +
187B CYS* 3.2 9.2 + - - +
189B MSE 1.3 90.4 - - + +
191B MSE 1.3 63.8 + - - +
193B LEU* 3.2 16.4 + - + +
194B GLY* 3.5 6.8 + - - -
200B VAL* 3.6 21.1 - - + +
201B TYR* 3.8 20.6 + - + +
204B ASP* 4.5 15.5 - - + -
205B PHE* 3.9 28.5 - - + -
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Residues in contact with MSE 191 (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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187B CYS 2.9 23.4 + - - +
188B GLN* 3.2 13.5 - - - +
190B LEU* 1.3 72.2 - - - +
192B ILE* 1.3 63.1 + - + +
194B GLY* 3.2 11.1 + - - -
195B LEU 4.3 0.3 + - - -
196B GLU* 4.8 1.7 + - - -
197B GLY* 3.4 23.2 + - - +
198B ARG* 3.9 25.4 - - + +
201B TYR* 3.5 30.7 - - + +
253B ASP* 3.4 40.4 - - + +
255B SER* 5.2 0.7 - - - +
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Residues in contact with ILE 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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109B TRP* 3.9 30.7 - - + +
113B GLN* 4.7 8.5 - - - +
140B TYR* 5.2 5.4 - - + +
144B LEU* 3.7 30.5 - - + +
188B GLN* 3.0 41.0 + - + +
189B MSE 3.1 5.4 + - - +
191B MSE 1.3 73.5 - - + +
193B LEU* 1.3 57.7 + - - +
194B GLY 3.0 5.1 + - - -
195B LEU* 3.1 13.3 + - - -
196B GLU 4.5 2.9 + - - +
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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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109B TRP* 3.8 23.8 - - + -
144B LEU* 3.7 30.7 - - + +
147B PHE* 4.4 4.0 - - + -
148B ARG* 3.4 43.5 + - + +
152B VAL* 3.8 38.8 - - + -
189B MSE 3.0 32.0 + - + +
190B LEU* 3.6 12.6 - - + +
191B MSE 3.2 0.6 - - - -
192B ILE* 1.3 75.9 - - - +
194B GLY* 1.3 54.9 + - - +
195B LEU* 3.3 8.4 + - - +
200B VAL* 3.9 10.5 - - + -
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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