Contacts of the helix formed by residues 179 - 195 (chain A) in PDB entry 2W3C
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 ARG 179 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A PHE* 3.0 32.3 + - - +
136A PHE* 3.6 46.0 - - + +
139A ARG* 3.9 5.3 - - - +
177A ASP* 2.8 45.7 + - - +
178A SER* 1.3 82.8 + - - +
180A GLU* 1.3 59.8 + - - +
181A VAL* 3.3 2.5 - - + +
182A ILE* 3.2 32.8 + - + +
183A ARG 3.3 8.1 + - - -
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Residues in contact with GLU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A SER 3.4 7.7 + - - +
179A ARG* 1.3 68.8 - - - +
181A VAL* 1.3 66.6 + - + +
182A ILE 3.2 1.3 - - - -
183A ARG* 3.9 33.9 + - + +
184A ASN* 3.0 46.9 + - - +
220A GLU* 4.5 13.9 - - - +
228A VAL* 5.5 1.7 - - - +
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Residues in contact with VAL 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A PHE* 4.1 24.9 - - + -
140A TRP* 3.8 34.2 + - + +
179A ARG* 3.3 1.3 - - + -
180A GLU* 1.3 82.5 - - + +
182A ILE* 1.3 59.4 + - - +
184A ASN* 4.4 3.1 - - - +
185A ASP* 3.5 25.9 + - - +
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Residues in contact with ILE 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A PHE* 3.8 31.0 - - + +
139A ARG* 3.8 31.6 - - + +
140A TRP* 4.1 20.6 - - + +
143A VAL* 4.4 11.5 - - + +
174A LEU* 4.1 6.7 - - + +
177A ASP* 3.8 21.3 - - + +
179A ARG* 3.2 37.0 + - - +
181A VAL* 1.3 78.9 - - - +
183A ARG* 1.3 60.8 + - - +
184A ASN 3.3 0.2 - - - -
185A ASP* 3.8 2.7 - - - +
186A GLY* 2.8 24.9 + - - -
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Residues in contact with ARG 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A LEU 3.5 19.7 + - - +
175A LEU* 4.0 15.1 + - - +
177A ASP* 3.8 18.2 + - - +
179A ARG 3.3 6.8 + - - +
180A GLU* 4.0 29.3 + - + +
182A ILE* 1.3 75.4 - - - +
184A ASN* 1.3 94.4 + - - +
186A GLY* 3.4 0.9 - - - +
187A VAL* 2.9 35.6 + - - +
216A ILE* 3.7 49.6 - - - +
219A GLU* 4.0 16.0 + - - -
220A GLU* 3.8 16.0 + - - +
228A VAL* 4.0 5.7 - - - +
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Residues in contact with ASN 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A GLU* 3.0 36.6 + - - +
181A VAL* 4.4 3.7 - - - +
183A ARG* 1.3 102.6 + - - +
185A ASP* 1.3 68.0 + - - +
187A VAL* 3.2 20.3 + - - +
188A LEU* 3.3 15.4 + - - +
228A VAL* 3.5 34.0 - - + +
231A ASP* 5.1 2.5 - - - +
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Residues in contact with ASP 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A TRP* 2.7 32.3 + - + +
143A VAL* 3.6 25.6 - - + +
144A LYS* 3.8 12.5 - - + +
147A THR* 4.4 1.4 + - - -
181A VAL* 3.5 17.1 + - - +
182A ILE 4.3 1.1 - - - +
184A ASN* 1.3 74.9 - - - +
186A GLY* 1.3 65.8 + - - +
188A LEU* 3.4 20.9 + - - +
189A LEU 3.0 18.4 + - - -
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Residues in contact with GLY 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A VAL* 4.1 4.7 - - - +
174A LEU* 4.5 18.8 - - - +
175A LEU* 4.6 0.9 - - - -
182A ILE 2.8 21.3 + - - -
183A ARG* 3.4 4.7 - - - -
184A ASN 3.1 0.8 - - - -
185A ASP* 1.3 76.5 - - - +
187A VAL* 1.3 55.8 + - - +
189A LEU* 3.0 12.5 + - - +
190A LEU* 3.0 35.3 + - - +
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Residues in contact with VAL 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A LEU* 3.5 22.8 - - + +
183A ARG* 2.9 24.1 + - - +
184A ASN* 3.4 13.0 - - - +
186A GLY* 1.3 73.7 - - - +
188A LEU* 1.3 61.6 + - - +
190A LEU* 3.3 3.5 + - - +
191A GLN* 3.2 23.4 + - - +
213A LEU* 4.9 0.9 - - + -
216A ILE* 4.9 5.4 - - + -
228A VAL* 5.7 2.5 - - + +
231A ASP* 3.5 40.6 - - + +
232A CYS* 3.9 19.7 - - - +
235A LEU* 4.1 16.6 - - + +
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Residues in contact with LEU 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A THR* 3.7 17.5 - - + +
151A LYS* 5.8 0.2 - - - +
184A ASN 3.3 7.3 + - - +
185A ASP* 3.6 26.0 - - - +
186A GLY 3.2 0.4 - - - -
187A VAL* 1.3 75.9 - - - +
189A LEU* 1.3 63.5 + - - +
191A GLN* 3.2 38.1 - - - +
192A ALA* 3.5 5.7 + - - +
231A ASP* 3.8 30.7 - - - +
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Residues in contact with LEU 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LEU* 5.1 0.4 - - + -
143A VAL* 3.4 32.8 - - + +
146A LEU* 3.8 25.4 - - + -
147A THR* 3.5 21.2 + - - +
150A LEU* 3.9 12.7 - - + +
171A LEU* 4.1 27.8 - - + -
174A LEU* 4.3 13.5 - - + -
185A ASP 3.0 11.4 + - - +
186A GLY* 3.0 14.0 + - - +
188A LEU* 1.3 76.1 - - - +
190A LEU* 1.3 69.1 + - + +
192A ALA* 3.1 7.2 + - - +
193A LEU* 2.9 25.1 + - + -
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Residues in contact with LEU 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A LEU* 4.3 23.8 - - + +
172A MET* 3.9 25.6 - - + -
174A LEU* 6.0 0.4 - - + -
175A LEU* 3.8 42.8 - - + +
186A GLY 3.0 16.5 + - - +
187A VAL 3.3 3.8 + - - +
189A LEU* 1.3 76.2 - - + +
191A GLN* 1.3 54.9 + - - +
192A ALA 3.3 0.2 - - - -
193A LEU* 3.3 25.7 + - + +
194A THR* 2.8 41.2 + - + +
204A VAL* 4.8 6.7 - - + -
235A LEU* 3.7 20.9 - - + -
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Residues in contact with GLN 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A VAL 3.2 13.0 + - - +
188A LEU* 3.2 30.5 - - - +
190A LEU* 1.3 75.3 - - - +
192A ALA* 1.3 55.6 + - - +
194A THR* 3.8 0.7 - - - -
195A ARG* 3.1 17.5 + - - +
231A ASP* 2.7 49.0 + - - +
234A ILE* 3.7 31.5 - - + +
235A LEU* 3.8 15.1 - - + +
238A ASN* 3.0 26.8 + - - +
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Residues in contact with ALA 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A THR* 4.3 9.9 - - + -
150A LEU* 3.6 33.1 - - + +
151A LYS* 4.3 17.7 - - + +
158A GLN* 2.8 21.1 + - - -
188A LEU 3.5 8.3 + - - +
189A LEU 3.1 9.5 + - - +
191A GLN* 1.3 77.6 - - - +
193A LEU* 1.3 60.5 + - - +
195A ARG* 3.9 6.9 + - - +
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Residues in contact with LEU 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A LEU* 4.1 13.2 - - + +
158A GLN* 2.9 27.5 + - + +
161A ILE* 3.5 40.6 - - + -
168A VAL* 4.2 13.0 - - + -
171A LEU* 3.8 22.7 - - + -
189A LEU* 2.9 13.4 + - + +
190A LEU* 3.6 29.6 - - + +
191A GLN 3.2 0.4 - - - -
192A ALA* 1.3 78.8 - - - +
194A THR* 1.3 58.0 - - - +
197A ASN* 4.2 0.5 - - - +
200A ILE* 3.8 34.3 - - + +
204A VAL* 4.9 2.0 - - + -
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Residues in contact with THR 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A LEU* 2.8 23.9 + - + +
193A LEU* 1.3 78.3 - - + +
195A ARG* 1.3 68.1 + - - +
197A ASN 3.0 8.4 + - - +
200A ILE* 4.3 11.9 - - + +
201A GLN* 2.9 36.5 + - - -
204A VAL* 3.7 30.1 - - + -
235A LEU* 3.7 7.3 - - + +
238A ASN* 2.9 30.7 + - - +
239A LEU* 4.1 13.9 - - + -
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Residues in contact with ARG 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A LYS 5.8 2.0 + - - -
158A GLN* 3.1 19.4 + - - +
191A GLN 3.1 19.9 + - - +
192A ALA* 4.2 9.4 - - - +
193A LEU 3.4 1.8 - - - -
194A THR* 1.3 74.2 - - - +
196A SER* 1.3 80.5 + - - +
197A ASN 3.0 1.6 + - - -
238A ASN* 3.8 15.0 - - - +
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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