Contacts of the helix formed by residues 187 - 201 (chain A) in PDB entry 2Y4U
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 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A LYS 3.4 0.6 + - - -
118A GLN 3.2 21.7 - - - +
119A GLY* 3.3 22.7 - - - +
158A ARG* 4.9 2.1 + - - -
181A LEU* 4.5 0.8 - - + +
184A CYS* 3.6 17.1 + - + +
185A VAL 3.6 1.4 + - - -
186A TRP* 1.3 72.6 - - - +
188A ALA* 1.3 59.7 + - - +
189A GLU* 2.9 22.8 + - - +
190A LEU* 2.8 39.2 + - + +
191A ARG* 3.1 27.5 + - - +
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Residues in contact with ALA 188 (chain A).
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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186A TRP 3.5 4.5 + - - +
187A ASP* 1.3 70.5 - - - +
189A GLU* 1.3 75.1 + - - +
191A ARG* 3.3 11.4 + - - +
192A GLU* 2.9 30.2 + - - +
214A ALA* 4.4 8.6 - - - +
217A LEU* 4.3 16.8 - - + -
218A LYS* 4.2 32.1 - - + -
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Residues in contact with GLU 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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118A GLN 5.1 1.2 - - - +
120A LYS* 6.1 1.6 - - - +
158A ARG* 6.2 1.8 - - - +
187A ASP* 2.9 16.7 - - - +
188A ALA* 1.3 80.4 + - + +
190A LEU* 1.3 66.0 + - + +
192A GLU* 3.6 13.4 - - - +
193A LEU* 3.3 18.9 + - - +
218A LYS* 5.7 6.7 - - - +
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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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119A GLY 5.4 0.2 - - - +
158A ARG* 4.5 28.9 - - + +
162A LEU* 4.5 22.4 - - + -
177A LEU* 4.2 16.1 - - + +
180A ILE* 4.3 24.5 - - + -
181A LEU* 4.2 12.8 - - + -
184A CYS* 5.3 2.5 - - + -
187A ASP* 2.8 39.7 + - + +
188A ALA 3.1 0.4 - - - -
189A GLU* 1.3 80.0 - - + +
191A ARG* 1.3 66.5 + - - +
193A LEU* 2.8 21.1 + - + +
194A ARG* 2.8 13.7 + - - +
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Residues in contact with ARG 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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181A LEU* 4.1 22.8 + - + +
184A CYS 5.4 0.2 + - - -
185A VAL* 2.9 35.1 + - - +
187A ASP 3.1 21.7 + - - +
188A ALA* 3.6 8.7 - - - +
190A LEU* 1.3 76.5 - - - +
192A GLU* 1.3 52.1 + - - +
194A ARG* 2.8 24.9 + - - +
195A ALA* 2.7 34.7 + - - +
209A SER* 4.6 6.7 + - - -
210A ASP* 3.7 36.2 + - + +
213A ALA* 3.9 31.0 - - - +
214A ALA* 4.8 3.1 - - + +
217A LEU* 5.0 5.1 - - - +
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Residues in contact with GLU 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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188A ALA 2.9 20.4 + - - +
189A GLU* 3.6 11.9 - - - +
191A ARG* 1.3 75.7 - - - +
193A LEU* 1.3 57.8 + - - +
195A ALA* 3.2 8.2 + - - +
196A GLU* 2.8 29.7 + - - +
211A LEU* 4.4 13.7 - - + +
214A ALA* 4.0 17.2 - - + +
218A LYS* 3.1 36.8 + - - -
224A ALA* 5.0 5.5 - - - +
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Residues in contact with LEU 193 (chain A).
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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161A ALA 5.5 0.4 - - - -
162A LEU* 3.9 31.9 - - + +
165A PHE* 3.4 55.9 - - + -
177A LEU* 4.3 21.3 - - + -
189A GLU 3.3 11.0 + - - +
190A LEU* 2.8 18.3 + - + +
192A GLU* 1.3 75.7 - - - +
194A ARG* 1.3 61.4 + - - +
196A GLU* 3.2 7.9 + - + +
197A CYS* 3.0 24.6 + - - -
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Residues in contact with ARG 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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174A ILE* 4.5 9.0 - - + -
177A LEU* 3.9 35.9 - - + +
178A ASP* 2.8 48.2 + - - +
181A LEU* 3.4 21.4 - - + +
190A LEU 2.8 10.9 + - - +
191A ARG* 3.3 19.6 - - - +
193A LEU* 1.3 73.8 - - - +
195A ALA* 1.3 67.1 + - - +
197A CYS* 2.9 17.2 + - + +
198A PHE* 3.1 35.8 + - + -
210A ASP* 2.9 33.5 + - - +
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Residues in contact with ALA 195 (chain A).
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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191A ARG 2.7 15.6 + - - +
192A GLU 3.4 8.7 - - - +
194A ARG* 1.3 74.1 - - - +
196A GLU* 1.3 61.0 + - - +
198A PHE* 3.2 8.3 + - - +
199A ILE* 3.2 20.6 + - + +
207A ALA* 3.6 21.5 - - + +
210A ASP* 3.8 13.4 - - + +
211A LEU* 3.6 34.1 - - + -
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Residues in contact with GLU 196 (chain A).
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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165A PHE* 4.6 15.9 - - + -
192A GLU 2.8 13.8 + - - +
193A LEU* 3.4 13.2 - - + +
194A ARG 3.1 0.2 - - - -
195A ALA* 1.3 77.0 - - - +
197A CYS* 1.3 62.5 + - - +
199A ILE* 3.2 32.1 - - - +
200A LYS* 2.9 52.4 + - + +
227A LYS* 4.6 11.6 + - - -
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Residues in contact with CYS 197 (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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165A PHE* 3.6 26.9 - - - -
170A TYR* 4.5 22.0 - - + +
173A ALA* 4.6 4.0 - - - -
174A ILE* 3.8 22.2 - - + -
177A LEU* 4.5 11.4 - - - -
193A LEU 3.0 20.3 + - - -
194A ARG* 2.9 14.0 + - - +
196A GLU* 1.3 74.3 - - - +
198A PHE* 1.3 64.8 + - - +
200A LYS* 2.9 10.5 + - - +
201A GLU* 2.8 24.3 + - - +
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Residues in contact with PHE 198 (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 ILE* 3.9 37.0 - - + -
178A ASP* 5.2 3.1 - - - -
194A ARG* 3.1 34.3 + - + -
195A ALA* 3.4 9.0 - - - +
197A CYS* 1.3 77.2 - - - +
199A ILE* 1.3 58.3 + - - +
201A GLU* 2.9 17.8 + - - +
202A GLY 3.0 0.2 + - - -
203A GLU* 2.9 42.0 + - - +
206A LYS* 3.3 53.4 - - + -
207A ALA* 3.7 8.1 - - + +
210A ASP* 4.0 11.4 - - - -
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Residues in contact with ILE 199 (chain A).
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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195A ALA 3.2 3.7 + - - +
196A GLU* 3.2 46.2 - - - +
198A PHE* 1.3 76.5 - - - +
200A LYS* 1.3 59.4 + - + +
202A GLY* 2.8 19.7 + - - +
203A GLU 4.3 3.6 - - - +
204A PRO* 3.6 23.7 - - + +
207A ALA* 3.6 27.4 - - + -
211A LEU* 5.6 5.8 - - + -
227A LYS* 4.8 11.9 - - - +
231A LEU* 4.6 9.9 - - + -
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Residues in contact with LYS 200 (chain A).
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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165A PHE* 5.6 3.4 - - + -
170A TYR* 3.5 50.2 - - + +
196A GLU* 2.9 40.9 + - + +
197A CYS 3.4 8.7 - - - +
199A ILE* 1.3 78.0 - - + +
201A GLU* 1.3 59.5 + - - +
202A GLY* 3.4 0.9 + - - -
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Residues in contact with GLU 201 (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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170A TYR* 3.3 31.5 + - + +
171A THR* 3.6 26.3 + - + +
174A ILE* 5.0 5.6 - - + -
197A CYS 2.8 12.9 + - - +
198A PHE* 2.9 10.7 + - - +
200A LYS* 1.3 78.3 - - - +
202A GLY* 1.3 60.7 + - - -
203A GLU* 3.3 25.2 + - - +
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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
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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