Contacts of the helix formed by residues 202 - 217 (chain A) in PDB entry 4O5A
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 HIS 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A ASP* 6.4 2.0 - - + -
161A LEU* 4.7 3.5 - - + +
172A ASP* 3.5 16.6 - - - +
193A ARG* 5.6 0.2 - - - -
200A LEU* 3.1 35.4 - - + +
201A GLY* 1.3 75.6 - - - +
203A SER* 1.3 67.6 + - - +
204A TYR 3.3 1.8 - - - -
205A ILE* 3.5 11.0 + - + +
206A ARG* 3.1 69.4 + - - +
228A TYR* 4.0 8.6 + - - -
253A ASP* 4.3 4.9 - - - -
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Residues in contact with SER 203 (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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193A ARG* 5.0 4.1 + - - +
197A PRO 4.2 7.2 - - - -
198A GLU* 3.7 29.2 + - - +
200A LEU* 3.0 18.6 + - - -
201A GLY 3.3 0.2 - - - -
202A HIS* 1.3 85.8 + - - +
204A TYR* 1.3 68.5 + - - +
206A ARG* 3.9 3.4 - - - +
207A ASP* 3.0 29.8 + - - +
225A HIS* 4.0 14.4 - - - -
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Residues in contact with TYR 204 (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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137A ILE* 3.6 32.5 - - + -
198A GLU* 4.2 21.5 + - + +
200A LEU 4.6 2.4 + - - -
201A GLY 4.5 2.7 + - - +
202A HIS 3.3 0.4 - - - -
203A SER* 1.3 90.0 - - - +
205A ILE* 1.3 66.8 + - + +
206A ARG 3.4 0.2 - - - -
207A ASP* 4.2 7.8 - - + +
208A ALA* 3.1 25.6 + - - +
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Residues in contact with ILE 205 (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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158A ASP* 4.1 25.4 - - + +
160A SER* 3.7 25.4 - - - +
161A LEU* 5.5 4.3 - - + -
172A ASP* 4.2 21.1 - - + +
173A ALA* 4.4 14.3 - - + +
201A GLY 4.4 13.7 + - - +
202A HIS* 3.8 9.6 - - + +
203A SER 3.4 0.2 - - - -
204A TYR* 1.3 78.6 - - + +
206A ARG* 1.3 64.2 + - + +
208A ALA* 3.5 4.4 + - - +
209A ALA* 3.1 23.0 + - - +
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Residues in contact with ARG 206 (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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172A ASP* 2.9 40.6 + - + +
176A SER* 4.6 5.6 - - - -
193A ARG* 3.7 24.7 - - - +
202A HIS* 3.1 47.4 + - - +
203A SER* 3.9 1.8 - - - +
205A ILE* 1.3 77.8 - - - +
207A ASP* 1.3 57.9 + - - +
209A ALA* 3.3 1.7 + - - +
210A PHE* 2.9 34.7 + - - -
228A TYR* 5.3 0.8 + - - -
253A ASP* 3.4 30.7 + - - +
281A TRP* 3.5 50.6 - - + +
299A ARG* 6.2 2.2 - - - +
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Residues in contact with ASP 207 (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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193A ARG* 4.0 8.6 - - - +
203A SER* 3.0 19.4 + - - +
204A TYR* 4.2 11.0 - - + +
206A ARG* 1.3 75.1 - - - +
208A ALA* 1.3 59.0 + - - +
210A PHE* 3.4 2.4 + - - +
211A SER* 2.9 45.9 + - - -
221A TYR* 4.2 6.6 - - - -
223A OCS 3.5 26.3 + - - +
225A HIS* 6.3 1.8 - - + +
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Residues in contact with ALA 208 (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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204A TYR 3.1 19.9 + - - +
205A ILE* 3.9 4.7 - - - +
207A ASP* 1.3 80.8 + - - +
209A ALA* 1.3 56.3 + - - +
211A SER* 3.5 4.4 + - - -
212A GLU* 3.0 31.2 + - - +
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Residues in contact with ALA 209 (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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173A ALA* 3.8 34.5 - - + +
176A SER* 3.8 13.0 - - - +
205A ILE 3.1 16.8 + - - +
206A ARG 3.7 3.4 - - - +
207A ASP 3.3 0.2 - - - -
208A ALA* 1.3 77.2 - - - +
210A PHE* 1.3 62.8 + - - +
212A GLU* 3.4 3.9 + - - -
213A ILE* 3.0 36.2 + - + +
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Residues in contact with PHE 210 (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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176A SER* 3.4 31.9 - - - -
179A MSE 4.3 8.7 - - + -
180A ILE* 3.6 25.8 - - + -
191A ILE* 4.5 4.7 - - + -
193A ARG* 3.8 23.3 - - + -
206A ARG 2.9 19.3 + - - +
207A ASP 4.0 1.3 - - - +
209A ALA* 1.3 75.8 - - - +
211A SER* 1.3 55.2 + - - +
214A THR* 2.6 41.8 + - + +
221A TYR* 3.5 40.2 - + + +
251A ILE* 3.6 34.3 - - + -
281A TRP* 3.7 17.7 - + - -
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Residues in contact with SER 211 (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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207A ASP* 2.9 35.8 + - - -
208A ALA* 3.9 4.7 - - - -
210A PHE* 1.3 75.8 - - - +
212A GLU* 1.3 62.8 + - - +
214A THR* 3.4 4.6 + - - -
215A THR* 2.9 32.4 + - - -
221A TYR* 4.1 12.0 - - - -
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Residues in contact with GLU 212 (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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208A ALA 3.0 18.7 + - - +
209A ALA* 4.0 4.0 - - - +
211A SER* 1.3 77.8 - - - +
213A ILE* 1.3 67.7 + - - +
215A THR* 3.8 3.3 - - - -
216A GLU* 3.0 55.2 + - + +
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Residues in contact with ILE 213 (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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173A ALA 4.3 7.2 - - - +
176A SER* 4.2 1.3 - - - -
177A GLY* 3.5 35.0 - - - +
180A ILE* 3.7 32.8 - - + -
181A ARG* 5.6 4.3 - - + +
209A ALA* 3.0 22.2 + - + +
212A GLU* 1.3 87.1 - - - +
214A THR* 1.3 65.7 + - - +
216A GLU* 3.2 6.1 + - - +
217A LEU* 3.0 34.4 + - + +
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Residues in contact with THR 214 (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 ILE* 4.1 17.9 - - + -
191A ILE* 4.0 24.0 - - + -
210A PHE* 2.6 26.9 + - + +
211A SER* 3.4 4.9 + - - -
213A ILE* 1.3 77.6 - - - +
215A THR* 1.3 62.9 + - - +
217A LEU 3.1 1.7 + - - -
218A GLY 3.0 4.3 + - - -
219A MSE 2.8 52.6 + - + -
221A TYR* 3.4 31.3 - - + +
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Residues in contact with THR 215 (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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211A SER* 2.9 24.4 + - - -
212A GLU* 3.8 4.3 - - - -
214A THR* 1.3 76.6 + - - +
216A GLU* 1.3 67.2 + - + +
218A GLY* 3.1 14.2 + - - +
219A MSE 4.7 3.8 - - - +
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Residues in contact with GLU 216 (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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212A GLU* 3.0 45.6 + - + +
213A ILE* 3.8 5.4 - - - +
214A THR 3.2 0.2 - - - -
215A THR* 1.3 81.9 - - + +
217A LEU* 1.3 64.2 + - + +
218A GLY 3.3 0.8 + - - -
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Residues in contact with LEU 217 (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 ILE* 4.2 5.4 - - + -
181A ARG* 5.0 10.8 - - + -
184A ALA* 4.3 14.8 - - + -
189A LYS* 6.1 0.3 - - - +
213A ILE* 3.0 35.1 + - + +
214A THR 3.1 1.1 + - - +
216A GLU* 1.3 82.4 - - + +
218A GLY* 1.3 64.6 + - - +
219A MSE 3.3 31.6 + - - +
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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