Contacts of the helix formed by residues 202 - 216 (chain A) in PDB entry 4U2M
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 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A GLU 3.4 5.2 + - - +
201A ILE* 1.3 79.8 - - - +
203A PRO* 1.3 73.4 - - - +
204A GLU* 2.9 35.5 + - - +
205A GLY* 2.9 10.6 + - - +
206A PHE 3.1 17.2 + - - -
227A ALA* 4.1 26.5 - - + +
231A THR* 4.3 6.4 + - - +
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Residues in contact with PRO 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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161A VAL* 3.8 29.8 - - + +
162A SER* 4.7 9.0 - - - -
163A ARG* 5.5 0.9 - - + +
164A GLU* 3.8 36.1 - - + +
166A PHE* 3.8 5.8 - - + -
201A ILE 3.3 9.8 - - - +
202A ASN* 1.3 87.6 - - - +
204A GLU* 1.3 57.7 + - - +
206A PHE* 3.1 4.1 + - + +
207A CYS* 2.9 29.1 + - - +
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Residues in contact with GLU 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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164A GLU* 5.4 0.8 + - - -
202A ASN* 2.9 15.0 + - - +
203A PRO* 1.3 75.8 - - - +
205A GLY* 1.3 63.4 + - - +
207A CYS* 3.3 8.1 + - + +
208A ILE* 3.1 50.4 + - + +
223A GLY 5.5 0.7 - - - +
224A ASN* 3.9 22.4 + - - +
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Residues in contact with GLY 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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202A ASN* 2.9 15.9 + - - -
204A GLU* 1.3 77.1 - - - +
206A PHE* 1.3 62.7 + - - +
208A ILE* 3.4 2.6 + - - +
209A LEU* 3.1 27.9 + - - +
224A ASN* 6.2 0.2 - - - -
227A ALA* 4.5 4.7 - - - +
228A VAL* 4.2 22.5 - - - +
231A THR* 4.1 16.2 - - - -
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Residues in contact with PHE 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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159A ILE* 3.7 23.8 - - + -
161A VAL* 4.0 13.2 - - + -
166A PHE* 3.7 42.2 - + + -
173A LEU* 5.3 0.4 - - + -
180A PHE* 4.1 15.9 - + - -
197A LEU* 4.0 20.4 - - + -
201A ILE* 4.7 2.0 - - + -
202A ASN 3.1 10.8 + - - +
203A PRO 3.1 9.3 + - - +
205A GLY* 1.3 78.1 - - - +
207A CYS* 1.3 53.4 + - - +
209A LEU* 3.0 3.6 + - - +
210A LEU* 2.8 54.2 + - + -
213A MET* 5.4 2.5 - - + -
231A THR* 4.0 12.5 - - + +
235A LEU* 4.0 27.6 - - + -
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Residues in contact with CYS 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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149A ARG* 6.3 0.2 - - - -
164A GLU* 5.8 0.7 - - - +
166A PHE* 3.7 27.6 - - + -
203A PRO 2.9 12.6 + - - +
204A GLU* 3.5 13.2 - - + +
206A PHE* 1.3 77.9 - - - +
208A ILE* 1.3 58.3 + - + +
210A LEU* 3.4 5.3 + - - +
211A ASP* 3.0 49.7 + - - +
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Residues in contact with ILE 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 GLU* 3.1 36.0 + - + +
205A GLY 3.7 3.8 - - - +
207A CYS* 1.3 78.1 - - + +
209A LEU* 1.3 59.0 + - - +
211A ASP* 3.6 8.4 + - - +
212A PHE* 3.0 25.1 + - - +
217A ARG 4.7 1.4 - - - +
218A LEU* 4.2 17.7 - - + +
219A ASN* 4.0 27.5 + - + +
220A LEU* 5.2 0.2 - - + -
224A ASN* 3.3 34.3 - - + +
228A VAL* 3.9 20.2 - - + -
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Residues in contact with LEU 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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205A GLY 3.1 7.0 + - - +
206A PHE 3.0 8.9 + - - +
208A ILE* 1.3 76.1 - - - +
210A LEU* 1.3 59.4 + - - +
212A PHE* 3.1 6.6 + - + +
213A MET* 2.9 32.9 + - - +
218A LEU* 4.0 12.8 - - + -
228A VAL* 3.8 11.7 - - + +
231A THR* 3.5 25.6 - - + -
232A ALA* 3.4 33.2 - - + +
235A LEU* 4.0 9.4 - - + -
237A MET* 4.3 20.8 - - + +
240A VAL* 3.7 32.1 - - + -
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Residues in contact with LEU 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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149A ARG* 3.5 24.5 - - - +
159A ILE* 6.3 0.2 - - + -
166A PHE* 3.8 36.3 - - + -
167A ARG 4.3 8.3 - - - +
168A ALA* 4.3 6.3 - - + -
173A LEU* 3.6 30.7 - - + -
206A PHE* 2.8 33.8 + - + +
207A CYS* 3.7 5.6 - - - +
209A LEU* 1.3 68.9 - - - +
211A ASP* 1.3 65.2 + - - +
213A MET* 3.1 22.3 + - - +
214A TYR* 3.3 31.1 + - + -
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Residues in contact with ASP 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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149A ARG* 3.0 32.2 + - - +
207A CYS* 3.0 36.7 + - - +
208A ILE* 3.8 8.7 - - - +
210A LEU* 1.3 74.8 - - - +
212A PHE* 1.3 58.7 + - - +
214A TYR 3.3 1.6 + - - -
215A THR* 2.7 41.6 + - + +
217A ARG 4.3 3.1 - - - +
219A ASN* 5.2 8.8 - - - +
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Residues in contact with PHE 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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3A PHE* 3.6 43.1 - + + -
6A HIS* 3.6 32.3 + + - -
176A CYS* 5.8 1.3 - - + -
208A ILE 3.0 15.9 + - - +
209A LEU* 3.1 14.8 + - + +
211A ASP* 1.3 75.8 - - - +
213A MET* 1.3 68.4 + - + +
215A THR* 4.0 0.4 - - - -
216A SER* 2.8 46.1 + - - -
217A ARG 3.3 18.8 + - - +
218A LEU* 3.9 20.9 - - + -
237A MET* 5.1 5.6 - - + -
240A VAL* 3.7 24.0 - - + -
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Residues in contact with MET 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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6A HIS* 2.8 25.1 + - - -
142A LEU* 3.6 11.1 - - - +
172A VAL* 4.4 4.5 - - + +
173A LEU* 3.6 33.9 - - + -
176A CYS* 3.6 31.8 - - + -
177A SER* 4.1 15.3 - - - -
180A PHE* 4.5 4.9 - - + -
206A PHE* 5.4 1.8 - - + -
209A LEU 2.9 17.9 + - - +
210A LEU* 3.1 15.9 + - + +
212A PHE* 1.3 82.8 - - + +
214A TYR* 1.3 65.2 + - + +
235A LEU* 4.3 5.2 - - + -
237A MET* 3.1 37.5 - - + -
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Residues in contact with TYR 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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142A LEU* 3.4 31.2 - - + +
143A LEU* 5.1 1.2 - - - -
145A LEU* 3.7 15.9 - - + -
146A ASN* 3.3 44.5 - - - +
149A ARG* 3.5 29.4 - - - +
168A ALA* 3.8 3.9 - - + +
169A HIS* 2.7 52.1 + - - +
172A VAL* 3.7 31.6 - - + +
173A LEU* 5.0 1.3 - - + -
210A LEU* 3.3 33.2 + - + +
211A ASP 4.0 2.5 - - - +
212A PHE 3.2 0.6 - - - -
213A MET* 1.3 80.6 - - + +
215A THR* 1.3 57.5 + - - +
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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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142A LEU* 4.4 3.4 - - - -
146A ASN* 3.6 23.3 - - - +
149A ARG* 5.2 0.9 - - - +
211A ASP* 2.7 28.8 + - + +
214A TYR* 1.3 82.1 - - + +
216A SER* 1.3 73.0 + - - +
217A ARG* 3.0 43.0 + - - +
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Residues in contact with SER 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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2A ASP* 3.9 2.1 + - - -
3A PHE* 3.5 43.1 + - - -
6A HIS* 3.1 28.0 - - - +
7A SER* 3.9 6.6 + - - -
142A LEU* 3.7 8.1 - - - +
212A PHE* 2.8 21.9 + - - -
215A THR* 1.3 80.1 + - - +
217A ARG* 1.3 63.4 + - - +
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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