Contacts of the helix formed by residues 194 - 209 (chain A) in PDB entry 1XO2
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 SER 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A GLU* 3.4 26.9 + - - -
32A LEU* 6.6 0.2 - - - -
193A LEU* 1.3 73.8 - - - +
195A PRO* 1.4 72.9 - - - +
197A LEU* 3.5 25.2 + - - +
198A ILE* 3.0 25.3 + - - +
230A PHE* 4.4 10.1 - - - -
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Residues in contact with PRO 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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31A GLU* 2.9 29.6 - - + +
150A VAL* 3.8 24.7 - - + +
151A LEU 3.7 6.3 - - - +
152A ALA* 3.4 44.9 - - + +
155A PHE* 3.9 3.6 - - + -
193A LEU 4.5 1.8 - - - +
194A SER* 1.4 83.4 - - - +
196A GLY* 1.3 59.1 + - - -
198A ILE* 4.2 4.7 - - + -
199A CYS* 3.1 20.6 + - - +
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Residues in contact with GLY 196 (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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31A GLU* 2.8 23.6 + - - -
155A PHE* 3.5 24.0 - - - -
159A LEU* 4.3 3.1 - - - +
194A SER 3.1 0.8 - - - -
195A PRO* 1.3 77.7 - - - +
197A LEU* 1.3 60.0 + - - +
199A CYS* 3.5 3.5 - - - +
200A ALA 3.2 16.1 + - - -
228A LEU* 3.7 19.4 - - - +
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Residues in contact with LEU 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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193A LEU* 5.0 6.7 - - + -
194A SER* 3.3 20.9 + - - +
196A GLY* 1.3 71.2 - - - +
198A ILE* 1.3 68.4 + - - +
199A CYS 2.8 3.2 + - - -
200A ALA* 3.0 5.7 + - + +
201A GLY 2.9 21.3 + - - -
228A LEU* 3.4 24.9 - - + -
230A PHE* 3.5 49.6 - - + -
234A THR* 3.8 16.8 - - + -
235A VAL* 4.8 11.9 - - + -
238A VAL* 3.4 28.9 - - + +
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Residues in contact with ILE 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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152A ALA* 3.6 18.8 - - + -
181A ILE* 4.0 17.1 - - + +
184A ALA* 5.8 0.9 - - + -
185A LEU* 4.1 17.5 - - + -
190A ILE* 3.5 30.3 - - + +
191A ALA* 5.5 0.9 - - - -
193A LEU* 3.4 33.9 - - + +
194A SER 3.0 22.8 + - - +
195A PRO* 3.9 8.5 - - + +
197A LEU* 1.3 76.1 - - - +
199A CYS* 1.3 59.5 + - - +
202A GLY* 3.3 16.1 + - - -
238A VAL* 4.3 6.7 - - - +
242A VAL* 3.8 13.9 - - + +
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Residues in contact with CYS 199 (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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152A ALA 3.3 22.0 - - - +
155A PHE* 3.5 12.6 - - + -
156A LEU* 3.2 54.7 - - - -
159A LEU* 4.0 6.1 - - + -
181A ILE* 3.9 9.0 - - - +
195A PRO 3.1 11.7 + - - +
196A GLY 3.5 5.6 - - - +
197A LEU 2.8 1.4 + - - -
198A ILE* 1.3 74.3 - - - +
200A ALA* 1.3 58.3 + - - +
202A GLY* 2.6 23.9 + - - -
203A LEU* 2.8 11.9 + - - +
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Residues in contact with ALA 200 (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 LEU* 4.0 10.0 - - + +
196A GLY 3.2 2.8 + - - +
197A LEU* 3.0 9.4 + - + +
199A CYS* 1.3 76.5 - - - +
201A GLY* 1.3 65.8 + - - +
203A LEU* 2.7 18.9 + - - +
204A LEU* 2.9 17.6 + - - +
224A LEU* 3.7 26.7 - - + -
228A LEU* 3.8 20.4 - - + -
235A VAL* 4.4 12.8 - - + -
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Residues in contact with GLY 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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197A LEU 2.9 9.9 + - - -
198A ILE 4.3 0.4 - - - -
200A ALA* 1.3 76.2 - - - +
202A GLY* 1.3 55.6 + - - +
204A LEU* 3.5 8.0 + - - +
205A THR* 2.9 35.6 + - - -
235A VAL 5.2 0.2 + - - -
238A VAL* 3.8 15.1 - - - +
239A LYS* 3.7 24.1 - - - -
242A VAL* 4.3 4.5 - - - -
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Residues in contact with GLY 202 (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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177A ALA* 4.3 1.6 - - - -
180A THR* 4.0 4.3 + - - -
181A ILE* 3.8 26.9 - - - -
198A ILE 3.3 7.2 + - - -
199A CYS 2.6 16.0 + - - -
201A GLY* 1.3 69.6 - - - +
203A LEU* 1.3 57.9 + - - -
205A THR* 3.8 3.6 - - - -
206A THR* 2.9 32.9 + - - -
242A VAL* 4.1 10.5 - - - +
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Residues in contact with LEU 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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156A LEU* 3.6 27.4 - - + +
159A LEU* 4.4 17.9 - - + -
160A CYS* 3.9 30.1 - - - +
163A LEU* 4.3 17.5 - - + -
165A ILE* 4.2 11.0 - - + -
173A LEU* 4.2 14.6 - - + +
174A TYR* 6.0 0.2 - - - -
177A ALA* 3.8 10.1 - - + -
181A ILE* 4.8 0.6 - - - +
199A CYS* 2.8 8.6 + - - +
200A ALA* 2.7 17.0 + - - +
202A GLY* 1.3 70.2 - - - +
204A LEU* 1.3 56.1 + - + +
206A THR* 3.1 3.3 + - - -
207A ILE* 2.7 51.7 + - + +
224A LEU* 5.7 2.0 - - + -
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Residues in contact with LEU 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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163A LEU* 6.0 0.7 - - + -
200A ALA 2.9 15.1 + - - +
201A GLY* 3.7 5.6 - - - +
203A LEU* 1.3 77.9 - - + +
205A THR* 1.3 57.2 + - - +
207A ILE* 3.3 13.6 + - + +
208A GLU* 2.8 31.6 + - - +
217A TRP* 3.7 34.4 - - + +
220A TYR* 5.0 3.4 - - + -
221A LEU* 4.8 9.2 - - + +
224A LEU* 3.6 21.3 - - + -
235A VAL* 3.6 31.4 - - + +
239A LYS* 3.7 37.5 - - + -
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Residues in contact with THR 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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180A THR* 4.7 17.5 - - + +
201A GLY 2.9 22.3 + - - -
202A GLY* 3.8 7.4 - - - +
204A LEU* 1.3 75.3 - - - +
206A THR* 1.3 63.9 + - - +
208A GLU* 3.4 12.4 + - - +
209A THR* 2.9 35.7 + - + +
239A LYS* 3.2 23.5 + - - +
242A VAL* 4.6 3.5 - - + +
243A SER* 3.7 28.0 + - - +
246A PHE* 5.3 7.4 - - + -
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Residues in contact with THR 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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173A LEU* 4.1 17.7 - - + +
176A ALA* 3.2 31.8 + - + +
177A ALA* 3.2 23.6 + - - +
180A THR* 3.5 13.0 + - + +
202A GLY 2.9 23.0 + - - -
203A LEU* 3.6 3.8 - - - -
205A THR* 1.3 74.4 - - - +
207A ILE* 1.3 69.3 + - - +
208A GLU 3.3 0.3 + - - -
209A THR* 3.8 4.6 + - - -
210A ASP* 3.6 24.6 + - + +
212A THR* 5.7 2.0 - - + +
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Residues in contact with ILE 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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163A LEU* 5.6 0.7 - - + -
165A ILE* 4.2 10.5 - - + -
173A LEU* 4.0 20.2 - - + -
203A LEU* 2.7 47.1 + - + +
204A LEU* 3.5 10.5 - - + +
206A THR* 1.3 73.0 - - - +
208A GLU* 1.3 62.5 + - - +
210A ASP 2.6 25.8 - - - +
211A ASN* 3.7 4.2 + - - -
212A THR* 4.7 3.8 - - - +
214A CYS* 4.0 24.5 - - + +
215A ARG 4.7 0.4 - - - +
217A TRP* 3.5 26.2 - - + +
220A TYR* 3.9 26.9 - - + -
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Residues in contact with GLU 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 LEU 2.8 14.1 + - - +
205A THR* 3.4 11.9 + - - +
207A ILE* 1.3 77.2 - - - +
209A THR* 1.3 68.2 + - + +
210A ASP* 2.3 23.8 + - - -
211A ASN* 3.7 2.9 + - - +
217A TRP* 3.1 48.3 - - + -
239A LYS* 3.3 20.5 + - - -
243A SER* 5.1 5.5 + - - -
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Residues in contact with THR 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 THR* 2.9 21.8 + - + +
206A THR* 4.0 4.6 + - - -
208A GLU* 1.3 90.7 - - + +
210A ASP* 1.3 63.8 + - - +
243A SER* 6.0 1.6 - - - +
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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