Contacts of the helix formed by residues 198 - 211 (chain A) in PDB entry 1UXI
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 ALA 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A PHE 4.3 0.2 + - - -
197A ILE* 1.3 76.8 - - - +
199A PRO* 1.3 63.4 - - + +
200A ASP* 3.2 18.8 - - - +
201A ARG* 3.0 8.3 + - + +
202A LEU* 2.7 31.9 + - - +
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Residues in contact with PRO 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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194A SER* 6.5 1.1 - - - -
197A ILE 3.7 3.8 - - - +
198A ALA* 1.3 86.0 - - + +
200A ASP* 1.3 56.7 + - - +
202A LEU* 3.2 10.3 + - + +
203A ALA* 2.8 31.4 + - - +
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Residues in contact with ASP 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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198A ALA* 3.2 21.8 - - - +
199A PRO* 1.3 76.4 - - - +
201A ARG* 1.3 81.6 + - - +
203A ALA* 3.4 8.8 + - - +
204A GLN* 3.2 29.4 + - - +
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Residues in contact with ARG 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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159A GLU* 3.3 45.5 + - + +
197A ILE* 3.5 9.0 - - + -
198A ALA* 3.0 12.1 + - + +
200A ASP* 1.3 88.3 + - - +
202A LEU* 1.3 66.8 - - - +
204A GLN* 3.1 30.7 + - - +
205A ILE* 3.1 26.6 + - + +
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Residues in contact with LEU 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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152A TYR* 4.1 17.3 - - + +
156A ILE* 5.0 0.9 - - + -
183A PRO* 3.7 31.2 - - + -
193A VAL* 3.9 28.9 - - + -
194A SER* 4.9 17.3 - - - +
197A ILE* 3.5 19.5 - - + +
198A ALA 2.7 20.5 + - - +
199A PRO* 3.6 9.6 - - + +
201A ARG* 1.3 72.0 - - - +
203A ALA* 1.3 57.5 - - - +
205A ILE* 3.2 12.5 + - + +
206A VAL* 2.9 31.7 + - + +
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Residues in contact with ALA 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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199A PRO 2.8 16.8 + - - +
200A ASP* 3.4 9.2 - - - +
201A ARG 3.1 0.2 - - - -
202A LEU* 1.3 75.1 - - - +
204A GLN* 1.3 65.2 + - + +
206A VAL* 3.1 10.0 + - - +
207A GLU* 2.9 23.8 + - - +
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Residues in contact with GLN 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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200A ASP* 3.3 15.3 - - - +
201A ARG* 3.1 47.6 + - - +
203A ALA* 1.3 78.3 - - + +
205A ILE* 1.3 57.9 + - + +
207A GLU* 3.4 8.1 + - - +
208A ARG* 2.8 29.0 + - - +
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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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152A TYR* 3.8 25.8 - - + -
155A PHE* 3.7 32.3 - - + +
156A ILE* 4.3 5.8 - - + -
159A GLU* 3.8 25.6 - - + +
197A ILE* 3.7 32.1 - - + -
201A ARG* 3.1 14.4 + - + +
202A LEU* 3.4 9.9 - - + +
203A ALA 3.1 0.2 - - - -
204A GLN* 1.3 76.1 - - + +
206A VAL* 1.3 64.5 + - - +
208A ARG* 3.7 7.3 - - + +
209A THR* 2.8 29.3 + - - -
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Residues in contact with VAL 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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152A TYR* 4.4 8.5 - - + -
181A PRO* 3.2 29.8 - - + +
183A PRO* 3.6 32.3 - - + -
202A LEU* 2.9 20.5 + - + +
203A ALA* 3.4 10.8 - - - +
205A ILE* 1.3 76.2 - - - +
207A GLU* 1.3 63.7 + - - +
209A THR* 3.3 5.8 - - - -
210A ARG* 3.2 31.4 + - - +
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Residues in contact with GLU 207 (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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203A ALA 2.9 12.0 + - - +
204A GLN* 3.5 12.1 - - - +
206A VAL* 1.3 76.6 - - - +
208A ARG* 1.3 65.2 + - - +
210A ARG* 2.8 37.5 + - - +
211A LYS* 3.1 46.3 + - + +
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Residues in contact with ARG 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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155A PHE* 3.2 47.0 - - + +
158A MET* 4.6 16.4 - - - +
204A GLN 2.8 20.7 + - - +
205A ILE* 3.2 8.0 + - - +
207A GLU* 1.3 73.4 - - - +
209A THR* 1.3 52.8 + - - +
211A LYS* 3.2 5.1 + - - -
212A GLY* 2.7 34.3 + - - -
215A GLU* 3.0 39.3 + - + +
44B LEU* 3.9 16.8 - - - +
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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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148A ASP* 3.4 27.1 - - - +
151A ARG* 4.7 5.9 + - + -
152A TYR* 3.3 36.7 - - + +
155A PHE* 3.7 11.3 - - - -
171A LEU* 4.0 18.6 - - + -
179A MET* 3.9 10.6 - - - +
181A PRO* 4.4 2.5 - - + -
205A ILE 2.8 18.3 + - - -
206A VAL 3.3 9.0 - - - -
208A ARG* 1.3 76.7 - - - +
210A ARG* 1.3 64.9 + - - +
212A GLY* 2.9 14.2 + - - -
213A GLY 4.8 0.3 + - - -
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Residues in contact with ARG 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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88A ARG* 5.0 4.7 + - - -
176A GLY 4.3 3.8 - - - +
177A ASP* 3.4 32.0 + - - +
178A GLU* 5.0 4.2 - - - +
179A MET* 3.1 54.1 + - + +
181A PRO* 3.8 12.3 - - + -
206A VAL* 3.2 20.7 + - - +
207A GLU* 2.8 33.8 + - - +
209A THR* 1.3 79.8 - - - +
211A LYS* 1.3 63.9 + - + +
212A GLY 3.6 0.5 + - - -
213A GLY 5.0 1.2 + - - -
291A LEU* 5.1 13.3 - - - +
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Residues in contact with LYS 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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177A ASP* 3.1 36.9 + - - +
207A GLU* 3.1 38.6 + - + +
208A ARG* 3.3 5.4 - - - +
210A ARG* 1.3 78.1 - - + +
212A GLY* 1.3 64.3 + - - +
213A GLY 3.4 2.7 - - - -
214A GLY* 3.2 7.6 + - - +
215A GLU* 3.1 20.8 + - - +
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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