Contacts of the helix formed by residues 174 - 184 (chain A) in PDB entry 1UIR
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 THR 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A ARG* 3.6 3.8 + - - -
170A ARG 3.5 17.9 - - - +
171A LEU* 3.8 5.6 + - - -
172A LEU 3.6 1.8 - - - -
173A TYR* 1.3 80.5 - - - +
175A VAL* 1.3 65.0 + - - +
176A GLU* 3.5 8.0 + - - -
177A PHE* 3.0 24.8 + - - +
178A TYR* 3.2 15.1 + - - -
212A THR* 3.8 2.7 - - - -
293A SER* 3.5 10.8 - - - +
294A THR 3.5 21.3 - - - +
295A ASP* 2.8 30.3 + - - +
298A PRO* 4.0 6.3 - - + -
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Residues in contact with VAL 175 (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 THR* 1.3 72.1 - - - +
176A GLU* 1.3 82.5 + - - +
178A TYR* 3.3 5.6 + - - +
179A ARG* 3.0 51.0 + - - +
212A THR* 3.5 16.0 - - + +
215A GLU* 3.7 33.7 - - + +
216A ALA* 4.0 2.7 - - + -
292A VAL* 4.2 7.0 - - + -
293A SER 2.7 20.5 + - - +
294A THR* 4.2 11.9 - - + -
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Residues in contact with GLU 176 (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 ARG* 3.9 8.4 + - - +
174A THR* 3.1 1.3 + - - -
175A VAL* 1.3 91.9 - - + +
177A PHE* 1.3 59.6 + - - +
179A ARG* 3.1 17.0 + - - +
180A LEU* 2.9 28.8 + - - +
294A THR* 3.5 7.3 - - - +
295A ASP* 2.7 60.5 + - + +
296A GLN 5.0 0.7 + - - -
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Residues in contact with PHE 177 (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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84A VAL* 4.5 12.8 - - + -
141A ALA* 4.2 10.5 - - + -
142A ARG* 3.4 30.7 - - + +
145A LEU* 4.2 17.9 - - + -
157A ILE* 3.9 21.3 - - + -
159A LEU* 4.8 0.4 - - + -
171A LEU 3.8 9.0 - - - +
172A LEU* 2.9 51.1 - - + -
174A THR* 3.0 19.0 + - - +
176A GLU* 1.3 79.3 - - - +
178A TYR* 1.3 67.7 - + - +
180A LEU* 3.1 10.4 + - + +
181A VAL* 2.9 49.6 + - + +
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Residues in contact with TYR 178 (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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157A ILE* 4.0 11.7 - - + -
172A LEU 3.8 1.6 + - - -
173A TYR* 3.3 49.0 - - - -
174A THR 3.2 22.5 + - - -
175A VAL* 3.8 2.2 - - - +
176A GLU 3.3 0.2 - - - -
177A PHE* 1.3 92.2 - + - +
179A ARG* 1.3 57.3 + - - +
181A VAL* 3.4 6.0 + - + +
182A LYS* 2.9 28.1 + - - +
191A MET* 4.0 15.9 - - + -
193A MET* 3.5 23.6 - - + +
209A VAL* 3.8 4.4 - - + +
212A THR* 3.8 16.8 - - + -
213A VAL* 3.6 28.7 - - + -
216A ALA* 3.8 19.5 - - + -
217A PHE* 3.7 11.1 - - + -
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Residues in contact with ARG 179 (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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175A VAL* 3.0 40.8 + - - +
176A GLU* 3.1 19.0 + - - +
178A TYR* 1.3 73.6 - - - +
180A LEU* 1.3 60.8 + - - +
182A LYS* 3.3 13.6 + - - +
183A ALA* 2.9 28.2 + - - +
215A GLU* 3.1 34.4 + - - +
216A ALA* 3.9 15.6 - - + +
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Residues in contact with LEU 180 (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 ARG* 4.0 36.1 - - + +
145A LEU* 3.6 33.4 - - + +
146A GLU* 3.1 30.1 - - + +
176A GLU 2.9 12.8 + - - +
177A PHE* 3.1 10.3 + - + +
179A ARG* 1.3 77.8 - - - +
181A VAL* 1.3 60.3 + - - +
183A ALA* 3.2 11.5 + - + +
184A HIS* 2.9 47.2 + - + -
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Residues in contact with VAL 181 (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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82A LEU* 6.1 0.7 - - + -
84A VAL* 5.8 1.3 - - + -
145A LEU* 4.1 15.5 - - + -
155A VAL* 3.7 36.0 - - + +
157A ILE* 4.2 8.1 - - + -
177A PHE* 2.9 47.9 + - + +
178A TYR* 3.5 10.3 - - + +
180A LEU* 1.3 77.4 - - - +
182A LYS* 1.3 59.1 + - - +
184A HIS* 2.9 29.3 + - - +
185A LEU* 3.6 4.2 + - + +
191A MET* 4.2 16.8 - - + -
217A PHE* 5.0 2.9 - - + -
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Residues in contact with LYS 182 (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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178A TYR 2.9 18.0 + - - +
179A ARG* 3.6 15.0 - - - +
181A VAL* 1.3 76.2 - - - +
183A ALA* 1.3 61.9 + - - +
185A LEU* 3.1 25.4 + - + +
216A ALA* 2.8 29.2 + - - +
217A PHE* 3.5 29.6 - - + -
241A ASP* 2.9 32.5 + - + +
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Residues in contact with ALA 183 (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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151A ARG* 3.9 15.1 + - - +
179A ARG 2.9 13.5 + - - +
180A LEU* 3.3 16.4 - - + +
181A VAL 3.1 0.4 - - - -
182A LYS* 1.3 77.7 - - - +
184A HIS* 1.3 65.5 + - + +
185A LEU 3.2 4.0 + - - +
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Residues in contact with HIS 184 (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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82A LEU* 5.5 0.9 - - + -
145A LEU* 2.8 46.9 + - + +
148A THR* 3.3 27.6 + - + +
149A GLU* 4.2 4.9 - - - -
150A GLU 3.2 22.4 - - - +
151A ARG* 3.2 8.9 - - + -
152A TYR* 2.7 43.1 + + + +
155A VAL* 4.8 1.3 - - + +
180A LEU* 2.9 35.1 + - + -
181A VAL 2.9 12.0 + - - +
183A ALA* 1.3 84.1 - - + +
185A LEU* 1.3 52.7 + - - +
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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