Contacts of the helix formed by residues 174 - 185 (chain A) in PDB entry 2IBS
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 PHE 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A TYR* 3.8 22.7 - + - -
141A ASN* 3.7 27.4 - - + -
143A TYR* 3.4 34.8 - + - -
144A GLY* 4.3 4.9 - - - -
167A THR* 3.7 9.6 - - - -
168A TRP* 3.6 34.8 - - + +
171A LEU* 3.3 21.9 + - + +
172A GLU 3.0 1.4 - - - -
173A ASP* 1.3 89.2 - - + +
175A ALA* 1.3 58.4 + - - +
176A LEU 3.3 2.2 - - - -
177A LEU* 3.3 26.1 + - + +
178A ARG* 2.9 34.7 + - - +
4B C 5.0 2.2 - - - -
5B G 4.3 5.8 - - - -
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Residues in contact with ALA 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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137A LYS* 3.8 13.9 - - - +
171A LEU 3.8 0.6 + - - -
172A GLU* 3.1 24.2 + - - +
173A ASP 3.5 0.6 - - - -
174A PHE* 1.3 77.2 - - - +
176A LEU* 1.3 59.4 + - + +
178A ARG* 3.5 23.8 + - - +
179A GLU* 3.1 43.6 + - - +
240A GLY 4.5 1.6 - - - +
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Residues in contact with LEU 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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134A SER 3.6 19.7 - - - +
135A THR* 3.6 28.2 - - + +
136A TRP 4.3 4.7 - - - +
137A LYS* 4.2 27.6 - - + +
173A ASP 5.1 0.4 + - - -
174A PHE 3.3 0.4 - - - -
175A ALA* 1.3 76.5 - - + +
177A LEU* 1.3 60.3 + - - +
179A GLU* 3.5 18.8 + - - +
180A PHE* 2.9 29.3 + - - +
183A ARG* 5.2 1.1 + - - +
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Residues in contact with LEU 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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135A THR* 3.8 16.8 + - + +
140A TYR* 3.7 23.1 - - + +
144A GLY* 3.8 16.4 - - - +
147A LEU* 4.0 31.9 - - + -
148A GLU* 4.4 6.7 - - + +
168A TRP* 4.3 17.3 - - + -
174A PHE* 3.3 36.1 + - + +
176A LEU* 1.3 76.5 - - - +
178A ARG* 1.3 59.3 + - - +
180A PHE* 3.2 5.2 + - + +
181A LEU* 2.9 48.1 + - + +
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Residues in contact with ARG 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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168A TRP* 2.8 53.2 + - + +
169A LEU* 3.8 16.6 + - - +
171A LEU 2.8 35.6 + - - +
172A GLU* 4.9 3.4 + - - +
174A PHE 2.9 22.5 + - - +
175A ALA* 3.6 20.2 - - - +
177A LEU* 1.3 75.9 - - - +
179A GLU* 1.3 61.2 + - - +
181A LEU* 4.6 3.1 - - - -
182A ALA* 3.1 21.3 + - - +
238A TRP* 3.4 21.8 - - + -
240A GLY* 3.1 24.0 + - - +
241A GLU 3.6 18.7 + - - -
242A ILE* 3.8 20.1 - - - +
243A ILE* 4.6 1.8 - - - -
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Residues in contact with GLU 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 ALA* 3.1 31.1 + - - +
176A LEU* 3.8 22.3 - - - +
178A ARG* 1.3 73.0 - - - +
180A PHE* 1.3 65.2 + - - +
182A ALA* 3.6 2.4 + - - +
183A ARG* 3.2 44.3 + - - +
239A GLU 3.5 23.2 - - - +
240A GLY* 4.3 8.1 - - - +
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Residues in contact with PHE 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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134A SER* 4.4 4.5 - - - -
135A THR* 3.6 17.9 - - + -
148A GLU* 3.7 29.4 - - + -
151A VAL* 3.7 33.0 - - + -
152A ARG* 3.7 35.4 - - + -
176A LEU 2.9 19.7 + - - +
177A LEU* 3.3 8.1 - - + +
179A GLU* 1.3 75.6 - - - +
181A LEU* 1.3 67.8 + - + +
183A ARG* 3.1 22.3 + - - +
184A GLU* 2.9 59.0 + - + +
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Residues in contact with LEU 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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147A LEU* 5.2 9.2 - - + +
151A VAL* 3.9 27.4 - - + -
168A TRP* 3.8 29.6 - - + -
177A LEU* 2.9 40.3 + - + +
178A ARG* 4.0 3.4 - - - +
179A GLU 3.5 0.2 - - - -
180A PHE* 1.3 82.7 - - + +
182A ALA* 1.3 60.9 + - - +
183A ARG 3.3 0.5 + - - -
184A GLU* 4.7 0.2 - - - -
185A GLY 3.3 10.9 + - - +
187A THR* 3.9 13.1 + - - +
206A ILE* 3.9 20.6 - - + -
208A PHE* 3.3 35.4 - - + -
238A TRP* 4.4 3.4 - - + -
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Residues in contact with ALA 182 (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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178A ARG 3.1 18.2 + - - +
179A GLU 3.8 2.9 - - - +
180A PHE 3.3 0.2 - - - -
181A LEU* 1.3 76.2 - - - +
183A ARG* 1.3 58.1 - - - +
185A GLY 3.7 11.5 - - - +
213A LYS* 4.7 10.4 - - - +
214A GLY 5.1 1.5 + - - +
238A TRP* 3.4 44.2 - - + +
239A GLU* 3.6 19.7 - - - -
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Residues in contact with ARG 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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176A LEU* 5.2 1.0 + - - +
179A GLU* 3.2 39.7 + - - +
180A PHE* 3.1 41.7 + - - +
182A ALA* 1.3 77.7 - - - +
184A GLU* 1.3 71.3 + - + +
185A GLY 3.5 0.4 - - - -
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Residues in contact with GLU 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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151A VAL* 3.9 7.4 - - + +
152A ARG* 6.3 0.2 - - - -
180A PHE* 2.9 57.5 + - + +
181A LEU 3.4 0.4 + - - -
183A ARG* 1.3 92.7 + - - +
185A GLY* 1.3 55.5 + - - +
208A PHE* 3.5 18.4 - - + -
210A LYS* 3.7 42.8 + - + +
211A SER* 4.9 0.2 - - - -
212A GLY 5.0 0.2 - - - -
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Residues in contact with GLY 185 (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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181A LEU 3.3 14.0 + - - +
182A ALA* 3.7 8.7 - - - +
183A ARG 3.5 2.0 - - - -
184A GLU* 1.3 79.1 - - - +
186A LYS* 1.3 59.4 + - - -
187A THR 4.3 0.3 + - - -
208A PHE* 3.5 5.8 - - - -
209A GLN 3.3 12.1 - - - -
211A SER 3.7 4.7 - - - -
212A GLY 3.4 20.1 + - - -
213A LYS* 3.6 11.3 - - - -
214A GLY 4.2 1.7 + - - +
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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