Contacts of the helix formed by residues 182 - 193 (chain A) in PDB entry 4HI7
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 TYR 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A THR* 3.7 18.5 + - + +
139A TYR* 3.6 38.1 - + + +
140A ASP* 2.7 33.7 + - - -
143A GLU* 3.3 31.2 - - + +
177A VAL* 3.8 15.3 - - + -
178A ASP* 2.8 31.2 + - + +
179A ALA 3.6 3.4 - - - -
181A LYS* 1.3 112.2 - - + +
183A PRO* 1.3 58.9 - - - +
185A LEU* 3.9 7.4 - - + -
186A SER* 2.8 27.5 + - - -
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Residues in contact with PRO 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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143A GLU* 3.4 8.1 - - - +
179A ALA 3.4 13.5 - - - +
180A ALA 3.5 11.4 - - - +
181A LYS 3.2 10.3 - - - +
182A TYR* 1.3 89.4 - - - +
184A LYS* 1.3 63.0 + - + +
186A SER* 3.4 4.3 + - - -
187A ALA* 2.9 29.6 + - - +
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Residues in contact with LYS 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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143A GLU* 2.9 23.8 + - + +
146A PHE* 3.7 30.9 - - + -
147A LYS* 2.9 38.5 + - - +
183A PRO* 1.3 79.3 - - + +
185A LEU* 1.3 61.3 + - - +
187A ALA* 3.8 5.3 - - - +
188A TRP* 2.9 31.5 + - - +
191A ARG* 5.0 0.9 + - - -
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Residues in contact with LEU 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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139A TYR* 4.1 40.8 - - + +
142A VAL* 3.5 30.3 - - + -
143A GLU* 2.8 23.5 + - - +
146A PHE* 3.9 7.9 - - + -
168A ILE* 4.6 7.2 - - + -
177A VAL* 4.0 24.9 - - + -
182A TYR* 3.9 9.0 - - + +
183A PRO 3.4 0.2 - - - -
184A LYS* 1.3 72.9 - - - +
186A SER* 1.3 63.5 + - - +
188A TRP* 3.3 26.7 + - + +
189A ILE* 3.0 33.7 + - + +
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Residues in contact with SER 186 (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 VAL* 3.3 13.5 - - - +
179A ALA* 3.2 31.8 - - - +
182A TYR 2.8 21.9 + - - -
183A PRO* 3.6 5.2 - - - -
185A LEU* 1.3 77.5 - - - +
187A ALA* 1.3 61.0 + - - +
189A ILE* 3.4 12.8 + - - +
190A LYS* 3.1 28.4 + - - +
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Residues in contact with ALA 187 (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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183A PRO 2.9 17.8 + - - +
184A LYS* 3.8 6.7 - - - +
186A SER* 1.3 76.5 - - - +
188A TRP* 1.3 57.1 + - - +
190A LYS* 3.3 8.5 + - - +
191A ARG* 2.9 45.7 + - - +
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Residues in contact with TRP 188 (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 VAL* 4.9 2.0 - - + -
146A PHE* 3.4 26.9 - + + -
150A THR 3.6 12.3 - - - -
151A TYR* 4.2 4.3 - + - -
152A VAL* 3.8 16.9 - - + +
161A ASP* 2.9 35.8 + - - -
164A LEU* 3.8 12.3 - - + -
165A ILE* 3.6 36.8 - - + -
168A ILE* 4.4 9.0 - - + -
184A LYS 2.9 18.1 + - - +
185A LEU* 3.6 32.1 - - + +
187A ALA* 1.3 74.2 - - - +
189A ILE* 1.3 79.3 + - + +
191A ARG* 3.2 16.3 + - - +
192A LEU* 3.0 48.4 + - + +
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Residues in contact with ILE 189 (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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165A ILE* 3.9 21.9 - - + +
168A ILE* 4.1 20.6 - - + -
169A SER* 6.0 2.5 - - - +
172A VAL* 5.4 4.3 - - + -
177A VAL* 4.2 19.7 - - + -
185A LEU* 3.0 24.0 + - + +
186A SER* 3.6 10.1 - - - +
188A TRP* 1.3 88.7 - - + +
190A LYS* 1.3 59.8 + - + +
192A LEU* 3.3 2.5 + - - +
193A GLU* 2.9 50.8 + - + +
198A TYR* 5.0 1.6 - - - +
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Residues in contact with LYS 190 (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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186A SER* 3.1 19.2 + - - +
187A ALA* 3.6 10.3 - - - +
189A ILE* 1.3 77.2 - - + +
191A ARG* 1.3 62.3 + - - +
193A GLU* 3.5 30.6 + - - +
194A GLN* 3.5 18.5 - - - +
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Residues in contact with ARG 191 (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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146A PHE* 5.4 1.0 - - - -
150A THR* 2.8 59.4 + - - +
151A TYR* 3.7 39.0 - - + +
184A LYS 5.0 0.8 + - - -
187A ALA* 2.9 29.0 + - - +
188A TRP* 3.2 30.7 + - - +
190A LYS* 1.3 74.9 - - - +
192A LEU* 1.3 66.8 + - + +
194A GLN* 3.2 31.9 + - - +
195A LEU* 4.1 3.5 + - - +
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Residues in contact with LEU 192 (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 TYR* 4.2 14.4 - - + -
157A LEU* 3.5 32.1 - - + -
161A ASP* 4.1 7.9 - - + +
162A PHE* 5.6 1.3 - - + -
165A ILE* 3.5 38.1 - - + -
188A TRP* 3.0 44.5 + - + +
189A ILE 3.8 3.1 - - - +
191A ARG* 1.3 76.4 - - + +
193A GLU* 1.3 58.4 + - - +
194A GLN 3.0 0.4 - - - -
195A LEU* 3.0 36.0 + - + +
198A TYR* 3.3 25.3 - - + -
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Residues in contact with GLU 193 (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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189A ILE* 2.9 35.8 + - + +
190A LYS* 3.6 36.9 + - - +
191A ARG 3.2 0.4 - - - -
192A LEU* 1.3 74.4 - - - +
194A GLN* 1.3 59.6 + - + +
195A LEU 3.3 1.4 + - - +
198A TYR* 3.5 44.6 + - + +
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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