Contacts of the helix formed by residues 163 - 176 (chain A) in PDB entry 4P9O
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 ASP 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A THR* 3.6 11.9 - - - -
161A PHE 3.2 1.6 + - - +
162A GLY* 1.3 75.7 - - - +
164A LEU* 1.4 66.4 + - - +
165A SER* 3.3 14.8 - - - +
166A LYS* 3.2 51.3 + - - +
167A SER* 3.2 23.7 + - - -
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Residues in contact with LEU 164 (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 TYR* 4.2 17.5 - - + +
146A ALA* 3.6 39.0 - - + +
147A VAL* 3.6 23.1 - - + +
150A THR* 3.7 9.7 + - + +
163A ASP* 1.4 72.8 - - - +
165A SER* 1.4 52.0 - - - +
167A SER* 3.2 4.7 + - - -
168A LEU* 2.8 52.9 + - + +
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Residues in contact with SER 165 (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 ASP* 3.3 10.9 + - - +
164A LEU* 1.4 73.9 - - - +
166A LYS* 1.4 64.4 - - - +
168A LEU* 3.4 12.6 + - - +
169A TYR* 3.1 23.8 + - - +
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Residues in contact with LYS 166 (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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158A PRO* 2.7 34.3 + - - +
159A GLU* 3.6 26.7 + - - +
160A TRP 3.3 15.3 - - - +
162A GLY* 4.0 5.8 - - - +
163A ASP* 3.2 34.8 + - - +
164A LEU 3.5 0.2 - - - -
165A SER* 1.4 76.5 - - - +
167A SER* 1.4 50.6 + - - +
169A TYR* 3.4 8.7 + - - +
170A THR* 2.8 38.8 + - - -
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Residues in contact with SER 167 (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 ALA* 3.4 17.9 - - - -
149A ALA* 4.7 0.7 - - - -
150A THR* 2.8 29.4 + - - -
160A TRP 3.6 5.8 + - - -
161A PHE* 3.4 29.5 - - - +
163A ASP 3.2 4.9 + - - -
164A LEU 3.2 9.2 + - - -
166A LYS* 1.4 75.4 - - - +
168A LEU* 1.4 58.2 + - - +
170A THR* 3.4 1.2 + - - -
171A LEU* 2.9 35.3 + - - +
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Residues in contact with LEU 168 (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 PHE* 3.2 42.4 - - + +
143A TYR* 3.9 41.3 - - + +
146A ALA* 3.5 23.3 - - + +
164A LEU* 2.8 39.6 + - + +
165A SER* 3.4 9.2 + - - +
167A SER* 1.4 68.2 - - - +
169A TYR* 1.4 65.0 + - - +
172A PHE* 3.1 20.3 + - - +
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Residues in contact with TYR 169 (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 SER 3.1 13.4 + - - +
166A LYS* 3.5 11.4 - - - +
168A LEU* 1.4 73.1 - - - +
170A THR* 1.4 71.5 + - - +
172A PHE* 3.2 14.0 + + + +
173A GLN* 3.2 40.1 + - + +
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Residues in contact with THR 170 (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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160A TRP* 2.7 38.9 + - + +
161A PHE* 3.8 28.0 - - + -
166A LYS 2.8 9.9 + - - -
167A SER 3.9 3.4 - - - -
169A TYR* 1.4 83.5 - - - +
171A LEU* 1.3 51.2 + - - +
173A GLN* 3.1 12.2 + - - +
174A VAL* 2.8 39.8 + - + +
184A ILE* 4.2 23.3 - - + -
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Residues in contact with LEU 171 (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 PHE* 3.5 14.3 - - + +
145A ALA* 3.7 15.7 - - + +
146A ALA* 3.6 37.9 - - + +
149A ALA* 4.3 7.4 - - + -
161A PHE* 4.6 7.0 - - + -
167A SER 2.9 18.2 + - - +
170A THR* 1.3 72.8 - - - +
172A PHE* 1.4 59.1 + - - +
174A VAL* 3.8 5.4 - - + -
175A MET* 3.0 27.7 + - - +
198A PHE* 4.0 20.9 - - + -
199A PHE* 4.2 15.5 - - + -
202A PHE* 3.4 34.7 - - + -
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Residues in contact with PHE 172 (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 PHE* 3.3 13.7 - + + -
168A LEU 3.1 18.1 + - - +
169A TYR* 3.2 14.8 + + + +
171A LEU* 1.4 75.7 - - - +
173A GLN* 1.4 60.6 + - + +
175A MET* 3.3 27.5 - - + +
176A THR* 3.0 46.2 + - + +
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Residues in contact with GLN 173 (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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169A TYR* 3.2 31.9 + - + +
170A THR* 3.1 13.4 + - - +
172A PHE* 1.4 77.3 - - + +
174A VAL* 1.3 64.8 + - - +
176A THR* 2.8 21.6 + - - -
177A LEU 3.1 7.8 + - - -
178A GLU* 3.0 50.4 + - + +
179A SER* 4.1 7.7 - - - -
184A ILE* 3.6 33.7 - - - +
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Residues in contact with VAL 174 (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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170A THR* 2.8 37.7 + - + +
171A LEU* 3.9 8.7 - - + +
172A PHE 3.4 0.2 - - - -
173A GLN* 1.3 70.5 - - + +
175A MET* 1.4 58.5 + - - +
177A LEU* 2.9 27.9 + - - +
178A GLU 4.9 0.4 - - - -
180A TRP* 4.1 16.7 - - + +
184A ILE* 4.5 21.8 - - + -
185A VAL* 5.1 1.1 - - + -
199A PHE* 4.2 22.0 - - + -
202A PHE* 3.9 14.1 - - + -
203A ILE* 3.8 29.5 - - + +
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Residues in contact with MET 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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138A LEU* 5.2 4.0 - - + -
142A PHE* 4.6 13.5 - - - -
171A LEU 3.0 15.9 + - - +
172A PHE* 3.3 40.4 - - + +
173A GLN 3.2 0.2 - - - -
174A VAL* 1.4 76.9 - - - +
176A THR* 1.4 65.0 + - + +
177A LEU* 3.1 12.0 + - - +
202A PHE* 4.1 6.3 - - + -
203A ILE* 5.3 1.3 - - - -
206A THR* 3.6 29.6 - - - +
207A THR* 3.2 29.6 + - + +
210A VAL* 3.4 39.0 - - + -
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Residues in contact with THR 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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172A PHE* 3.0 40.3 + - + +
173A GLN* 2.8 25.7 + - - -
175A MET* 1.4 80.0 - - + +
177A LEU* 1.4 66.6 + - - +
178A GLU* 3.2 13.7 + - - +
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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