Contacts of the helix formed by residues 160 - 176 (chain A) in PDB entry 2RQP
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 LYS 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A PRO* 6.5 0.2 - - - -
158A ARG* 3.8 13.2 + - - +
159A PRO* 1.3 80.8 - - - +
161A MET* 1.3 70.6 + - - +
162A ASP* 3.0 2.9 - - - -
163A ALA* 2.9 24.0 + - + +
164A ILE* 3.1 24.4 + - + +
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Residues in contact with MET 161 (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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159A PRO* 5.9 1.3 - - + -
160A LYS* 1.3 79.6 - - - +
162A ASP* 1.3 66.0 + - - +
164A ILE* 3.1 22.9 + - + +
165A LEU* 3.1 24.9 + - + +
187A ILE* 5.5 9.9 - - + -
191A TYR* 6.0 6.3 - - + -
193A SER* 4.9 3.1 - - - +
197A GLU* 2.9 33.4 - - - +
202A LEU* 3.9 28.0 - - + -
203A LEU* 5.7 1.8 - - - -
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Residues in contact with ASP 162 (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 PRO* 4.2 18.9 - - + +
160A LYS* 2.9 3.5 + - - +
161A MET* 1.3 80.8 - - - +
163A ALA* 1.3 51.5 + - - +
165A LEU* 3.6 3.4 + - - +
166A THR* 2.5 35.2 + - - +
209A ARG* 5.9 0.3 + - - -
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Residues in contact with ALA 163 (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 LYS* 2.9 18.0 + - + +
162A ASP* 1.3 75.6 - - - +
164A ILE* 1.3 65.7 + - + +
165A LEU 3.2 0.7 - - - -
166A THR* 3.4 10.8 - - + -
167A GLU* 2.9 25.8 + - - +
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Residues in contact with ILE 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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160A LYS* 3.1 20.7 + - + +
161A MET* 3.1 33.6 + - + +
163A ALA* 1.3 78.1 - - + +
165A LEU* 1.3 59.8 + - - +
167A GLU* 3.6 9.4 - - - +
168A ALA* 3.6 14.0 + - - +
186A TYR* 3.1 41.7 + - + +
191A TYR* 5.4 14.6 - - + +
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Residues in contact with LEU 165 (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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161A MET* 3.1 15.5 + - + +
162A ASP* 4.1 3.4 - - - +
164A ILE* 1.3 75.2 - - + +
166A THR* 1.3 66.2 + - - +
167A GLU 3.1 2.0 - - - -
168A ALA* 3.0 21.6 + - + +
169A ILE* 3.0 14.3 + - + +
183A ILE* 3.4 31.4 - - + +
186A TYR* 5.3 9.4 - - + -
187A ILE* 5.3 7.4 - - + -
203A LEU* 5.1 13.7 - - + +
206A ALA* 5.2 10.1 - - + -
207A LEU* 3.7 35.0 - - + +
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Residues in contact with THR 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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162A ASP* 2.5 26.1 + - - +
163A ALA* 3.0 13.4 + - + -
165A LEU* 1.3 75.4 - - - +
167A GLU* 1.3 57.8 + - - +
169A ILE* 3.0 21.5 - - + +
170A LYS* 2.9 50.4 + - + +
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Residues in contact with GLU 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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163A ALA 2.9 15.0 + - - +
164A ILE* 3.6 9.8 - - - +
166A THR* 1.3 76.8 - - - +
168A ALA* 1.3 58.0 + - - +
170A LYS* 4.6 2.0 - - - -
171A ALA* 2.5 54.9 + - + +
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Residues in contact with ALA 168 (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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164A ILE 3.6 4.3 + - - +
165A LEU* 3.0 32.8 + - + +
167A GLU* 1.3 77.5 - - - +
169A ILE* 1.3 60.4 + - + +
172A CYS* 2.5 46.3 + - + +
173A PHE 2.8 3.6 + - - -
178A ALA* 4.2 4.0 - - + +
183A ILE* 5.5 2.7 - - + -
186A TYR* 5.3 12.8 - - + -
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Residues in contact with ILE 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 LEU* 3.0 17.6 + - + +
166A THR* 3.0 34.8 - - + +
168A ALA* 1.3 76.6 - - - +
170A LYS* 1.3 75.3 + - + +
173A PHE* 2.6 28.3 - - + +
178A ALA* 3.9 9.6 - - + -
207A LEU* 3.0 37.5 - - + -
210A GLU* 5.9 4.5 - - + -
216A ILE* 3.1 26.7 - - + -
219A VAL* 5.5 9.9 - - + -
231A VAL* 3.5 7.7 - - + +
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Residues in contact with LYS 170 (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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166A THR* 2.9 37.1 + - - +
167A GLU* 4.3 2.2 - - - +
169A ILE* 1.3 87.6 - - + +
171A ALA* 1.3 59.5 + - - +
174A GLN* 4.3 1.4 - - - +
219A VAL* 3.7 35.9 - - + -
220A LYS* 4.9 11.9 - - - +
231A VAL* 4.6 4.9 - - - -
232A GLN* 3.1 41.4 - - + +
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Residues in contact with ALA 171 (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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167A GLU* 2.5 40.1 + - + +
170A LYS* 1.3 75.8 - - + +
172A CYS* 1.3 60.5 + - - +
174A GLN* 3.9 2.6 + - - +
175A LYS* 3.3 26.2 + - - +
232A GLN* 5.2 2.7 - - - -
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Residues in contact with CYS 172 (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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167A GLU 3.3 0.2 + - - -
168A ALA* 2.5 36.8 + - + +
171A ALA* 1.3 71.2 - - - +
173A PHE* 1.3 46.6 + - - +
174A GLN 2.5 16.5 + - - -
175A LYS* 2.7 3.4 + - - -
176A SER* 2.5 57.9 + - - +
177A GLY 2.6 15.3 + - - +
178A ALA* 5.1 0.9 - - + -
182A ALA* 6.1 2.2 - - - -
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Residues in contact with PHE 173 (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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168A ALA 2.8 9.7 + - - -
169A ILE 2.6 25.3 + - - +
172A CYS* 1.3 71.2 - - - +
174A GLN* 1.3 56.7 + - - +
177A GLY* 3.2 7.9 + - - -
178A ALA* 3.3 47.1 - - + +
215A VAL* 5.1 2.0 - - + -
216A ILE* 3.7 31.4 - - + -
217A LYS* 4.2 18.2 - - - -
231A VAL* 3.7 21.8 - - + -
233A LYS* 2.8 68.8 + - + -
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Residues in contact with GLN 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 LYS 4.3 0.6 + - - +
171A ALA 3.9 6.8 + - - +
172A CYS 2.5 5.0 + - - -
173A PHE* 1.3 78.4 - - - +
175A LYS* 1.3 65.3 + - + +
176A SER 5.1 0.2 - - - -
177A GLY 4.7 0.3 + - - -
232A GLN* 2.7 62.4 - - + +
233A LYS* 3.1 29.9 + - - +
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Residues in contact with LYS 175 (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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171A ALA* 3.3 17.1 + - - +
172A CYS* 2.7 10.3 + - - +
174A GLN* 1.3 81.3 - - + +
176A SER* 1.3 60.3 + - - +
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Residues in contact with SER 176 (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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172A CYS* 2.5 37.7 + - - -
174A GLN 5.0 0.4 - - - -
175A LYS* 1.3 78.7 - - - +
177A GLY* 1.3 59.9 + - - +
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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