Contacts of the helix formed by residues 166 - 183 (chain A) in PDB entry 1RY2
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 166 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A CYS 3.3 23.1 - - - -
138A VAL* 3.8 17.6 - - + +
141A HIS* 3.5 25.8 - + + -
142A ALA* 3.7 18.9 - - - +
145A THR* 4.1 11.7 - - - +
148A LYS* 3.0 27.1 + - - +
149A LYS 3.9 3.8 - - - -
150A ALA* 3.4 34.8 - - + -
165A THR* 1.3 72.4 + - - +
167A LYS* 1.3 66.1 + - - +
169A LEU* 3.4 5.7 + - + +
170A LEU* 3.1 23.0 + - - +
377A LEU* 3.5 20.5 + - + +
380A GLY* 3.5 27.7 - - - -
381A CYS 3.0 22.1 + - - -
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Residues in contact with LYS 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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142A ALA* 4.1 12.5 - - + +
146A PRO* 3.3 32.6 + - + +
147A ASN* 5.7 4.0 - - - +
165A THR* 3.3 7.4 - - + -
166A TYR* 1.3 80.4 - - - +
168A GLU* 1.3 61.9 + - + +
170A LEU* 3.2 16.8 - - + +
171A GLU* 2.9 48.5 + - + +
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Residues in contact with GLU 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A SER 4.4 3.8 - - - +
164A ILE* 4.1 11.8 - - + -
165A THR* 3.2 36.4 + - + +
167A LYS* 1.3 79.2 - - + +
169A LEU* 1.3 61.9 + - - +
170A LEU 3.1 1.1 - - - -
171A GLU* 3.2 24.6 + - - +
172A GLU* 2.9 37.9 + - + +
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Residues in contact with LEU 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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138A VAL* 3.9 22.0 - - + -
150A ALA* 4.1 19.5 - - + -
151A ILE* 4.3 18.4 - - + -
164A ILE* 3.6 11.4 - - + +
165A THR 3.3 16.8 + - - +
166A TYR* 3.8 8.1 - - + +
167A LYS 3.4 0.2 - - - -
168A GLU* 1.3 78.7 - - - +
170A LEU* 1.3 56.8 + - - +
172A GLU* 3.2 2.5 + - + +
173A VAL* 2.8 49.2 + - + +
204A ILE* 3.5 31.9 - - + -
207A LEU* 4.0 11.9 - - + -
377A LEU* 4.5 9.0 - - + -
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Residues in contact with LEU 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A VAL* 3.6 19.0 - - + +
139A ASP* 3.9 27.1 - - + +
142A ALA* 3.8 20.6 - - + -
143A LEU* 5.4 8.7 - - + -
166A TYR 3.1 13.4 + - - +
167A LYS* 3.2 12.8 - - - +
169A LEU* 1.3 77.9 - - - +
171A GLU* 1.3 64.5 + - + +
173A VAL* 3.5 1.6 + - + -
174A CYS* 3.0 40.2 + - - -
211A ARG* 4.1 7.4 - - - +
302A THR 5.0 1.6 - - - +
303A TYR* 4.9 12.6 - - + -
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Residues in contact with GLU 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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167A LYS* 2.9 43.4 + - + +
168A GLU* 3.5 25.9 - - - +
170A LEU* 1.3 76.1 - - + +
172A GLU* 1.3 69.4 + - + +
174A CYS* 3.1 12.6 + - - +
175A GLN* 3.1 20.8 + - - +
302A THR* 3.3 40.7 + - + +
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Residues in contact with GLU 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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164A ILE* 5.6 7.6 - - + -
168A GLU* 2.9 25.3 + - + +
169A LEU* 3.6 6.7 - - - +
171A GLU* 1.3 78.4 - - - +
173A VAL* 1.3 65.2 + - - +
174A CYS 3.0 3.1 + - - -
175A GLN* 3.1 12.5 + - - +
176A VAL* 3.1 27.4 + - - +
204A ILE* 3.6 23.8 - - + +
297A LYS* 2.8 36.5 + - - +
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Residues in contact with VAL 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A CYS* 3.4 31.0 - - - -
138A VAL* 4.7 2.9 - - + -
169A LEU* 2.8 45.3 + - + +
170A LEU* 4.1 4.3 - - - +
172A GLU* 1.3 72.3 - - - +
174A CYS* 1.3 57.2 + - - +
176A VAL* 4.0 2.9 - - - -
177A ALA* 3.1 25.5 + - - +
204A ILE* 3.7 18.8 - - + -
207A LEU* 3.7 15.5 - - + +
208A ALA* 3.6 22.0 - - - +
211A ARG* 4.4 7.6 - - - +
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Residues in contact with CYS 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 LEU* 3.0 37.9 + - - +
171A GLU 3.4 0.4 - - - +
172A GLU 3.0 1.0 - - - -
173A VAL* 1.3 77.1 - - - +
175A GLN* 1.3 63.0 + - - +
176A VAL 3.2 0.4 - - - -
177A ALA* 3.8 3.6 - - - +
178A GLN* 3.1 31.6 + - - +
211A ARG* 3.7 7.6 - - - +
302A THR 2.8 28.9 - - - +
303A TYR* 3.8 3.1 - - - -
304A TYR* 3.2 40.7 - - + +
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Residues in contact with GLN 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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171A GLU* 3.1 13.3 + - - +
172A GLU* 3.1 14.7 + - - +
174A CYS* 1.3 75.8 - - - +
176A VAL* 1.3 58.2 + - - +
178A GLN* 3.4 4.1 + - - +
179A VAL* 2.9 30.7 + - - +
297A LYS* 3.2 55.2 + - + +
298A LYS* 4.2 6.6 - - - +
300A TYR* 2.9 25.9 - - - +
301A LYS 3.5 17.5 - - - +
302A THR* 4.2 16.0 - - + +
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Residues in contact with VAL 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 GLU 3.1 17.0 + - - +
173A VAL 4.1 0.4 - - - +
175A GLN* 1.3 74.8 - - - +
177A ALA* 1.3 64.1 + - - +
178A GLN 3.1 1.8 - - - -
179A VAL* 3.1 7.9 + - + +
180A LEU* 3.0 29.9 + - + +
204A ILE* 3.3 24.5 - - + -
205A THR* 4.5 9.9 - - + +
208A ALA* 3.5 22.9 - - + -
273A LEU* 4.9 10.8 - - + -
293A TRP* 4.0 18.2 - - + -
297A LYS* 3.7 20.6 - - + -
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Residues in contact with ALA 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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173A VAL 3.1 19.9 + - - +
174A CYS 3.8 5.6 - - - +
176A VAL* 1.3 77.6 - - - +
178A GLN* 1.3 59.1 + - - +
180A LEU* 3.4 5.3 + - - +
181A THR* 3.0 30.8 + - - -
208A ALA* 3.8 11.0 - - - +
211A ARG* 3.8 17.9 - - - -
212A ILE* 3.6 25.3 - - + +
304A TYR* 3.8 7.2 - - + -
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Residues in contact with GLN 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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174A CYS 3.1 17.6 + - - +
175A GLN 3.6 1.3 - - - +
176A VAL 3.1 0.6 - - - -
177A ALA* 1.3 77.8 - - - +
179A VAL* 1.3 57.9 + - - +
181A THR* 4.4 2.9 - - - +
182A TYR* 2.9 48.0 + - + +
300A TYR* 3.3 37.5 - - + +
301A LYS* 2.8 50.9 + - - +
303A TYR 4.0 0.4 + - - -
304A TYR* 3.5 39.9 - - + +
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Residues in contact with VAL 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 GLN 2.9 29.2 + - - +
176A VAL* 3.1 14.6 + - + +
178A GLN* 1.3 76.2 - - - +
180A LEU* 1.3 58.8 + - - +
183A SER* 2.8 38.1 + - - -
184A MET* 3.1 22.8 + - + +
273A LEU* 4.0 14.8 - - + -
293A TRP 5.3 0.2 - - - +
296A GLU* 3.6 20.9 - - + -
297A LYS* 3.9 22.4 - - + +
300A TYR* 3.5 20.4 - - + -
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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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176A VAL* 3.0 21.7 + - + +
177A ALA* 3.5 7.2 - - - +
178A GLN 3.2 0.2 - - - -
179A VAL* 1.3 77.8 - - - +
181A THR* 1.3 56.5 + - - +
184A MET* 3.2 35.0 - - + -
185A GLY 3.0 10.7 + - - -
186A VAL* 2.8 38.3 + - + +
192A VAL* 4.6 11.2 - - + -
205A THR* 4.9 1.6 - - + +
208A ALA* 3.9 35.0 - - + +
209A ILE* 4.0 14.8 - - + +
212A ILE* 4.0 17.0 - - + -
239A VAL* 5.4 0.4 - - + -
241A ILE* 4.2 15.5 - - + -
273A LEU* 5.2 1.1 - - + -
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Residues in contact with THR 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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177A ALA 3.0 16.4 + - - -
178A GLN* 4.0 3.1 - - - -
180A LEU* 1.3 79.5 - - - +
182A TYR* 1.3 76.9 + - + +
185A GLY* 3.4 19.9 - - - -
186A VAL 3.9 8.9 + - - +
187A ARG* 3.4 27.6 + - - +
212A ILE* 4.1 16.6 - - - +
304A TYR* 4.0 22.5 + - - +
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Residues in contact with TYR 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 GLN* 2.9 44.1 + - + +
181A THR* 1.3 85.4 - - + +
183A SER* 1.3 60.6 + - - +
184A MET 3.6 0.2 - - - -
185A GLY 4.5 1.0 + - - -
300A TYR* 3.4 29.2 - + + +
304A TYR* 4.3 28.0 + + - -
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Residues in contact with SER 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A VAL* 2.8 30.1 + - - -
182A TYR* 1.3 76.2 - - - +
184A MET* 1.3 58.5 + - - +
271A HIS* 3.5 17.2 + - - -
291A LEU* 3.7 19.5 - - - +
296A GLU* 3.3 22.2 + - - +
299A LYS* 4.3 2.9 + - - -
300A TYR* 2.9 20.3 + - - -
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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
------------------------------------------------------------
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