Contacts of the helix formed by residues 168 - 187 (chain A) in PDB entry 2RCY
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 CYS 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A THR* 2.8 20.3 + - - -
164A ALA* 3.4 7.2 - - - +
167A GLY* 1.3 72.4 - - - -
169A GLY* 1.3 65.6 + - - +
170A PRO* 3.3 2.5 - - - -
171A ALA* 3.0 20.4 + - - +
172A TYR* 3.2 29.9 + - + +
253A ALA* 4.4 0.2 - - - -
223E ILE* 3.3 4.2 - - - +
229E ILE* 3.7 21.1 - - - -
230E THR* 3.0 45.5 - - + +
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Residues in contact with GLY 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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164A ALA 3.8 0.6 + - - -
165A ILE 2.9 26.5 + - - -
168A CYS* 1.3 77.1 - - - +
170A PRO* 1.4 67.5 - - - +
172A TYR* 2.9 27.9 + - - +
173A VAL* 3.1 14.8 + - - +
180E LEU* 5.9 1.6 - - - -
201E THR* 3.6 11.2 - - - -
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Residues in contact with PRO 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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115A ASN* 3.8 23.1 - - + +
116A THR* 4.4 5.6 - - - +
117A PRO* 3.9 12.8 - - + -
166A SER 3.5 14.8 - - - +
167A GLY 3.5 4.0 - - - +
168A CYS 3.3 5.2 - - - -
169A GLY* 1.4 87.8 - - - +
171A ALA* 1.3 50.8 + - - +
173A VAL* 3.2 2.5 + - + +
174A TYR* 2.6 59.0 + - + -
201E THR* 3.5 4.7 - - + -
205E SER* 3.2 22.2 - - - +
223E ILE* 3.8 9.4 - - + -
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Residues in contact with ALA 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A CYS 3.0 13.2 + - - +
169A GLY 3.0 0.2 + - - -
170A PRO* 1.3 78.8 - - - +
172A TYR* 1.3 59.7 + - + +
174A TYR* 3.6 11.4 + - - +
175A LEU* 3.0 29.1 + - - +
220E LYS* 4.0 4.8 - - + +
223E ILE* 3.5 14.8 - - + +
230E THR* 3.6 25.4 - - + -
234E LEU* 3.9 21.0 - - + +
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Residues in contact with TYR 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 ALA 3.0 28.8 + - - -
165A ILE* 4.9 0.2 - - - -
168A CYS* 3.2 21.3 - - + +
169A GLY* 2.9 23.9 + - - +
171A ALA* 1.3 78.2 - - + +
173A VAL* 1.3 60.1 + - + +
175A LEU* 3.5 2.1 + - - +
176A PHE* 2.9 28.8 + - - +
246A VAL* 6.0 1.6 - - + -
249A ALA* 4.1 8.1 + - + -
250A VAL* 4.1 17.4 - - + -
253A ALA* 3.6 18.7 - - - +
176E PHE* 3.8 19.8 - - + -
180E LEU* 4.1 17.3 - - + -
230E THR 5.1 1.8 - - - -
233E GLY* 4.2 23.0 - - - -
234E LEU* 4.5 4.0 - - + -
237E LEU* 3.7 28.7 - - + -
242E PHE* 4.1 3.1 - - - -
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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
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169A GLY* 3.1 17.4 + - - +
170A PRO 3.6 4.7 - - - +
172A TYR* 1.3 74.6 - - + +
174A TYR* 1.3 59.3 + - - +
176A PHE* 3.2 7.9 + - + +
177A ILE* 2.8 48.1 + - + +
202A ILE* 5.4 2.7 - - + -
176E PHE* 4.1 13.2 - - + -
180E LEU* 5.3 3.4 - - + -
201E THR* 4.5 2.0 - - + -
202E ILE* 3.8 45.8 - - + +
205E SER* 3.7 26.9 - - - +
206E VAL* 4.9 0.7 - - + -
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Residues in contact with TYR 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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116A THR* 3.8 9.2 + - - -
117A PRO* 4.8 0.3 - - - +
170A PRO* 2.6 45.7 + - + +
171A ALA 3.8 6.1 - - - +
173A VAL* 1.3 71.9 - - - +
175A LEU* 1.3 56.2 + - - +
177A ILE* 3.5 2.1 + - + -
178A GLU* 2.8 30.2 + - - +
205E SER* 3.5 29.0 - - - -
208E MSE 3.2 37.5 - - + +
209E VAL* 3.9 9.4 - - + -
216E VAL* 3.4 27.3 - - + +
219E LEU* 3.2 39.9 - - + +
220E LYS* 3.6 22.7 - - + -
223E ILE* 4.5 1.8 - - + -
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Residues in contact with LEU 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 ALA 3.0 17.9 + - - +
172A TYR 3.8 4.3 - - - +
174A TYR* 1.3 73.8 - - - +
176A PHE* 1.3 53.5 + - - +
178A GLU* 3.4 29.5 - - - +
179A SER* 2.6 46.4 + - - +
220E LYS* 3.9 16.3 - - + +
234E LEU* 4.2 9.6 - - + -
237E LEU* 3.8 21.1 - - + -
238E GLU* 3.8 23.3 - - - +
242E PHE* 3.7 26.2 - - + -
243E LYS* 4.7 11.9 - - + +
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Residues in contact with PHE 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 TYR 2.9 18.3 + - - +
173A VAL* 3.3 10.8 - - + +
175A LEU* 1.3 74.8 - - - +
177A ILE* 1.3 62.4 + - - +
179A SER* 3.2 4.2 + - - -
180A LEU* 3.0 52.7 + - + +
202A ILE* 4.3 11.4 - - + -
242A PHE* 3.8 20.6 - + - -
172E TYR* 3.8 32.5 - - + -
173E VAL* 3.9 19.5 - - + -
176E PHE* 4.0 26.2 - + + -
242E PHE* 3.6 25.2 - + + -
246E VAL* 4.0 16.8 - - + -
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Residues in contact with ILE 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A VAL* 2.8 41.2 + - + +
174A TYR* 3.6 6.7 - - - +
176A PHE* 1.3 71.7 - - - +
178A GLU* 1.3 62.8 + - - +
180A LEU* 3.4 2.0 + - - +
181A ILE* 3.1 44.3 + - + +
198A VAL* 3.9 16.6 - - + +
199A LEU* 4.2 14.1 - - + -
202A ILE* 3.6 21.8 - - + -
205E SER 4.7 1.1 - - - +
206E VAL* 4.2 19.3 - - + +
209E VAL* 3.9 24.2 - - + -
216E VAL* 4.3 11.0 - - + -
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Residues in contact with GLU 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 TYR 2.8 19.6 + - - +
175A LEU* 3.4 15.6 - - - +
177A ILE* 1.3 74.3 - - - +
179A SER* 1.3 60.3 + - - +
181A ILE* 3.6 5.2 + - - +
182A ASP* 3.2 27.6 + - - +
178D GLU* 4.8 5.0 - - - +
216E VAL* 4.2 14.0 - - + +
217E GLN* 3.5 32.7 + - + +
220E LYS* 2.9 35.0 + - - +
243E LYS* 2.8 26.6 + - - +
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Residues in contact with SER 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 LEU* 2.6 32.2 + - - +
176A PHE* 3.7 4.6 - - - -
178A GLU* 1.3 71.3 - - - +
180A LEU* 1.3 64.6 + - - +
182A ASP* 3.5 1.1 + - - +
183A ALA* 3.1 19.1 + - - +
242E PHE* 4.4 1.7 - - - -
243E LYS* 3.3 42.7 - - - +
246E VAL* 3.8 25.8 - - - -
247E MSE 3.3 12.6 - - - +
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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 PHE* 3.0 50.6 + - + +
177A ILE 3.8 2.0 - - - +
179A SER* 1.3 74.1 - - - +
181A ILE* 1.3 64.6 + - - +
183A ALA* 3.4 6.7 + - - +
184A GLY 3.2 16.3 + - - -
198A VAL* 3.5 33.9 - - + -
202A ILE* 4.4 5.2 - - + -
165E ILE* 4.1 21.3 - - + +
169E GLY* 5.9 1.1 - - - -
172E TYR* 4.3 16.6 - - + -
173E VAL* 5.3 2.5 - - + -
246E VAL* 3.8 20.9 - - + -
250E VAL* 3.9 18.6 - - + -
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Residues in contact with ILE 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 ILE* 3.1 36.7 + - + +
178A GLU* 3.9 6.5 - - - +
180A LEU* 1.3 76.4 - - - +
182A ASP* 1.3 52.2 + - - +
184A GLY* 3.0 3.3 + - - -
185A VAL* 2.8 48.8 + - + +
191A ARG* 4.1 25.8 - - + +
194A SER* 3.8 18.8 + - - -
195A LYS* 3.8 40.2 - - + +
198A VAL* 4.0 8.7 - - + -
216E VAL* 4.9 10.1 - - + -
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Residues in contact with ASP 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 GLU* 3.2 17.7 + - - +
179A SER 3.7 5.4 - - - +
180A LEU 3.4 0.2 - - - -
181A ILE* 1.3 75.4 - - - +
183A ALA* 1.3 58.1 + - - +
185A VAL* 3.9 4.7 - - - +
186A LYS* 2.9 31.9 + - - +
191A ARG* 2.7 31.7 + - - -
217E GLN* 5.9 0.9 + - - -
243E LYS* 2.6 33.0 + - - -
247E MSE 3.7 20.7 - - + +
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Residues in contact with ALA 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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179A SER 3.1 14.0 + - - +
180A LEU 3.5 10.3 - - - +
181A ILE 3.3 0.2 - - - -
182A ASP* 1.3 75.8 - - - +
184A GLY* 1.3 60.5 + - - +
186A LYS* 3.7 2.1 + - - +
187A ASN* 3.1 31.0 + - - +
161E ILE* 3.6 6.0 - - - +
247E MSE 3.9 27.5 - - - +
250E VAL* 3.8 31.9 - - + -
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Residues in contact with GLY 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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180A LEU 3.2 4.2 + - - -
181A ILE 3.0 7.5 + - - -
183A ALA* 1.3 76.5 - - - +
185A VAL* 1.3 61.7 - - - +
187A ASN 3.3 9.0 + - - -
188A GLY 3.3 0.3 + - - -
189A LEU* 3.0 24.9 + - - +
194A SER* 3.6 12.1 - - - -
161E ILE* 4.0 5.2 - - - -
165E ILE* 3.4 26.2 - - - +
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Residues in contact with VAL 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 ILE* 2.8 26.2 + - + +
182A ASP* 3.9 4.3 - - - +
184A GLY* 1.3 72.7 - - - +
186A LYS* 1.3 63.0 + - - +
187A ASN 3.4 0.3 + - - -
188A GLY* 3.5 9.5 + - - -
189A LEU 3.3 13.5 - - - +
190A SER* 5.7 0.2 - - - -
191A ARG* 3.8 65.1 - - + +
194A SER* 4.2 1.8 - - - +
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Residues in contact with LYS 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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182A ASP 2.9 18.6 + - - +
183A ALA* 3.9 5.8 - - - +
184A GLY 3.3 0.2 - - - -
185A VAL* 1.3 77.5 - - - +
187A ASN* 1.3 64.1 + - - +
188A GLY 3.4 2.3 + - - -
247E MSE 4.2 18.4 - - + -
251E GLU* 2.9 40.3 + - - +
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Residues in contact with ASN 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 ALA* 3.1 16.6 + - - +
184A GLY 3.3 5.3 + - - -
185A VAL 3.2 0.8 - - - -
186A LYS* 1.3 86.4 + - - +
188A GLY* 1.3 55.6 + - - +
189A LEU 3.7 0.4 - - - -
157E LYS 5.6 0.7 - - - +
158E ASP* 4.8 1.7 - - - +
161E ILE* 3.5 44.2 - - + +
251E GLU* 3.3 42.3 + - - +
254E CYS* 4.6 12.4 - - - -
258E LYS* 5.3 10.2 + - - +
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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