Contacts of the helix formed by residues 181 - 200 (chain A) in PDB entry 3RCY
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 ALA 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A MET 3.6 1.8 + - - -
180A PRO* 1.3 76.8 - - - +
182A MET* 1.3 65.9 + - - +
183A THR* 3.1 17.7 - - - +
184A ASP* 2.9 28.8 + - - +
185A ILE* 3.2 11.6 + - - +
393A CYS* 4.5 0.2 - - - -
394A ASP 3.8 12.6 - - - +
395A TYR* 3.6 31.6 - - + +
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Residues in contact with MET 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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180A PRO 3.9 0.2 + - - -
181A ALA* 1.3 72.6 - - - +
183A THR* 1.3 59.0 + - + +
185A ILE* 3.3 16.8 + - + +
186A SER* 2.9 41.5 + - - +
220A ARG* 3.6 28.0 - - - +
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Residues in contact with THR 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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181A ALA* 3.6 14.0 - - - +
182A MET* 1.3 77.3 - - + +
184A ASP* 1.3 62.2 + - - -
186A SER* 4.2 5.5 - - - +
187A LEU* 2.9 32.7 + - - +
394A ASP 4.9 3.6 + - - -
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Residues in contact with ASP 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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168A PRO 4.4 5.1 - - - +
169A ALA* 3.4 31.6 - - + +
170A GLY* 4.0 8.1 - - - -
171A PRO* 5.2 1.4 - - - +
178A HIS* 5.1 1.0 + - - -
180A PRO* 3.8 11.5 - - + +
181A ALA* 2.9 35.6 + - - +
183A THR* 1.3 77.0 + - - +
185A ILE* 1.3 64.3 + - - +
187A LEU* 4.0 4.6 - - - +
188A SER* 2.8 31.1 + - - -
221A LEU* 4.7 1.8 - - + -
393A CYS* 3.7 15.5 - - - -
394A ASP 5.8 0.2 - - - -
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Residues in contact with ILE 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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180A PRO* 3.9 23.8 - - + +
181A ALA 3.2 10.5 + - - +
182A MET* 3.3 18.6 + - + +
184A ASP* 1.3 76.8 - - - +
186A SER* 1.3 64.2 + - - +
188A SER* 3.2 4.0 + - - -
189A VAL* 3.0 24.4 + - + +
220A ARG* 3.5 47.6 - - + +
221A LEU* 3.9 17.0 - - + -
224A ALA* 3.6 29.4 - - + -
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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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182A MET* 2.9 27.5 + - - +
183A THR* 4.2 5.6 - - - -
185A ILE* 1.3 77.7 - - - +
187A LEU* 1.3 57.4 + - - +
189A VAL* 3.4 8.5 + - - +
190A GLU* 2.9 29.0 + - - +
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Residues in contact with LEU 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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144A THR* 3.6 50.3 - - + +
146A ALA 5.0 0.9 - - - +
168A PRO* 3.6 20.2 - - + +
183A THR 2.9 19.8 + - - +
184A ASP* 4.0 4.5 - - - +
186A SER* 1.3 76.3 - - - +
188A SER* 1.3 57.5 + - - +
190A GLU* 3.2 24.0 + - - +
191A PHE* 2.9 50.0 + - + -
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Residues in contact with SER 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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168A PRO* 3.7 11.1 - - - +
169A ALA* 3.7 13.3 - - - -
184A ASP 2.8 21.5 + - - -
185A ILE 3.2 5.4 + - - -
187A LEU* 1.3 77.4 - - - +
189A VAL* 1.3 60.2 + - - +
191A PHE* 3.5 1.9 + - - +
192A CYS* 3.1 29.6 + - - -
207A PHE* 3.4 21.3 - - - -
221A LEU* 3.4 23.7 - - - +
225A ILE* 4.0 5.6 - - - -
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Residues in contact with VAL 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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185A ILE* 3.0 19.6 + - + +
186A SER* 3.6 9.9 - - - +
188A SER* 1.3 72.9 - - - +
190A GLU* 1.3 60.4 + - - +
192A CYS* 3.3 4.7 + - - +
193A ARG* 2.9 33.9 + - + +
224A ALA* 3.6 39.0 - - + +
225A ILE* 4.4 4.9 - - + -
228A TYR* 3.7 24.7 - - + +
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Residues in contact with GLU 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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146A ALA* 3.7 17.5 + - + +
147A ASP* 5.1 0.7 + - - -
186A SER 2.9 17.9 + - - +
187A LEU* 3.2 24.3 + - - +
189A VAL* 1.3 77.6 - - - +
191A PHE* 1.3 57.0 + - - +
193A ARG* 3.8 26.2 - - - +
194A LYS* 2.8 58.5 + - - +
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Residues in contact with PHE 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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142A PHE* 4.5 1.6 - + - -
143A TRP 3.7 22.4 - - - -
144A THR 3.9 3.8 - - - -
145A SER 3.6 17.9 - - - -
146A ALA* 3.4 28.0 - - + +
149A ALA* 3.4 18.8 - - + -
166A PHE* 3.8 28.7 - + + -
167A ASP 5.5 0.7 - - - -
168A PRO* 3.5 29.6 - - + -
187A LEU* 2.9 43.2 + - + +
188A SER 3.7 5.4 - - - +
190A GLU* 1.3 72.8 - - - +
192A CYS* 1.3 58.1 + - - +
194A LYS* 4.2 0.2 - - - +
195A ILE* 2.8 46.7 + - + +
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Residues in contact with CYS 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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166A PHE* 4.1 11.0 - - - -
188A SER 3.1 19.0 + - - +
189A VAL* 3.8 1.8 - - - +
191A PHE* 1.3 79.6 - - - +
193A ARG* 1.3 57.9 + - - +
196A ARG* 2.9 33.8 + - - +
205A LEU* 3.6 14.4 - - + +
207A PHE* 3.9 26.5 - - - -
225A ILE* 4.0 18.4 - - - -
228A TYR* 3.6 28.9 - - + -
230A PRO* 5.4 4.7 - - - -
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Residues in contact with ARG 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 VAL* 2.9 20.3 + - - +
190A GLU* 3.8 29.0 - - - +
192A CYS* 1.3 78.1 - - - +
194A LYS* 1.3 79.7 + - - +
196A ARG* 3.9 1.6 - - - +
197A ALA* 3.0 31.1 + - + +
228A TYR* 3.6 32.2 - - + +
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Residues in contact with LYS 194 (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* 3.8 18.4 - - + +
147A ASP* 2.8 34.7 + - - +
150A ALA* 3.7 17.3 - - + +
190A GLU* 2.8 46.5 + - + +
191A PHE 4.2 1.1 - - - +
193A ARG* 1.3 98.4 - - - +
195A ILE* 1.3 60.6 + - - +
197A ALA* 3.4 6.7 + - - +
198A ALA* 3.0 28.1 + - - +
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Residues in contact with ILE 195 (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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131A LEU* 3.7 22.7 - - + -
146A ALA 5.0 1.3 - - - +
149A ALA* 4.0 3.1 - - + -
150A ALA* 4.1 20.9 - - + +
153A ALA* 3.8 17.7 - - + -
164A VAL* 4.1 11.9 - - + -
166A PHE* 3.7 28.0 - - + -
191A PHE* 2.8 38.8 + - + +
192A CYS 4.3 1.1 - - - +
194A LYS* 1.3 71.0 - - - +
196A ARG* 1.3 58.9 + - - +
198A ALA* 3.1 5.8 + - - -
199A VAL* 2.9 30.7 + - + +
205A LEU* 3.8 24.0 - - + -
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Residues in contact with ARG 196 (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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192A CYS 2.9 20.9 + - - +
193A ARG 3.9 2.9 - - - +
195A ILE* 1.3 76.0 - - - +
197A ALA* 1.3 56.6 + - - +
199A VAL* 4.1 5.1 - - - +
200A GLY* 2.7 69.3 + - - -
201A ASP* 5.7 0.7 - - - -
203A ALA 3.0 19.4 + - - -
205A LEU* 3.8 32.5 - - + +
228A TYR* 2.9 40.0 + - + +
229A SER 3.3 15.6 + - - -
182B MET* 3.6 29.8 - - - +
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Residues in contact with ALA 197 (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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193A ARG* 3.0 20.5 + - + +
194A LYS* 3.7 8.1 - - - +
195A ILE 3.3 0.4 - - - -
196A ARG* 1.3 78.4 - - - +
198A ALA* 1.3 60.5 + - - +
200A GLY* 4.2 3.6 + - - -
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Residues in contact with ALA 198 (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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150A ALA* 3.7 29.8 - - + +
154A ALA* 4.7 16.5 - - + +
157A VAL* 5.8 1.2 - - - +
194A LYS 3.0 16.9 + - - +
195A ILE* 3.1 5.6 + - - +
197A ALA* 1.3 78.9 - - - +
199A VAL* 1.3 63.5 + - + +
202A LYS* 6.1 0.2 - - - +
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Residues in contact with VAL 199 (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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153A ALA* 3.8 25.4 - - + +
154A ALA 4.7 0.2 - - - +
157A VAL* 3.6 33.9 - - + -
164A VAL* 4.9 2.9 - - + -
195A ILE* 2.9 23.9 + - + +
196A ARG* 4.1 2.2 - - - +
198A ALA* 1.3 81.0 - - - +
200A GLY* 1.3 74.9 + - - +
201A ASP 3.4 0.2 + - - -
202A LYS* 2.9 29.9 + - - +
203A ALA* 3.7 22.0 - - + +
205A LEU* 3.8 17.0 - - + -
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Residues in contact with GLY 200 (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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196A ARG* 2.7 56.0 + - - -
197A ALA 4.2 3.4 + - - -
198A ALA 3.7 1.4 - - - -
199A VAL* 1.3 74.1 - - - +
201A ASP* 1.3 61.7 + - - -
203A ALA 3.8 0.3 - - - +
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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
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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