Contacts of the helix formed by residues 181 - 197 (chain A) in PDB entry 1C0F
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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155A SER* 4.4 4.3 - - - +
156A GLY 3.2 13.9 - - - +
157A ASP 3.7 2.5 - - - +
158A GLY 3.5 7.2 + - - -
159A VAL 3.4 32.3 - - - +
160A SER* 4.2 3.4 - - - +
180A LEU* 1.3 80.0 - - - +
182A GLY* 1.3 68.2 + - - +
183A ARG 3.3 1.6 - - - -
184A ASP* 2.9 21.1 + - - +
185A LEU* 3.2 14.6 + - - +
261A LEU* 5.2 0.7 - - - -
303A THR* 4.2 6.7 - - - -
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Residues in contact with GLY 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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156A GLY 2.8 14.3 + - - -
157A ASP 3.6 0.2 + - - -
181A ALA* 1.3 72.5 - - - +
183A ARG* 1.3 61.0 + - - +
185A LEU* 3.2 6.4 + - - +
186A THR* 3.0 18.9 + - - -
213A LYS* 3.0 15.0 + - - -
303A THR* 3.2 14.8 + - - -
376A ATP 3.2 23.3 - - - -
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Residues in contact with ARG 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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69A TYR* 5.3 18.2 + - - -
157A ASP* 3.0 44.3 + - - +
158A GLY* 5.4 2.0 - - - -
182A GLY* 1.3 76.3 - - - +
184A ASP* 1.3 61.2 + - - +
186A THR* 3.3 6.9 + - - -
187A ASP* 3.0 57.4 + - - +
206A ARG* 3.7 31.7 - - - +
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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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73A HIC 5.9 1.9 - - - -
157A ASP 5.4 0.3 - - - +
158A GLY 5.1 2.8 - - - +
179A ASP 3.9 4.0 - - - +
180A LEU* 3.3 13.0 + - + -
181A ALA* 2.9 29.5 + - - +
183A ARG* 1.3 78.9 + - - +
185A LEU* 1.3 60.5 + - - +
187A ASP* 3.7 8.0 + - - +
188A TYR* 3.0 27.4 + - - +
267A LEU* 4.0 21.1 - - + +
269A MET* 4.3 14.1 - - - +
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Residues in contact with LEU 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 LEU* 4.1 20.2 - - + -
181A ALA 3.2 4.3 + - - +
182A GLY* 3.4 9.4 - - - +
183A ARG 3.1 0.4 - - - -
184A ASP* 1.3 80.1 - - - +
186A THR* 1.3 59.4 + - - +
188A TYR* 3.3 3.1 + - - +
189A MET 2.9 23.7 + - - -
213A LYS* 4.1 9.0 - - + -
257A CYS* 3.4 39.6 - - - +
258A PRO* 4.3 1.6 - - + -
260A ALA* 3.9 18.4 - - + -
261A LEU* 3.9 14.4 - - + -
267A LEU* 4.9 1.1 - - + -
303A THR* 3.7 20.2 - - + -
306A PHE* 3.5 33.4 - - + -
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Residues in contact with THR 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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157A ASP* 5.6 0.3 + - - -
182A GLY 3.0 5.7 + - - -
183A ARG* 3.6 10.2 - - - -
185A LEU* 1.3 71.8 - - - +
187A ASP* 1.3 68.8 + - - +
189A MET* 3.0 7.8 + - - +
190A MET* 3.0 22.7 + - - +
206A ARG* 4.0 25.8 - - + +
209A VAL* 3.6 4.4 - - + +
210A ARG* 3.8 37.8 - - + +
213A LYS* 2.9 36.2 + - - +
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Residues in contact with ASP 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 ARG* 3.0 41.6 + - - +
184A ASP* 3.8 8.6 - - - +
186A THR* 1.3 74.2 - - - +
188A TYR* 1.3 62.9 + - - +
190A MET* 2.9 20.5 + - - +
191A LYS* 3.1 14.5 + - - +
206A ARG* 3.0 38.5 + - - -
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Residues in contact with TYR 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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184A ASP 3.0 19.0 + - - +
185A LEU* 3.6 5.2 - - - +
186A THR 3.2 0.2 - - - -
187A ASP* 1.3 75.8 - - - +
189A MET* 1.3 63.3 + - - +
190A MET 3.3 0.2 + - - -
191A LYS* 3.3 22.5 + - - -
192A ILE* 3.1 49.0 + - + +
256A ARG* 3.3 34.0 + - - +
257A CYS* 3.9 23.6 - - - -
260A ALA* 4.3 3.1 - - + -
266A PHE* 3.4 44.5 + + + +
267A LEU* 3.5 23.6 - - + -
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Residues in contact with MET 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 LEU 2.9 16.3 + - - +
186A THR* 3.0 7.1 + - - +
188A TYR* 1.3 76.9 - - - +
190A MET* 1.3 61.6 + - - +
192A ILE* 3.6 7.1 - - - +
193A LEU* 3.0 44.5 + - + +
209A VAL* 3.5 22.0 - - + +
212A ILE* 4.5 11.0 - - + -
213A LYS* 4.3 11.7 - - + -
216A LEU* 5.9 0.4 - - + -
217A ALA* 4.2 18.2 - - + +
250A ILE* 5.2 1.1 - - + -
253A GLU* 3.4 46.0 - - + +
254A ARG* 4.4 2.7 - - - -
257A CYS* 3.5 24.9 - - + -
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Residues in contact with MET 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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186A THR* 3.0 18.1 + - - +
187A ASP* 2.9 13.8 + - - +
189A MET* 1.3 79.3 - - - +
191A LYS* 1.3 53.6 + - - +
193A LEU* 4.0 1.6 - - - +
194A THR* 2.8 38.0 + - - -
200A PHE* 3.5 26.2 - - + +
201A THR* 3.9 21.8 - - - +
202A THR 4.1 0.4 - - - +
206A ARG* 3.7 62.8 - - + +
209A VAL* 3.6 26.9 - - + -
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Residues in contact with LYS 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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187A ASP 3.1 10.0 + - - +
188A TYR* 3.3 28.2 + - + +
190A MET* 1.3 80.0 - - - +
192A ILE* 1.3 58.1 + - + +
194A THR* 3.4 8.1 - - - +
195A GLU* 3.1 52.7 + - + +
266A PHE 5.3 3.4 - - - -
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Residues in contact with ILE 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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188A TYR* 3.1 55.3 + - + +
189A MET* 3.6 13.7 - - - +
191A LYS* 1.3 77.6 - - + +
193A LEU* 1.3 66.8 + - - +
194A THR 3.2 0.2 - - - -
195A GLU* 3.8 17.4 - - - +
196A ARG* 3.3 13.9 + - - -
253A GLU* 3.8 47.8 - - + +
256A ARG* 3.7 35.6 + - + +
257A CYS 4.4 2.2 - - - +
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Residues in contact with LEU 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 MET* 3.0 43.8 + - + +
190A MET 4.0 0.4 - - - +
192A ILE* 1.3 73.5 - - - +
194A THR* 1.3 67.7 + - - +
196A ARG* 3.0 26.0 + - - +
198A TYR* 3.4 19.4 + - + +
200A PHE* 3.8 30.7 - - + -
209A VAL* 4.5 5.2 - - + -
212A ILE* 4.1 20.9 - - + -
250A ILE* 3.7 26.7 - - + -
253A GLU* 3.7 27.6 - - + -
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Residues in contact with THR 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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190A MET 2.8 23.8 + - - -
191A LYS* 3.4 9.1 - - - +
193A LEU* 1.3 77.2 - - - +
195A GLU* 1.3 65.0 + - + +
197A GLY* 2.8 15.1 + - - -
198A TYR 2.9 22.3 - - - +
199A SER* 4.4 7.4 - - - +
200A PHE* 3.0 26.0 + - - -
201A THR* 4.3 9.3 - - + +
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Residues in contact with GLU 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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191A LYS* 3.1 49.2 + - + +
192A ILE* 3.9 21.3 - - - +
193A LEU 3.3 0.2 - - - -
194A THR* 1.3 76.9 - - + +
196A ARG* 1.3 60.7 + - - +
197A GLY* 3.2 1.0 + - - -
256A ARG* 4.5 6.6 + - - -
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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 ILE 3.3 5.9 + - - +
193A LEU* 3.0 17.3 + - - +
194A THR 3.0 0.4 + - - -
195A GLU* 1.3 76.0 - - - +
197A GLY* 1.3 56.4 + - - +
198A TYR* 3.7 16.4 + - + -
237A GLU* 4.1 18.4 + - - +
249A THR* 3.1 29.1 + - - +
251A GLY* 3.6 21.8 - - - +
252A ASN* 4.3 7.1 + - - +
253A GLU* 2.9 54.0 + - - +
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Residues in contact with GLY 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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194A THR 2.8 7.2 + - - -
195A GLU 3.1 1.9 - - - -
196A ARG* 1.3 80.3 - - - +
198A TYR* 1.3 69.6 + - - +
199A SER* 5.3 0.2 - - - -
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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