Contacts of the helix formed by residues 206 - 227 (chain A) in PDB entry 5ICN
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 THR 206 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204A PRO 4.2 0.4 + - - -
205A LEU* 1.3 74.0 - - - +
207A ASP* 1.3 76.6 + - - +
208A LYS* 3.5 14.5 + - + +
209A GLN* 3.0 44.6 + - + +
210A ILE* 3.1 16.9 + - - +
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Residues in contact with ASP 207 (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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206A THR* 1.3 77.0 + - - +
208A LYS* 1.3 56.6 + - - +
210A ILE* 4.4 2.4 - - - +
211A ASP* 2.8 35.4 + - - +
49B ARG* 2.9 42.9 + - - +
50B LYS* 5.4 8.2 - - - +
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Residues in contact with LYS 208 (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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206A THR* 3.1 15.2 + - + +
207A ASP* 1.3 79.5 - - - +
209A GLN* 1.3 52.7 + - + +
211A ASP* 3.2 7.1 + - - +
212A GLN* 2.7 64.5 + - + +
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Residues in contact with GLN 209 (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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204A PRO 4.3 2.9 - - - +
205A LEU* 3.5 29.2 - - + +
206A THR* 3.0 39.4 + - + +
208A LYS* 1.3 76.5 - - + +
210A ILE* 1.3 62.3 + - - +
212A GLN* 3.6 17.8 - - - +
213A PHE* 2.9 28.2 + - - +
265A ILE* 4.4 17.0 - - + +
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Residues in contact with ILE 210 (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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199A TRP* 4.2 22.4 - - + -
203A ASN* 4.3 4.9 - - - +
205A LEU* 4.0 31.0 - - + +
206A THR 3.1 21.3 + - - +
207A ASP* 3.8 1.3 - - - +
209A GLN* 1.3 72.1 - - - +
211A ASP* 1.3 66.3 + - - +
213A PHE* 3.0 7.5 + - - +
214A LEU* 2.8 25.9 + - + +
255A MET* 4.0 27.6 - - + -
258A LEU* 4.3 9.0 - - + -
265A ILE* 5.7 0.2 - - - -
49B ARG* 3.4 35.9 - - + +
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Residues in contact with ASP 211 (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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207A ASP* 2.8 19.9 + - - +
208A LYS* 3.3 7.7 - - + +
210A ILE* 1.3 75.7 - - - +
212A GLN* 1.3 62.9 + - + +
214A LEU* 3.1 19.3 + - - +
215A VAL* 3.1 18.9 + - - +
218A ARG* 5.1 0.9 + - - -
49B ARG* 2.7 39.8 + - - -
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Residues in contact with GLN 212 (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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208A LYS* 2.7 51.4 + - + +
209A GLN* 3.6 24.3 + - - +
211A ASP* 1.3 70.6 - - + +
213A PHE* 1.3 65.2 + - - +
215A VAL* 3.0 12.3 + - - +
216A VAL* 3.0 28.0 + - + +
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Residues in contact with PHE 213 (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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209A GLN 2.9 15.3 + - - +
210A ILE* 3.0 11.0 + - - +
212A GLN* 1.3 75.5 - - - +
214A LEU* 1.3 59.6 + - + +
216A VAL* 3.0 9.7 + - + +
217A ALA* 2.8 26.6 + - + -
254A ALA* 3.6 33.7 - - + -
257A THR* 4.5 4.7 - - + -
258A LEU* 3.8 23.8 - - + -
265A ILE* 4.4 15.3 - - + -
268A ALA* 3.9 25.6 - - + -
269A ILE* 3.5 40.2 - - + -
272A LEU* 3.3 28.9 - - + -
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Residues in contact with LEU 214 (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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210A ILE* 2.8 19.6 + - + +
211A ASP* 3.3 10.1 - - - +
213A PHE* 1.3 80.8 - - + +
215A VAL* 1.3 61.1 + - - +
217A ALA* 3.4 4.5 + - - +
218A ARG* 3.0 36.2 + - - +
251A LEU* 4.3 27.5 - - + +
254A ALA* 3.6 28.3 - - + -
255A MET* 4.0 27.8 - - + -
258A LEU* 5.3 0.7 - - + -
43B LEU* 5.7 4.5 - - + -
49B ARG* 4.5 19.3 - - - +
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Residues in contact with VAL 215 (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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211A ASP* 3.1 16.7 + - + +
212A GLN* 3.0 11.4 + - - +
214A LEU* 1.3 75.4 - - - +
216A VAL* 1.3 60.4 + - + +
218A ARG* 3.1 27.0 + - + +
219A SER* 2.9 37.4 + - - +
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Residues in contact with VAL 216 (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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212A GLN* 3.0 19.8 + - + +
213A PHE* 3.3 13.0 - - + +
215A VAL* 1.3 78.7 - - + +
217A ALA* 1.3 61.7 + - - +
219A SER* 3.0 18.6 + - - -
220A VAL* 3.0 25.9 + - + +
269A ILE* 4.5 23.8 - - + -
272A LEU* 4.8 2.9 - - + -
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Residues in contact with ALA 217 (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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213A PHE* 2.8 17.9 + - + +
214A LEU 3.6 4.9 - - - +
216A VAL* 1.3 73.3 - - - +
218A ARG* 1.3 60.3 + - + +
220A VAL* 3.9 4.2 + - - +
221A GLY* 3.4 15.6 + - - -
250A THR* 3.9 17.9 - - + +
251A LEU* 6.1 0.9 - - + -
254A ALA* 3.5 32.8 - - + -
272A LEU* 4.2 26.2 - - + +
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Residues in contact with ARG 218 (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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211A ASP 5.1 0.6 + - - -
214A LEU* 3.0 22.7 + - - +
215A VAL* 3.3 37.5 - - + +
217A ALA* 1.3 76.9 - - - +
219A SER* 1.3 64.9 + - - +
221A GLY 3.4 0.9 + - - -
222A THR* 3.1 28.4 + - + +
245A ALA* 3.4 25.1 - - + +
246A SER* 3.1 34.3 + - - +
250A THR* 5.0 1.3 - - + -
251A LEU* 3.9 21.7 - - + +
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Residues in contact with SER 219 (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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215A VAL* 2.9 23.2 + - - +
216A VAL* 3.0 12.3 + - - -
218A ARG* 1.3 73.0 - - - +
220A VAL* 1.3 67.5 + - - +
222A THR* 2.6 26.7 + - - -
223A PHE* 2.9 10.4 + - - +
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Residues in contact with VAL 220 (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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216A VAL* 3.0 32.5 + - + +
217A ALA* 4.0 5.4 - - - +
219A SER* 1.3 74.1 - - - +
221A GLY* 1.3 52.7 + - - +
223A PHE* 3.0 9.4 + - - +
224A ALA* 2.5 36.4 + - - +
272A LEU* 3.7 30.1 - - + +
273A VAL* 4.5 15.9 - - + -
278A PRO* 3.4 27.5 - - + +
279A VAL* 4.0 9.9 - - + +
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Residues in contact with GLY 221 (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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217A ALA 3.4 11.9 + - - -
218A ARG 3.7 4.5 - - - -
219A SER 3.2 1.0 - - - -
220A VAL* 1.3 80.6 - - - +
222A THR* 1.3 57.5 + - - +
224A ALA* 3.4 8.7 - - - +
225A ARG* 2.8 49.3 + - - -
245A ALA* 3.8 4.0 - - - -
250A THR* 5.3 2.9 - - - -
279A VAL 4.2 7.4 - - - -
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Residues in contact with THR 222 (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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218A ARG* 3.1 17.0 + - + +
219A SER* 2.6 22.4 + - - -
221A GLY* 1.3 73.1 - - - +
223A PHE* 1.3 63.1 + - - +
225A ARG* 3.3 10.9 + - - +
226A ALA* 3.0 26.6 + - - +
238A LEU* 6.2 3.6 - - - -
241A SER* 4.4 6.2 - - - -
242A ALA* 3.4 31.2 - - + +
245A ALA* 3.3 17.7 - - + -
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Residues in contact with PHE 223 (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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219A SER 2.9 8.7 + - - +
220A VAL* 3.4 10.3 - - - +
222A THR* 1.3 79.0 + - - +
224A ALA* 1.3 63.5 + - - +
226A ALA* 3.4 11.9 + - + +
227A LEU* 3.3 48.9 + - + +
278A PRO* 4.1 16.4 - - + -
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Residues in contact with ALA 224 (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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220A VAL 2.5 19.8 + - - +
221A GLY 3.4 7.0 - - - +
222A THR 3.2 0.2 - - - -
223A PHE* 1.3 73.4 - - - +
225A ARG* 1.3 57.5 + - - +
227A LEU* 3.1 27.2 + - - +
228A ASP 4.2 2.9 - - - +
278A PRO* 3.7 28.4 - - + +
279A VAL 3.7 18.2 - - - +
280A LEU* 3.8 17.5 - - + +
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Residues in contact with ARG 225 (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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221A GLY* 2.8 27.8 + - - +
222A THR* 3.6 8.1 - - - +
224A ALA* 1.3 76.6 - - - +
226A ALA* 1.3 62.8 + - - +
227A LEU 3.3 0.2 - - - -
228A ASP* 3.7 16.9 + - - +
241A SER* 3.7 36.4 + - - +
244A ALA* 3.6 14.2 + - - +
245A ALA* 3.7 22.4 - - - +
250A THR* 4.1 5.9 + - - +
279A VAL 5.3 0.2 + - - -
280A LEU* 3.4 28.5 - - + +
281A CYS 3.4 22.4 + - - +
282A ARG* 6.0 0.7 - - - -
286A GLU* 2.7 49.8 + - - +
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Residues in contact with ALA 226 (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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222A THR 3.0 13.9 + - - +
223A PHE* 3.5 20.0 - - + +
224A ALA 3.1 0.2 - - - -
225A ARG* 1.3 78.4 - - - +
227A LEU* 1.3 58.9 + - + +
228A ASP* 3.2 6.6 + - - +
241A SER* 5.8 0.7 - - - -
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Residues in contact with LEU 227 (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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223A PHE* 3.3 39.9 - - + +
224A ALA 3.1 9.0 + - - +
226A ALA* 1.3 78.6 - - + +
228A ASP* 1.3 68.9 + - - +
278A PRO* 3.9 30.1 - - + -
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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