Contacts of the helix formed by residues 213 - 228 (chain C) in PDB entry 1R4N
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 PRO 213 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199C TYR* 4.1 13.7 - - + +
211C HIS 4.1 3.6 - - - +
212C THR* 1.3 94.6 - - + +
214C TRP* 1.3 65.0 + - - +
215C ILE 3.3 0.6 + - - +
216C VAL* 3.4 11.6 + - + -
217C ILE* 3.2 16.5 + - - +
332C MET* 3.2 25.6 - - + -
333C ILE 4.2 1.1 - - - +
334C ALA* 3.6 24.6 - - + -
338C LYS* 4.3 20.0 - - + +
339C TYR* 4.3 2.7 - - - -
342C LEU* 3.7 16.2 - - + -
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Residues in contact with TRP 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C GLU* 6.1 0.7 - - + -
183C LEU* 4.7 11.9 - - + +
212C THR 3.3 2.7 + - - -
213C PRO* 1.3 70.0 - - - +
215C ILE* 1.3 79.2 + - + +
217C ILE* 3.2 13.6 + - - +
218C ILE* 3.0 34.9 + - + +
264C ASN* 4.2 7.6 - - + +
267C GLU* 3.6 21.1 - - + +
268C ALA* 3.9 17.4 - - + +
271C ASN* 3.0 46.3 - - + +
275C ALA* 4.8 7.0 - - + +
330C PRO* 3.7 29.6 - - + -
331C ASP 3.5 20.2 - - - -
332C MET* 3.2 34.8 - - + +
333C ILE 4.6 1.6 + - - -
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Residues in contact with ILE 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C LEU* 3.7 26.5 - - + -
185C LEU* 3.8 20.2 - - + -
196C PHE* 3.7 28.0 - - + -
213C PRO 3.2 0.6 - - - -
214C TRP* 1.3 95.0 - - + +
216C VAL* 1.3 54.9 + - - +
218C ILE* 2.7 7.6 + - - +
219C ALA 2.5 34.0 + - - -
329C ILE* 4.9 3.6 - - + -
332C MET* 3.7 29.4 - - + +
342C LEU* 3.9 12.6 - - + -
346C TYR* 3.6 22.7 - - + +
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Residues in contact with VAL 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C HIS* 4.7 6.3 - - - +
196C PHE* 4.2 21.8 - - + +
199C TYR* 3.3 57.4 - - + +
212C THR* 4.1 6.5 - - + -
213C PRO* 3.7 26.2 - - + +
214C TRP 3.4 0.2 - - - -
215C ILE* 1.3 73.7 - - - +
217C ILE* 1.3 55.9 + - + +
219C ALA* 3.0 8.2 + - - -
220C LYS* 2.7 42.6 + - + +
342C LEU* 4.8 3.6 - - + -
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Residues in contact with ILE 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C HIS* 4.9 3.6 - - + +
212C THR* 3.5 33.0 - - + +
213C PRO 3.2 14.8 - - - +
214C TRP* 3.2 13.2 - - - +
215C ILE 3.0 0.2 - - - -
216C VAL* 1.3 76.4 - - + +
218C ILE* 1.3 60.7 + - - +
220C LYS* 3.7 3.3 + - - +
221C TYR* 3.2 32.0 + - + +
247C ILE* 4.2 15.9 - - + -
264C ASN* 4.4 4.0 - - - +
265C PHE* 3.5 41.7 - - + -
268C ALA* 3.9 18.6 - - + -
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Residues in contact with ILE 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C LEU* 4.0 19.1 - - + -
214C TRP* 3.0 25.2 + - + +
215C ILE* 2.7 10.6 + - - +
217C ILE* 1.3 71.6 - - - +
219C ALA* 1.3 60.9 + - - +
221C TYR* 4.6 0.4 - - - +
222C LEU* 2.8 35.5 + - + +
243C PHE* 3.7 19.7 - - + -
247C ILE* 4.1 7.2 - - + -
268C ALA* 3.1 38.1 - - + +
271C ASN* 4.1 0.7 - - + -
272C VAL* 3.6 22.9 - - + +
275C ALA* 4.0 14.8 - - + -
276C LEU* 4.8 8.5 - - + -
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Residues in contact with ALA 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C LEU* 3.9 12.5 - - + +
196C PHE* 3.7 49.3 - - + -
215C ILE 2.5 19.5 + - - +
216C VAL 3.4 4.5 - - - +
218C ILE* 1.3 73.4 - - - +
220C LYS* 1.3 56.6 + - - +
222C LEU* 3.4 8.1 + - - +
223C ALA* 2.9 28.4 + - - +
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Residues in contact with LYS 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C PHE* 2.7 37.2 + - + +
197C GLN* 3.8 10.5 + - - +
199C TYR* 3.9 29.9 - - + -
216C VAL* 2.7 25.6 + - + +
217C ILE* 3.9 5.4 - - - +
219C ALA* 1.3 70.5 - - - +
221C TYR* 1.3 68.7 + - + +
222C LEU 2.9 4.0 - - - -
223C ALA* 2.9 24.3 + - + +
224C GLN* 3.0 13.3 + - - +
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Residues in contact with TYR 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C ILE* 3.2 22.1 + - + +
220C LYS* 1.3 87.3 - - + +
222C LEU* 1.3 59.6 + - - +
224C GLN* 4.0 17.4 - - - +
225C TRP* 3.5 12.0 + - - +
243C PHE* 2.8 21.4 - - + -
246C LEU* 3.2 45.4 - - + +
247C ILE* 3.4 35.2 - - + -
249C GLN 4.4 1.5 + - - -
250C GLY* 2.9 30.7 + - - -
265C PHE* 4.3 13.6 - + - -
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Residues in contact with LEU 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C LEU* 4.1 32.8 - - + +
186C ASP* 5.8 0.9 - - - -
218C ILE* 2.8 21.2 + - + +
219C ALA* 3.4 9.4 - - - +
220C LYS 2.9 0.2 - - - -
221C TYR* 1.3 78.1 - - - +
223C ALA* 1.3 66.1 + - - +
224C GLN 3.1 1.3 - - - -
225C TRP* 3.0 7.1 + - + +
226C TYR* 3.0 20.9 + - + +
232C ARG* 4.5 7.2 - - - +
233C ILE* 3.3 31.4 - - + -
243C PHE* 3.5 8.3 - - + -
276C LEU* 4.3 15.5 - - + -
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Residues in contact with ALA 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C ALA 2.9 14.8 + - - +
220C LYS* 3.3 15.5 - - + +
222C LEU* 1.3 79.0 - - - +
224C GLN* 1.3 60.8 + - - +
226C TYR* 3.1 22.8 + - - +
227C SER* 3.6 7.1 + - - -
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Residues in contact with GLN 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C LYS 3.0 13.3 + - - +
221C TYR* 4.1 17.9 - - - +
223C ALA* 1.3 73.7 - - - +
225C TRP* 1.3 59.3 + - - +
226C TYR 2.8 10.3 + - - -
227C SER* 2.9 19.2 + - - -
228C GLU* 3.3 36.8 + - + +
246C LEU* 3.6 31.7 - - - +
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Residues in contact with TRP 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C TYR 3.5 13.2 + - - +
222C LEU* 3.0 10.6 + - + +
224C GLN* 1.3 78.1 - - - +
226C TYR* 1.3 61.3 + - - +
227C SER 3.4 0.2 - - - -
228C GLU* 4.1 10.7 - - - +
229C THR* 3.4 32.5 + - + -
230C ASN 4.0 0.2 + - - -
231C GLY* 3.9 16.3 - - - -
232C ARG* 3.8 6.4 - - - +
233C ILE* 3.2 39.2 - - + +
239C GLU* 4.0 40.8 - - + -
242C ASP* 4.7 9.9 - - + -
243C PHE* 4.0 32.3 - + + -
246C LEU* 4.2 15.7 - - + +
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Residues in contact with TYR 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222C LEU* 3.0 10.4 + - + +
223C ALA* 3.1 18.4 - - - +
224C GLN 2.8 1.0 + - - -
225C TRP* 1.3 81.9 - - - +
227C SER* 1.3 57.6 + - - +
230C ASN* 2.6 60.3 + - + +
231C GLY 3.4 15.9 - - - -
232C ARG* 6.5 0.2 - - + -
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Residues in contact with SER 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223C ALA 3.6 6.1 + - - -
224C GLN* 2.9 11.2 + - - -
226C TYR* 1.3 78.4 - - - +
228C GLU* 1.3 57.9 + - - -
229C THR* 2.6 17.9 + - - -
230C ASN* 4.8 6.3 + - - +
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Residues in contact with GLU 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C GLN* 3.3 38.4 + - + +
225C TRP* 4.1 9.3 - - - +
227C SER* 1.3 74.3 - - - +
229C THR* 1.3 67.3 + - - +
246C LEU* 5.1 5.5 - - - +
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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
------------------------------------------------------------
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