Contacts of the helix formed by residues 213 - 228 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199G TYR* 4.1 13.2 - - + +
211G HIS 4.1 3.6 - - - +
212G THR* 1.3 98.3 - - + +
214G TRP* 1.3 65.0 + - - +
215G ILE 3.3 0.7 + - - +
216G VAL* 3.4 12.7 + - + -
217G ILE* 3.2 16.1 + - - +
332G MET* 3.2 25.1 - - + -
333G ILE 4.2 1.3 - - - +
334G ALA* 3.6 24.6 - - + -
338G LYS* 4.2 19.7 - - + +
339G TYR* 4.3 2.9 - - - -
342G LEU* 3.7 17.5 - - + -
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Residues in contact with TRP 214 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181G GLU* 6.1 0.7 - - + -
183G LEU* 4.7 11.7 - - + +
185G LEU* 6.0 0.4 - - - +
212G THR 3.3 2.3 + - - -
213G PRO* 1.3 69.9 - - - +
215G ILE* 1.3 79.9 + - + +
217G ILE* 3.2 13.3 - - - +
218G ILE* 3.0 35.2 + - + +
264G ASN* 4.1 7.4 - - + +
267G GLU* 3.7 20.9 - - - +
268G ALA* 3.9 18.8 - - + +
271G ASN* 3.0 45.8 - - + +
275G ALA* 4.7 6.4 - - + +
330G PRO* 3.7 29.6 - - + -
331G ASP 3.5 21.3 - - - -
332G MET* 3.2 35.4 - - + +
333G ILE 4.6 2.0 + - - -
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Residues in contact with ILE 215 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183G LEU* 3.7 25.6 - - + -
185G LEU* 3.8 21.5 - - + -
196G PHE* 3.6 27.6 - - + -
213G PRO 3.2 0.8 - - - -
214G TRP* 1.3 94.5 - - + +
216G VAL* 1.3 58.5 + - - +
218G ILE* 2.7 7.7 + - - +
219G ALA 2.5 33.6 + - - -
329G ILE* 4.8 3.4 - - + -
332G MET* 3.7 19.7 - - + +
342G LEU* 3.9 22.7 - - + -
346G TYR* 3.7 21.5 - - + +
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Residues in contact with VAL 216 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195G HIS* 4.8 6.7 - - - +
196G PHE* 4.2 20.9 - - + +
199G TYR* 3.3 57.4 - - + +
212G THR* 4.1 6.5 - - + -
213G PRO* 3.7 25.8 - - + +
215G ILE* 1.3 75.3 - - - +
217G ILE* 1.3 56.1 + - + +
219G ALA* 2.9 7.7 + - - -
220G LYS* 2.7 42.6 + - + +
342G LEU* 4.8 4.0 - - + -
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Residues in contact with ILE 217 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209G HIS* 4.9 3.8 - - + +
212G THR* 3.5 33.2 - - + +
213G PRO 3.2 15.0 - - - +
214G TRP* 3.2 12.6 - - - +
215G ILE 3.0 0.2 - - - -
216G VAL* 1.3 77.6 - - + +
218G ILE* 1.3 61.0 + - - +
220G LYS* 3.9 2.9 - - - +
221G TYR* 3.2 32.1 + - + +
247G ILE* 4.2 16.4 - - + -
264G ASN* 4.4 4.7 - - - +
265G PHE* 3.5 41.5 - - + -
268G ALA* 3.8 18.2 - - + -
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Residues in contact with ILE 218 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185G LEU* 4.0 19.3 - - + -
214G TRP* 3.0 26.8 + - + +
215G ILE* 2.7 13.0 + - - +
217G ILE* 1.3 71.5 - - - +
219G ALA* 1.3 58.7 + - - +
221G TYR 3.7 0.5 - - - -
222G LEU* 2.8 35.7 + - + +
243G PHE* 3.7 20.0 - - + -
247G ILE* 4.1 7.0 - - + -
268G ALA* 3.1 37.5 - - + +
271G ASN* 4.0 0.4 - - + -
272G VAL* 3.5 23.1 - - + +
275G ALA* 4.0 14.6 - - + -
276G LEU* 4.8 8.1 - - + -
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Residues in contact with ALA 219 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185G LEU* 3.9 12.3 - - + +
196G PHE* 3.7 47.8 - - + -
215G ILE 2.5 16.9 + - - +
216G VAL* 3.4 7.0 - - + +
218G ILE* 1.3 74.1 - - - +
220G LYS* 1.3 57.1 + - - +
222G LEU* 3.4 7.7 - - - +
223G ALA* 2.9 28.6 + - - +
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Residues in contact with LYS 220 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196G PHE* 2.7 38.6 + - + +
197G GLN* 3.8 9.9 + - - +
199G TYR* 3.9 29.2 - - + -
216G VAL* 2.7 25.1 + - + +
217G ILE* 3.9 5.2 - - - +
219G ALA* 1.3 69.8 - - - +
221G TYR* 1.3 67.9 + - + +
222G LEU 2.9 3.8 - - - -
223G ALA* 2.9 25.0 + - + +
224G GLN* 3.0 13.9 + - - +
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Residues in contact with TYR 221 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217G ILE* 3.2 22.8 + - + +
220G LYS* 1.3 88.9 - - + +
222G LEU* 1.3 57.9 + - - +
224G GLN* 4.0 17.2 - - - +
225G TRP* 3.5 11.6 + - - +
243G PHE* 2.8 23.3 - - + -
246G LEU* 3.2 45.0 - - + +
247G ILE* 3.4 36.3 - - + -
249G GLN 4.4 1.7 + - - -
250G GLY* 2.9 31.3 + - - -
265G PHE* 4.3 13.3 - + - -
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Residues in contact with LEU 222 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185G LEU* 4.1 34.3 - - + +
186G ASP* 5.8 0.7 - - - -
218G ILE* 2.8 21.1 + - + +
219G ALA* 3.4 9.9 - - - +
221G TYR* 1.3 76.9 - - - +
223G ALA* 1.3 66.6 + - - +
224G GLN 3.1 1.3 - - - -
225G TRP* 3.0 6.5 + - + +
226G TYR* 3.0 20.7 + - + +
232G ARG* 4.5 7.4 - - - +
233G ILE* 3.3 31.6 - - + -
243G PHE* 3.5 7.4 - - + -
276G LEU* 4.3 14.8 - - + -
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Residues in contact with ALA 223 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219G ALA 2.9 14.3 + - - +
220G LYS* 3.3 15.3 - - + +
222G LEU* 1.3 78.4 - - - +
224G GLN* 1.3 60.4 + - - +
226G TYR* 3.1 22.2 - - - +
227G SER* 3.6 7.3 + - - -
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Residues in contact with GLN 224 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220G LYS 3.0 14.6 + - - +
221G TYR* 4.2 17.0 - - - +
222G LEU 3.1 0.2 - - - -
223G ALA* 1.3 73.5 - - - +
225G TRP* 1.3 58.1 + - - +
226G TYR 2.8 9.8 + - - -
227G SER* 2.8 19.7 + - - -
228G GLU* 3.3 35.6 + - + +
246G LEU* 3.6 31.6 - - - +
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Residues in contact with TRP 225 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221G TYR 3.5 13.0 + - - +
222G LEU* 3.0 10.2 + - + +
224G GLN* 1.3 78.6 - - - +
226G TYR* 1.3 61.2 + - - +
228G GLU* 4.2 10.7 - - - +
229G THR* 3.5 32.1 + - + -
231G GLY* 3.9 16.9 - - - -
232G ARG 3.8 5.4 - - - +
233G ILE* 3.1 39.9 - - + +
239G GLU* 4.0 40.8 - - + -
242G ASP* 4.7 10.1 - - + -
243G PHE* 4.0 31.9 - + + -
246G LEU* 4.2 15.6 - - + +
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Residues in contact with TYR 226 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222G LEU* 3.0 10.4 + - + +
223G ALA* 3.1 19.5 - - - +
224G GLN 2.8 0.8 + - - -
225G TRP* 1.3 81.6 - - - +
227G SER* 1.3 56.6 + - - +
230G ASN* 2.6 61.2 + - + +
231G GLY 3.4 16.4 - - - -
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Residues in contact with SER 227 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223G ALA 3.6 6.0 + - - -
224G GLN* 2.8 11.2 + - - -
226G TYR* 1.3 77.6 - - - +
228G GLU* 1.3 56.3 + - - -
229G THR* 2.6 18.6 + - - -
230G ASN* 4.8 6.8 + - - +
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Residues in contact with GLU 228 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224G GLN* 3.3 39.6 + - + +
225G TRP* 4.0 8.9 + - - +
226G TYR 3.6 0.2 - - - -
227G SER* 1.3 74.7 - - - +
229G THR* 1.3 67.7 + - - +
246G LEU* 5.1 5.7 - - - +
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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
------------------------------------------------------------
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