Contacts of the helix formed by residues 224 - 235 (chain D) 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 LEU 224 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329C ILE 5.8 0.7 - - - +
331C ASP* 3.7 31.4 - - + +
339C TYR* 4.4 13.2 - - + +
343C GLN* 5.0 6.1 - - - +
213D PHE* 5.7 2.7 - - + -
223D ARG* 1.3 88.7 - - + +
225D PRO* 1.3 76.1 - - + +
226D GLU* 3.8 20.2 - - + +
227D HIS* 2.8 50.1 + - + +
228D CYS* 3.5 3.1 + - - -
273D ILE* 3.7 7.9 - - - +
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Residues in contact with PRO 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224D LEU* 1.3 86.2 - - + +
226D GLU* 1.3 71.8 + - - +
228D CYS* 3.1 14.6 + - + +
229D ILE* 3.2 19.4 + - - +
273D ILE* 3.7 10.3 - - + -
274D ARG 3.1 26.7 - - - +
275D GLY* 3.3 31.4 - - - +
276D VAL* 3.7 13.9 - - + +
280D LEU* 3.7 11.9 - - + -
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Residues in contact with GLU 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D PHE* 3.8 25.1 - - + -
224D LEU* 3.8 16.8 - - + +
225D PRO* 1.3 94.2 - - - +
227D HIS* 1.3 58.5 + - - +
228D CYS 3.1 0.3 + - - -
229D ILE* 3.2 2.0 + - - +
230D GLU* 2.9 32.2 + - - +
280D LEU* 3.9 17.0 - - + +
284D VAL* 4.2 24.1 - - + +
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Residues in contact with HIS 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331C ASP* 3.8 7.3 + - - -
213D PHE* 3.5 40.7 - + + -
214D PRO* 6.3 0.4 - - - +
217D THR* 4.7 9.9 + - - -
218D ILE* 3.7 15.9 - - + +
221D MET 4.7 0.4 + - - -
222D PRO* 4.0 18.4 - - + +
223D ARG* 3.1 47.0 + - - -
224D LEU* 2.8 43.1 + - + +
226D GLU* 1.3 75.1 - - - +
228D CYS* 1.3 62.1 + - - +
230D GLU* 4.2 4.9 - - - -
231D TYR* 3.5 17.8 + - - +
267D ARG* 3.9 3.4 + - - -
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Residues in contact with CYS 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222D PRO* 4.4 5.6 - - - -
224D LEU 3.5 2.7 + - - -
225D PRO* 3.1 8.9 + - + +
226D GLU 3.1 0.8 - - - -
227D HIS* 1.3 76.7 - - - +
229D ILE* 1.3 71.3 + - - +
231D TYR* 2.9 12.3 + - - +
232D VAL* 3.0 14.4 + - - +
264D SER* 3.8 20.0 - - - +
267D ARG* 3.9 18.3 + - + +
268D ALA* 3.4 34.8 - - + +
271D TYR* 5.7 0.9 - - - -
273D ILE* 4.0 25.4 - - - -
276D VAL* 4.8 0.9 - - + -
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Residues in contact with ILE 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D PRO 3.2 12.4 + - - +
226D GLU 3.7 4.5 - - - +
228D CYS* 1.3 74.4 - - - +
230D GLU* 1.3 54.7 + - - +
231D TYR 2.6 13.2 + - - -
232D VAL* 2.7 15.2 + - - +
233D ARG* 3.0 10.4 + - + +
260D ILE* 4.3 2.2 - - + -
264D SER* 3.0 27.6 + - - +
276D VAL* 4.5 7.0 - - + -
280D LEU* 3.6 15.0 - - + -
281D THR* 3.2 50.7 - - + +
284D VAL* 3.4 35.9 - - + -
285D VAL* 4.1 9.2 - - + -
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Residues in contact with GLU 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D ASN* 5.4 2.1 + - - -
213D PHE* 3.8 22.3 + - + +
218D ILE* 3.7 24.9 - - + +
226D GLU 2.9 20.7 + - - +
227D HIS 4.3 4.5 - - - +
229D ILE* 1.3 73.1 - - - +
231D TYR* 1.3 56.8 + - - +
233D ARG* 3.0 31.2 + - - -
234D MET* 2.9 50.9 + - + +
284D VAL* 3.7 10.2 - - + +
287D ARG* 2.9 33.3 + - - -
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Residues in contact with TYR 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218D ILE* 3.4 23.8 - - - +
219D ALA* 4.4 7.6 - - + -
227D HIS 3.5 8.1 + - - +
228D CYS 2.9 5.1 + - - +
229D ILE 2.6 5.3 + - - -
230D GLU* 1.3 71.4 - - - +
232D VAL* 1.3 71.1 + - + +
233D ARG 2.6 15.5 + - - -
234D MET* 5.0 0.4 - - - -
235D LEU* 2.9 52.7 + - + +
236D GLN* 3.2 36.1 + - + +
267D ARG* 3.0 52.9 + - - +
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Residues in contact with VAL 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D CYS 3.7 4.3 - - - +
229D ILE 2.7 5.7 + - - +
231D TYR* 1.3 81.2 - - + +
233D ARG* 1.3 56.5 + - - +
236D GLN* 3.7 23.1 - - - +
237D TRP* 3.6 20.4 + - - +
259D TRP* 4.0 8.8 - - + -
260D ILE* 3.4 28.4 - - + +
263D LYS* 3.3 34.3 - - + +
264D SER* 3.3 37.9 - - - +
267D ARG* 4.4 2.5 - - + -
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Residues in contact with ARG 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D ILE 3.0 11.9 + - - +
230D GLU* 3.0 31.0 + - - +
231D TYR 2.6 6.3 + - - -
232D VAL* 1.3 75.2 - - - +
234D MET* 1.3 92.5 + - - +
235D LEU 3.1 2.6 + - - -
237D TRP* 3.9 2.9 - - - +
238D PRO* 3.3 20.1 - - - +
249D LEU* 3.7 27.9 - - + +
260D ILE* 4.7 3.1 - - + -
284D VAL* 4.6 0.9 - - - -
285D VAL* 3.9 44.7 + - + +
287D ARG* 4.4 17.7 - - - +
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Residues in contact with MET 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D ASN* 5.5 7.6 - - - +
213D PHE 5.6 3.4 - - - +
215D MET* 5.2 14.1 - - - +
218D ILE* 4.3 22.0 - - + -
230D GLU* 2.9 47.0 + - - +
231D TYR* 5.0 0.2 - - - -
233D ARG* 1.3 91.0 - - - +
235D LEU* 1.3 73.2 + - + +
238D PRO* 4.0 11.1 - - - +
287D ARG* 5.0 3.1 - - - +
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Residues in contact with LEU 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D MET* 4.4 29.8 - - + -
218D ILE* 5.0 6.1 - - + -
219D ALA* 4.3 15.5 - - + -
231D TYR* 2.9 39.0 + - + +
233D ARG 3.1 0.8 - - - -
234D MET* 1.3 96.7 - - + +
236D GLN* 1.3 65.8 + - - +
237D TRP 3.2 2.2 - - - -
238D PRO* 3.0 15.1 - - + +
239D LYS* 3.1 16.5 + - - +
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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
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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