Contacts of the helix formed by residues 235 - 249 (chain D) in PDB entry 1YCH
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 ASP 235 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180D ASP* 3.2 15.9 + - - +
232D TRP* 4.2 7.1 - - - -
234D LYS* 1.3 85.2 - - + +
236D PRO* 1.3 67.7 - - - +
237D GLY* 3.1 13.4 + - - -
238D ARG* 3.5 37.1 + - + +
239D ILE 4.2 1.9 + - - -
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Residues in contact with PRO 236 (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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221D ILE* 4.1 14.8 - - + +
222D LYS* 3.6 26.5 - - - +
223D THR* 4.0 1.8 - - - -
224D ILE* 3.7 22.2 - - + -
232D TRP* 3.1 32.1 - - + +
233D ARG 4.4 0.2 - - - +
234D LYS 3.8 4.7 - - - +
235D ASP* 1.3 87.7 - - - +
237D GLY* 1.3 65.9 - - - +
238D ARG 3.3 0.2 + - - -
239D ILE* 3.3 5.1 + - + +
240D ILE* 3.0 28.0 + - + +
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Residues in contact with GLY 237 (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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235D ASP* 3.1 8.7 + - - -
236D PRO* 1.3 81.1 - - - +
238D ARG* 1.3 56.7 + - - +
240D ILE* 3.0 8.1 + - - +
241D GLU* 2.8 45.6 + - - +
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Residues in contact with ARG 238 (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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185D ALA* 2.9 48.2 + - - +
186D GLY* 4.5 4.0 - - - +
188D ILE* 4.8 4.2 - - - +
189D MET* 3.1 43.2 - - + +
232D TRP* 5.1 5.7 - - + -
235D ASP* 3.5 32.5 + - - +
237D GLY* 1.3 75.2 - - - +
239D ILE* 1.3 58.5 + - - +
241D GLU* 3.4 14.7 + - - +
242D ALA* 3.0 28.8 + - - +
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Residues in contact with ILE 239 (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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169D PHE* 3.4 24.0 - - + +
189D MET* 4.5 4.7 - - + +
192D ALA* 4.3 13.5 - - + -
224D ILE* 4.3 5.8 - - + -
232D TRP* 3.0 62.1 - - + +
235D ASP 4.2 0.6 + - - -
236D PRO 3.3 10.8 + - - +
238D ARG* 1.3 77.0 - - - +
240D ILE* 1.3 67.4 + - - +
242D ALA* 4.2 9.4 - - + -
243D TYR* 3.1 50.8 + - + +
246D TRP* 4.6 2.0 - - + -
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Residues in contact with ILE 240 (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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163D LEU* 5.7 0.4 - - + -
169D PHE* 4.2 18.4 - - + -
211D LEU* 4.2 20.3 - - + +
214D ILE* 6.0 2.0 - - + -
221D ILE* 3.9 23.6 - - + -
224D ILE* 3.8 25.6 - - + -
236D PRO* 3.0 28.8 + - + +
237D GLY* 3.0 9.2 + - - +
239D ILE* 1.3 73.9 - - - +
241D GLU* 1.3 68.9 + - + +
243D TYR* 3.2 5.0 + - - +
244D ALA* 3.1 22.1 + - + +
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Residues in contact with GLU 241 (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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237D GLY* 2.8 36.8 + - - +
238D ARG* 3.7 11.7 - - - +
240D ILE* 1.3 75.1 - - + +
242D ALA* 1.3 57.8 + - - +
244D ALA* 3.2 8.9 + - - +
245D ARG* 2.9 58.1 + - - +
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Residues in contact with ALA 242 (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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189D MET* 4.0 13.2 - - - -
238D ARG 3.0 18.5 + - - +
239D ILE* 3.7 7.2 - - + +
241D GLU* 1.3 73.7 - - - +
243D TYR* 1.3 67.1 + - - +
245D ARG* 3.1 13.1 + - - +
246D TRP* 2.9 57.2 + - + -
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Residues in contact with TYR 243 (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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168D ALA* 4.6 4.7 - - + -
169D PHE* 2.9 55.0 + + + -
170D GLY 4.1 2.8 + - - -
192D ALA* 4.8 3.1 + - + -
195D TYR* 4.2 8.7 - - - -
196D TYR* 3.7 19.0 + + + +
200D LEU* 3.4 28.9 - - + +
207D ILE* 4.1 14.8 - - + +
211D LEU* 4.1 11.7 - - + -
239D ILE* 3.1 43.1 + - + +
240D ILE 3.6 4.7 - - - +
242D ALA* 1.3 78.2 - - - +
244D ALA* 1.3 57.7 + - - +
246D TRP* 3.8 23.8 - + - +
247D ALA* 2.9 32.7 + - - +
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Residues in contact with ALA 244 (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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208D THR* 5.2 3.8 + - - +
211D LEU* 3.9 16.5 - - + +
240D ILE* 3.1 13.5 + - + +
241D GLU* 3.3 13.2 - - - +
242D ALA 3.1 0.2 - - - -
243D TYR* 1.3 76.8 - - - +
245D ARG* 1.3 56.5 + - + +
247D ALA* 3.9 2.7 - - - +
248D GLU* 3.0 32.2 + - - +
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Residues in contact with ARG 245 (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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241D GLU* 2.9 48.5 + - - +
242D ALA* 3.1 10.9 + - - +
244D ALA* 1.3 76.4 - - + +
246D TRP* 1.3 69.6 + - + +
248D GLU* 3.3 12.2 + - - +
249D GLY* 3.2 18.4 + - - -
250D GLN* 4.3 4.3 + - - +
251D GLY 5.4 1.2 + - - -
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Residues in contact with TRP 246 (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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189D MET* 4.1 18.4 - - + -
192D ALA* 3.9 8.1 - - + -
193D ALA* 3.6 31.2 - - + +
196D TYR* 3.6 50.6 - + + -
204D SER* 4.0 6.8 + - - -
239D ILE* 4.6 0.7 - - + -
242D ALA* 2.9 40.5 + - + +
243D TYR* 3.8 27.8 - + - +
245D ARG* 1.3 80.2 - - + +
247D ALA* 1.3 62.8 + - - +
249D GLY* 3.4 12.5 + - - -
302D LEU* 3.6 35.2 - - + +
303D ASP* 4.7 15.1 + - - -
335D LYS* 5.5 0.3 - - - +
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Residues in contact with ALA 247 (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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196D TYR* 3.4 17.4 + - - +
204D SER* 3.3 31.7 - - - +
207D ILE* 3.8 11.0 - - + -
208D THR* 3.6 11.7 - - - +
243D TYR 2.9 19.9 + - - +
244D ALA* 3.9 3.6 - - - +
246D TRP* 1.3 74.3 - - - +
248D GLU* 1.3 54.3 + - - +
249D GLY 3.4 0.2 + - - -
335D LYS* 2.5 32.3 + - - +
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Residues in contact with GLU 248 (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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208D THR* 4.5 5.7 + - + -
244D ALA 3.0 19.2 + - - +
245D ARG* 3.6 11.5 - - - +
246D TRP 3.3 0.2 - - - -
247D ALA* 1.3 75.1 - - - +
249D GLY* 1.3 62.5 + - - +
250D GLN* 4.0 30.3 - - + +
335D LYS* 3.1 23.0 + - - +
336D ASN* 5.8 0.5 - - - +
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Residues in contact with GLY 249 (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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245D ARG 3.2 7.5 + - - -
246D TRP* 3.4 11.0 + - - -
247D ALA 3.2 2.0 - - - -
248D GLU* 1.3 79.8 - - - +
250D GLN* 1.3 66.5 + - - +
251D GLY* 3.1 4.8 + - - -
302D LEU 5.7 3.4 - - - -
335D LYS* 4.2 18.1 - - - +
336D ASN* 3.2 23.7 + - - +
337D LYS* 5.1 5.3 + - - -
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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