Contacts of the helix formed by residues 214 - 234 (chain A) in PDB entry 5Y7G
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 214 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU* 4.1 5.8 - - - +
212A PHE* 4.2 2.9 - - - +
213A ARG* 1.3 116.0 - - + +
215A ARG* 1.3 64.7 + - - +
216A ALA* 3.8 18.6 - - + +
217A ASP* 3.2 36.2 + - - +
218A VAL 3.5 4.2 + - - -
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Residues in contact with ARG 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 3.3 46.0 + - + +
41A LEU 5.9 0.4 - - - -
42A ASP* 3.9 16.9 + - - +
45A GLU* 2.4 43.5 + - - -
174A ARG* 3.5 30.3 - - - +
178A MET* 5.5 2.0 - - - -
213A ARG 3.9 0.6 + - - -
214A LEU* 1.3 69.0 - - - +
216A ALA* 1.3 62.0 + - - +
217A ASP 3.0 1.6 - - - -
218A VAL* 3.0 5.5 + - + +
219A ASP* 2.8 45.9 + - - +
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Residues in contact with ALA 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A LEU* 3.3 16.7 - - + +
215A ARG* 1.3 78.3 - - - +
217A ASP* 1.3 59.5 + - - +
219A ASP* 4.1 9.5 - - - +
220A ALA* 3.0 28.9 + - - +
254A LEU* 4.6 0.3 - - - +
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Residues in contact with ASP 217 (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 PHE* 4.0 16.5 - - + -
213A ARG* 4.1 10.9 + - - +
214A LEU* 3.2 38.9 + - - +
215A ARG 3.0 0.8 - - - -
216A ALA* 1.3 76.8 - - - +
218A VAL* 1.3 64.5 + - - +
220A ALA* 3.3 1.7 + - - +
221A TYR* 3.0 24.3 + - - +
250A ALA* 5.5 3.1 - - - +
251A ASN* 3.1 35.9 + - - +
253A TRP* 6.2 0.4 - - + -
254A LEU* 3.7 21.9 - - + +
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Residues in contact with VAL 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 4.4 5.4 - - + -
174A ARG* 3.9 25.4 - - + +
177A LEU* 4.4 2.5 - - + -
178A MET* 3.4 31.4 - - + -
212A PHE* 3.4 35.4 - - + -
214A LEU 3.5 3.9 + - - +
215A ARG* 3.0 11.7 + - + +
217A ASP* 1.3 78.2 - - - +
219A ASP* 1.3 66.4 + - - +
221A TYR* 3.1 1.9 + - - +
222A LEU* 2.9 43.6 + - + +
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Residues in contact with ASP 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ARG* 2.4 38.4 + - - +
215A ARG* 2.8 44.7 + - - +
216A ALA* 4.1 7.1 - - - +
218A VAL* 1.3 73.4 - - - +
220A ALA* 1.3 57.3 + - - +
222A LEU* 3.3 6.5 + - - +
223A HIS* 2.9 27.9 + - - +
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Residues in contact with ALA 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 ALA 3.0 19.5 + - - +
218A VAL 3.2 0.2 - - - -
219A ASP* 1.3 74.8 - - - +
221A TYR* 1.3 67.3 + - - +
223A HIS* 3.0 14.3 + - - +
224A LEU* 3.0 17.3 + - - +
249A TYR* 3.5 37.8 + - + +
254A LEU* 3.7 17.7 - - + -
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Residues in contact with TYR 221 (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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177A LEU* 3.6 36.6 - - + -
182A ASN* 3.9 13.3 + - - -
183A LEU* 3.7 31.4 + - + +
184A TRP* 5.8 0.2 - - - -
212A PHE* 4.3 6.5 - + + -
217A ASP 3.0 13.9 + - - +
218A VAL 3.6 6.7 - - - +
220A ALA* 1.3 75.4 - - - +
222A LEU* 1.3 66.7 + - + +
224A LEU* 3.1 6.4 + - - +
225A PHE* 2.9 30.2 + + + -
253A TRP* 4.5 20.0 - + - -
254A LEU* 3.8 20.0 - - + +
257A ARG* 3.2 44.3 + - + -
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Residues in contact with LEU 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ASP* 5.0 5.8 - - + +
174A ARG* 4.3 31.0 - - + +
177A LEU* 3.4 35.4 - - + -
183A LEU* 3.9 23.8 - - + -
218A VAL* 2.9 29.3 + - + +
219A ASP* 3.6 9.6 - - - +
221A TYR* 1.3 78.3 - - + +
223A HIS* 1.3 56.6 - - - +
225A PHE* 3.4 7.5 + - + +
226A ASP* 2.9 27.7 + - - +
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Residues in contact with HIS 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 ASP 2.9 14.3 + - - +
220A ALA* 3.0 9.4 + - - +
222A LEU* 1.3 74.8 - - - +
224A LEU* 1.3 67.5 + - - +
226A ASP* 3.0 21.3 + - - +
227A CYS* 2.9 38.9 + - - +
230A ARG* 5.3 4.0 + - - -
243A GLY* 3.1 39.1 + - - -
244A LEU* 3.9 11.1 - - + +
245A PRO* 4.8 1.7 - - + +
249A TYR* 4.4 10.4 + - - +
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Residues in contact with LEU 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ALA 3.0 14.9 + - - +
221A TYR* 3.6 10.3 - - - +
223A HIS* 1.3 74.7 - - - +
225A PHE* 1.3 62.0 + - - +
227A CYS* 2.9 15.3 + - - +
228A ARG* 3.1 14.4 + - - +
244A LEU* 3.6 28.3 - - + -
249A TYR* 4.0 20.0 - - + +
254A LEU* 4.1 5.2 - - + +
257A ARG* 3.6 26.5 - - + -
258A ARG* 3.4 46.9 - - + +
261A LEU* 4.4 14.3 - - + +
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Residues in contact with PHE 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ASP* 5.4 6.7 - - + -
176A ARG* 5.8 2.0 - - - -
183A LEU* 3.5 46.2 - - + -
221A TYR* 2.9 24.5 + + + +
222A LEU* 3.6 14.6 - - + +
224A LEU* 1.3 76.6 - - - +
226A ASP* 1.3 59.0 + - - +
228A ARG* 3.6 31.6 - - - +
229A GLN* 3.0 59.7 + - + +
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Residues in contact with ASP 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A LEU 2.9 14.6 + - - +
223A HIS* 3.0 21.9 + - + +
225A PHE* 1.3 76.5 - - - +
227A CYS* 1.3 60.5 + - - +
229A GLN* 3.7 7.1 - - - +
230A ARG* 2.9 67.3 + - - +
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Residues in contact with CYS 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 HIS* 2.9 30.2 + - - +
224A LEU 2.9 7.5 + - - +
226A ASP* 1.3 80.4 - - - +
228A ARG* 1.3 58.1 + - - +
230A ARG* 3.7 5.0 - - - +
231A PHE* 2.8 29.6 + - - +
240A LEU* 4.2 29.9 - - + +
243A GLY* 5.2 0.7 - - - -
244A LEU* 3.8 27.1 - - + -
261A LEU* 3.9 17.7 - - + -
265A PHE* 4.6 6.7 - - + -
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Residues in contact with ARG 228 (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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224A LEU 3.1 12.0 + - - +
225A PHE* 3.6 34.0 - - - +
227A CYS* 1.3 72.8 - - - +
229A GLN* 1.3 84.8 + - - +
231A PHE* 4.0 8.7 - - + -
232A ASP* 2.6 64.1 + - - +
261A LEU* 4.1 24.4 - - + +
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Residues in contact with GLN 229 (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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225A PHE* 3.0 50.1 + - + +
226A ASP* 3.7 9.0 - - - +
228A ARG* 1.3 105.0 - - - +
230A ARG* 1.3 63.2 + - + +
232A ASP* 3.4 4.0 + - - +
233A LEU* 3.2 34.9 + - + +
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Residues in contact with ARG 230 (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 HIS* 5.3 6.7 + - - -
226A ASP* 2.9 50.3 + - - +
227A CYS* 3.9 6.0 - - - +
229A GLN* 1.3 76.9 - - + +
231A PHE* 1.3 52.9 + - - +
233A LEU* 4.0 4.7 - - - +
234A GLY* 2.7 30.9 + - - -
235A GLU* 3.2 41.6 + - - +
239A GLU* 4.7 12.1 + - - +
240A LEU* 4.0 24.0 - - + +
243A GLY* 6.4 0.4 - - - -
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Residues in contact with PHE 231 (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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227A CYS 2.8 17.9 + - - +
228A ARG* 3.6 6.1 - - + +
230A ARG* 1.3 75.0 - - - +
232A ASP* 1.3 79.7 + - - +
233A LEU 2.9 12.4 + - - +
234A GLY* 3.1 12.9 + - - +
235A GLU 5.2 3.6 - - - -
237A LEU* 3.5 34.3 - - + -
240A LEU* 3.8 11.2 - - + -
261A LEU* 5.6 0.7 - - + -
264A GLN* 4.8 7.9 - - + -
265A PHE* 3.4 33.9 - + + -
268A HIS* 3.7 41.7 - + + -
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Residues in contact with ASP 232 (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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228A ARG* 2.6 55.3 + - - +
229A GLN* 4.3 5.4 - - - +
231A PHE* 1.3 92.0 - - - +
233A LEU* 1.3 66.1 + - + +
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Residues in contact with LEU 233 (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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229A GLN* 3.2 25.5 + - + +
230A ARG* 4.0 4.7 - - - +
231A PHE 2.9 4.0 - - - +
232A ASP* 1.3 84.7 - - + +
234A GLY* 1.3 67.9 + - - +
235A GLU* 5.6 0.7 - - - +
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Residues in contact with GLY 234 (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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230A ARG 2.7 24.1 + - - -
231A PHE 3.1 9.1 + - - -
233A LEU* 1.3 81.9 - - - +
235A GLU* 1.3 67.4 + - - -
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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