Contacts of the helix formed by residues 220 - 237 (chain A) in PDB entry 2E4Y
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 GLY 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A SER* 4.8 8.3 - - - -
219A GLU* 1.3 76.2 - - - +
221A ASP* 1.3 54.7 + - - -
222A TYR* 2.6 19.0 + - - -
223A GLY 3.0 4.2 + - - -
224A GLU* 2.6 39.2 + - - -
249A ARG* 6.3 1.3 - - - -
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Residues in contact with ASP 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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151A SER* 4.8 0.7 - - - -
152A SER* 4.4 18.6 + - - +
155A ILE* 3.5 31.0 - - + +
156A GLN* 6.2 0.3 - - - +
175A SER* 3.9 3.8 + - - -
177A LYS* 3.3 33.4 + - - +
220A GLY* 1.3 68.9 - - - -
222A TYR* 1.3 53.1 + - - +
224A GLU* 4.1 5.2 + - - -
225A THR* 2.5 44.6 + - + +
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Residues in contact with TYR 222 (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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151A SER* 3.6 18.6 - - - -
152A SER* 4.1 12.6 + - - +
174A THR* 3.4 9.4 - - - -
175A SER* 4.8 0.4 - - - -
194A ASP* 3.8 15.3 - - - +
219A GLU 6.0 0.4 - - - +
220A GLY 2.6 7.0 + - - -
221A ASP* 1.3 73.4 - - - +
223A GLY* 1.3 72.4 + - - +
225A THR* 3.4 1.9 + - - -
226A GLY* 3.0 27.5 + - - -
275A PHE* 4.0 14.1 - + - -
276A MET 3.9 21.1 - - - -
277A ARG* 4.2 20.4 - - + -
300A SER* 3.0 20.0 + - - -
301A ASP* 2.5 26.0 + - - -
302A GLY* 3.4 1.8 + - - -
1001A 52A 3.3 51.8 - - - +
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Residues in contact with GLY 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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217A ALA* 3.7 3.7 - - - +
218A SER* 3.4 17.1 + - - -
220A GLY 3.0 3.8 + - - -
222A TYR* 1.3 81.6 - - - +
224A GLU* 1.3 67.1 + - - +
226A GLY 3.6 0.2 - - - -
227A ILE* 2.8 27.2 + - - +
275A PHE* 3.1 26.5 - - - +
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Residues in contact with GLU 224 (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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217A ALA* 5.1 1.8 - - - -
218A SER 3.5 6.5 + - - +
219A GLU* 3.7 12.9 - - + +
220A GLY* 2.6 44.9 + - - +
221A ASP* 4.1 3.5 + - - -
223A GLY* 1.3 73.6 - - - +
225A THR* 1.3 60.5 + - + +
227A ILE* 2.8 23.9 + - - +
228A GLU* 2.9 28.0 + - + +
246A LYS* 5.1 12.9 + - + +
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Residues in contact with THR 225 (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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175A SER* 3.2 26.3 + - - +
176A ALA* 4.4 10.0 + - - +
177A LYS* 4.4 21.8 - - + +
194A ASP* 5.7 0.2 - - - -
221A ASP* 2.5 33.6 + - - +
222A TYR 3.4 2.1 + - - -
224A GLU* 1.3 77.0 - - + +
226A GLY* 1.3 58.7 + - - +
228A GLU* 3.3 15.9 + - - +
229A ALA* 3.0 28.1 + - - +
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Residues in contact with GLY 226 (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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194A ASP* 4.0 12.3 - - - -
222A TYR 3.0 7.6 + - - -
225A THR* 1.3 84.1 + - - +
227A ILE* 1.3 60.6 + - - +
229A ALA* 3.4 3.7 - - - +
230A PHE 3.4 10.7 + - - -
275A PHE* 3.2 50.9 - - - -
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Residues in contact with ILE 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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215A THR* 4.1 24.9 - - + +
216A VAL 5.2 0.2 - - - -
217A ALA* 3.6 25.4 - - + -
223A GLY 2.8 11.7 + - - +
224A GLU* 2.8 8.9 + - - +
226A GLY* 1.3 74.8 - - - +
228A GLU* 1.3 58.1 + - + +
229A ALA 2.8 5.2 - - - -
230A PHE* 2.7 35.9 + - + -
231A GLU* 2.5 58.3 + - + +
273A VAL* 4.4 6.5 - - + -
275A PHE* 3.8 11.9 - - + +
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Residues in contact with GLU 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 GLU* 2.9 27.3 + - - +
225A THR* 3.6 16.9 + - - +
227A ILE* 1.3 80.2 - - + +
229A ALA* 1.3 60.3 + - - +
231A GLU* 3.4 21.9 - - - +
232A GLN* 3.4 34.6 + - - +
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Residues in contact with ALA 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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176A ALA* 5.9 4.0 - - + -
194A ASP* 4.3 9.6 - - + +
195A PHE* 4.7 15.7 - - + -
198A ALA* 3.6 15.9 - - + -
225A THR 3.0 16.6 + - - +
226A GLY* 3.4 10.5 - - - +
228A GLU* 1.3 78.4 - - - +
230A PHE* 1.3 64.9 + - - +
231A GLU 3.5 0.2 + - - -
232A GLN* 3.5 8.7 + - - +
233A GLU* 3.3 26.3 + - - +
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Residues in contact with PHE 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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198A ALA* 3.5 16.1 - - + +
201A MET* 4.3 9.6 - - + -
202A ALA* 3.8 38.4 - - + -
205A LEU* 3.7 15.9 - - + -
213A VAL* 4.7 4.7 - - + -
215A THR* 3.6 24.0 - - + -
226A GLY 3.4 8.0 + - - +
227A ILE* 2.7 37.5 + - + +
229A ALA* 1.3 72.9 - - - +
231A GLU* 1.3 54.5 + - - +
233A GLU* 3.3 1.9 + - - -
234A ALA* 2.7 47.8 + - + +
239A ILE* 5.2 2.0 - - + -
241A ILE* 4.2 12.1 - - + -
273A VAL* 3.5 28.3 - - + -
275A PHE* 4.7 5.4 - - + -
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Residues in contact with GLU 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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215A THR* 5.3 1.6 + - - +
227A ILE* 2.5 40.4 + - + +
228A GLU* 3.4 26.3 - - - +
229A ALA 3.3 0.2 - - - -
230A PHE* 1.3 71.6 - - - +
232A GLN* 1.3 62.1 - - + +
234A ALA* 3.0 20.0 + - - +
235A ARG* 3.1 28.4 + - - +
241A ILE* 4.3 22.3 - - + +
244A ALA* 5.1 11.1 - - - +
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Residues in contact with GLN 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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195A PHE* 5.6 5.7 - - - -
228A GLU* 3.4 22.1 + - - +
229A ALA* 3.8 9.1 - - - +
230A PHE 3.2 0.6 - - - -
231A GLU* 1.3 74.7 - - + +
233A GLU* 1.3 73.1 + - - +
234A ALA 2.8 6.2 + - - -
235A ARG* 3.0 26.2 + - - +
236A LEU* 3.2 21.7 + - + +
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Residues in contact with GLU 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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195A PHE* 4.1 19.0 - - + +
198A ALA* 4.5 3.8 - - + +
199A LYS* 3.2 45.3 + - + +
202A ALA* 3.8 16.5 - - + +
229A ALA 3.3 17.5 + - - +
230A PHE 3.9 3.6 - - - +
232A GLN* 1.3 84.8 - - - +
234A ALA* 1.3 59.4 + - - +
236A LEU* 3.9 18.8 + - - +
237A ARG* 3.1 54.5 + - - +
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Residues in contact with ALA 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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202A ALA* 4.6 2.7 - - - -
230A PHE* 2.7 38.3 + - + +
231A GLU* 3.0 13.5 - - - +
232A GLN 2.8 1.4 + - - -
233A GLU* 1.3 76.7 - - - +
235A ARG* 1.3 62.9 + - + +
237A ARG 3.3 5.7 + - - -
239A ILE* 3.1 47.7 + - + +
241A ILE* 4.6 7.4 - - + -
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Residues in contact with ARG 235 (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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231A GLU* 3.5 24.1 + - - +
232A GLN* 3.0 14.3 + - - +
234A ALA* 1.3 74.9 - - + +
236A LEU* 1.3 60.9 + - + +
238A ASN* 2.8 31.7 + - - +
239A ILE 4.1 9.6 + - - +
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Residues in contact with LEU 236 (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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232A GLN* 3.2 20.8 + - + +
233A GLU* 4.0 25.8 - - - +
234A ALA 3.3 0.2 - - - -
235A ARG* 1.3 81.6 - - + +
237A ARG* 1.3 64.1 + - + +
238A ASN* 3.3 5.5 + - - -
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Residues in contact with ARG 237 (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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199A LYS* 4.1 17.1 - - - +
202A ALA* 3.7 28.2 - - - +
203A GLU* 3.2 37.7 + - - +
206A ARG* 2.6 61.6 + - + +
233A GLU* 3.1 43.7 + - - +
234A ALA 3.3 1.8 + - - -
235A ARG 2.9 1.4 + - - -
236A LEU* 1.3 82.1 - - + +
238A ASN* 1.3 60.5 + - - +
239A ILE* 3.5 9.8 - - + +
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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