Contacts of the helix formed by residues 223 - 239 (chain A) in PDB entry 4EE5
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 ASN 223 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A GLN* 3.0 9.9 + - - -
222A PHE* 1.3 75.1 - - - +
224A ARG* 1.3 63.5 + - - +
225A ALA* 3.6 4.7 + - - +
226A LYS* 3.2 23.0 + - - +
227A LEU* 3.2 25.7 + - - +
305A ASN 2.7 27.8 + - - +
307A TYR 3.1 20.1 + - - +
308A TRP* 3.3 32.5 - - + -
394A ILE* 3.5 19.5 - - + -
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Residues in contact with ARG 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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183A PRO* 4.0 16.2 - - + +
222A PHE* 3.7 23.0 + - + -
223A ASN* 1.3 71.0 + - - +
225A ALA* 1.3 62.8 + - - +
227A LEU* 3.2 8.4 + - - +
228A LEU* 3.1 47.2 + - + +
246A PHE* 4.9 7.3 + - - +
247A SER 5.0 0.6 - - - -
248A ASP* 2.7 38.6 + - - +
287A GLY* 5.5 0.6 - - - -
288A GLY 3.7 19.3 + - - +
307A TYR 4.6 2.8 + - - -
309A GLY 5.6 3.4 + - - +
313A GLU* 2.8 44.2 + - + +
314A ASP* 4.7 7.5 - - - +
317A ILE* 5.0 5.3 - - - +
349A ASN* 6.2 0.4 - - - +
404A UDP 4.2 7.4 - - - +
406A GOL 3.9 23.3 + - - +
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Residues in contact with ALA 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ASN* 3.4 4.1 + - - +
224A ARG* 1.3 76.2 - - - +
226A LYS* 1.3 66.1 + - - +
228A LEU* 3.4 13.3 + - + +
229A ASN* 3.0 25.6 + - - -
303A PHE* 4.1 15.3 - - + +
304A PRO* 3.2 22.0 - - + +
307A TYR* 5.2 1.9 + - + -
313A GLU* 3.7 29.0 - - + +
317A ILE* 4.9 1.8 - - + -
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Residues in contact with LYS 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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223A ASN* 3.2 36.8 + - + +
225A ALA* 1.3 77.6 - - - +
227A LEU* 1.3 57.9 + - - +
229A ASN* 3.1 4.2 + - - +
230A VAL* 2.9 31.3 + - - +
304A PRO 4.1 1.0 + - - -
305A ASN* 3.5 35.2 - - + +
308A TRP* 4.6 7.0 - - + -
374A LEU* 3.8 13.5 - - + +
375A THR* 3.2 29.6 + - - +
394A ILE* 2.7 48.1 + - + +
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Residues in contact with LEU 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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183A PRO* 4.2 8.3 - - + -
184A PHE 4.1 2.7 - - - +
214A ILE* 3.5 42.9 - - + +
216A GLN* 3.8 24.2 - - + +
222A PHE* 3.5 40.4 - - + -
223A ASN 3.2 14.6 - - - +
224A ARG 3.2 7.1 + - - +
226A LYS* 1.3 77.3 - - - +
228A LEU* 1.3 57.6 + - - +
230A VAL* 3.1 6.9 + - - +
231A GLY 2.8 24.9 + - - -
392A VAL* 4.0 17.0 - - + -
394A ILE* 4.1 14.4 - - + -
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Residues in contact with LEU 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ILE* 4.0 15.9 - - + +
183A PRO* 3.8 31.2 - - + -
224A ARG* 3.1 46.9 + - + +
225A ALA* 3.5 10.5 - - + +
227A LEU* 1.3 75.7 - - - +
229A ASN* 1.3 62.2 + - - +
231A GLY* 3.1 2.9 + - - -
232A PHE* 3.0 22.5 + - - +
246A PHE* 3.8 31.7 - - + -
303A PHE* 3.7 29.8 - - + -
317A ILE* 5.3 0.4 - - + -
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Residues in contact with ASN 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 ALA 3.0 14.4 + - - -
226A LYS 3.4 7.4 - - - +
228A LEU* 1.3 74.7 - - - +
230A VAL* 1.3 65.5 + - - +
232A PHE* 3.3 4.2 + - - +
233A GLN* 3.0 24.3 + - - +
297A PHE* 3.2 17.7 - - - -
302A GLY 4.8 0.2 - - - -
303A PHE* 2.8 49.6 + - - +
304A PRO 4.5 0.2 + - - -
305A ASN* 2.9 22.9 + - - +
370A GLY 4.1 8.1 - - - -
371A LEU* 4.7 8.5 - - + +
374A LEU* 3.8 17.1 - - + +
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Residues in contact with VAL 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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214A ILE* 4.0 15.9 - - + -
226A LYS 2.9 19.5 + - - +
227A LEU* 3.3 8.5 - - - +
229A ASN* 1.3 76.2 - - - +
231A GLY* 1.3 60.6 + - - +
233A GLN* 3.1 1.6 + - - +
234A GLU* 2.7 45.0 + - + +
374A LEU* 4.7 3.4 - - + -
376A TYR* 3.7 44.4 - - + -
390A ILE* 4.8 4.7 - - + -
392A VAL* 4.2 9.9 - - + -
394A ILE* 3.8 21.5 - - + -
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Residues in contact with GLY 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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181A ILE* 3.5 13.5 - - - +
212A TYR* 5.3 0.5 - - - -
214A ILE* 3.6 30.1 - - - -
227A LEU 2.8 11.9 + - - -
228A LEU 3.1 3.7 + - - -
230A VAL* 1.3 77.4 - - - +
232A PHE* 1.3 56.3 + - - +
234A GLU* 4.8 1.3 - - - -
235A ALA* 2.9 34.7 + - - +
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Residues in contact with PHE 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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181A ILE* 4.1 2.4 - - - +
228A LEU 3.0 10.1 + - - +
229A ASN 3.5 6.5 - - - +
230A VAL 3.3 0.2 - - - -
231A GLY* 1.3 77.1 - - - +
233A GLN* 1.3 73.0 + - + +
236A LEU* 3.4 43.5 + - + +
244A PHE* 3.6 52.8 - + + -
246A PHE* 4.7 2.7 - - + -
294A LYS* 4.3 9.0 - - + -
297A PHE* 3.3 56.3 - + + -
298A LEU* 3.9 21.1 - - + -
371A LEU* 3.9 21.3 - - + -
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Residues in contact with GLN 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 ASN 3.0 16.7 + - - +
230A VAL 3.8 0.7 - - - +
232A PHE* 1.3 89.4 - - + +
234A GLU* 1.3 63.6 + - - +
236A LEU* 3.5 15.5 + - + +
237A LYS* 3.8 16.7 + - - +
371A LEU* 3.9 22.1 - - + +
374A LEU* 4.1 12.8 + - + +
376A TYR* 3.3 35.0 + - + +
410A SO4 4.3 8.9 + - - -
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Residues in contact with GLU 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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212A TYR* 5.2 0.4 - - - -
230A VAL* 2.7 35.8 + - + +
231A GLY 4.3 0.7 - - - +
233A GLN* 1.3 70.5 - - - +
235A ALA* 1.3 68.7 + - - +
237A LYS* 2.5 57.5 + - - +
238A ASP* 3.7 5.7 + - - +
376A TYR* 2.7 22.1 + - + +
378A VAL* 3.6 23.2 - - + +
381A VAL* 5.4 4.3 - - - +
390A ILE* 3.6 29.5 - - + +
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Residues in contact with ALA 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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179A ALA* 3.8 28.7 - - + -
181A ILE* 4.2 1.3 - - + -
212A TYR* 3.8 31.3 - - + -
231A GLY 2.9 20.3 + - - +
232A PHE 4.2 2.0 - - - +
234A GLU* 1.3 78.0 - - - +
236A LEU* 1.3 58.1 + - - +
238A ASP* 2.9 25.2 + - - +
239A TYR 3.5 0.5 + - - -
241A TYR* 3.4 11.9 - - + -
244A PHE* 4.4 2.9 - - + -
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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 PHE* 3.4 48.1 + - + +
233A GLN* 3.8 10.5 - - + +
234A GLU 3.1 1.0 - - - -
235A ALA* 1.3 77.2 - - - +
237A LYS* 1.3 61.9 + - + +
238A ASP 3.2 0.4 - - - -
239A TYR 3.4 20.4 + - - +
240A ASP* 5.1 1.7 - - - -
241A TYR* 3.6 25.6 - - + +
244A PHE* 3.7 14.1 - - + -
294A LYS* 4.0 25.1 - - - +
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Residues in contact with LYS 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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233A GLN* 4.1 16.0 - - - +
234A GLU* 2.5 52.6 + - - +
236A LEU* 1.3 78.4 - - + +
238A ASP* 1.3 66.6 + - - +
376A TYR* 4.0 4.6 + - - -
378A VAL* 5.8 0.4 - - - +
410A SO4 4.9 6.3 + - - -
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Residues in contact with ASP 238 (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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166A ARG* 4.5 12.2 + - - +
212A TYR* 2.5 38.0 + - - +
234A GLU 4.6 3.8 - - - +
235A ALA 2.9 7.6 + - - +
237A LYS* 1.3 83.4 - - - +
239A TYR* 1.3 65.8 + - + +
383A ARG* 2.9 42.3 + - - -
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Residues in contact with TYR 239 (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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166A ARG* 3.4 28.5 - - - +
177A LYS* 3.8 26.7 - - + +
208A ASP* 2.6 40.0 + - - -
235A ALA 3.5 0.9 + - - +
236A LEU* 3.4 17.8 + - - +
237A LYS 3.5 2.0 - - - -
238A ASP* 1.3 83.3 - - + +
240A ASP* 1.3 65.8 + - + +
241A TYR* 2.7 58.2 + + + -
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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