Contacts of the helix formed by residues 271 - 288 (chain A) in PDB entry 5E2Q
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 271 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A ALA* 3.5 4.6 - - - +
270A ALA* 1.3 82.6 - - - +
272A SER* 1.3 60.4 + - - +
273A HIS* 3.2 12.8 + - + +
274A GLN* 2.8 46.1 + - - +
275A GLY* 3.1 22.9 + - - -
303A ASP* 2.8 22.5 + - - -
306A PRO* 6.0 0.4 - - - +
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Residues in contact with SER 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ASN* 1.3 73.6 - - - +
273A HIS* 1.3 69.9 + - - +
275A GLY* 4.2 3.4 - - - +
276A GLN* 2.8 50.4 + - - +
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Residues in contact with HIS 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ASN* 3.2 13.3 + - + +
272A SER* 1.3 86.0 + - - +
274A GLN* 1.3 59.7 + - - +
276A GLN* 4.6 3.9 + - - +
277A MET* 3.2 28.8 + - - +
299A PHE* 3.7 29.3 + + - +
302A GLN* 3.2 56.8 + - - +
303A ASP* 3.9 12.3 - - + -
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Residues in contact with GLN 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TYR* 3.6 32.4 + - + +
269A ALA* 4.1 7.4 - - + -
270A ALA* 3.0 33.2 + - - +
271A ASN* 2.8 25.3 + - - +
273A HIS* 1.3 70.8 - - - +
275A GLY* 1.3 64.5 + - - +
277A MET* 3.2 26.0 - - + +
278A LEU* 3.3 17.5 - - - +
303A ASP* 2.9 33.6 + - - +
306A PRO* 3.7 16.0 - - - +
307A ILE 5.4 0.4 - - - +
308A VAL* 4.3 8.5 + - - +
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Residues in contact with GLY 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A LYS* 3.6 23.8 - - - +
269A ALA* 4.0 12.3 - - - +
271A ASN 3.1 13.7 + - - -
272A SER* 3.3 4.7 + - - -
274A GLN* 1.3 78.8 - - - +
276A GLN* 1.3 60.4 + - - +
278A LEU 3.6 0.2 + - - -
279A ALA* 3.3 17.8 + - - +
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Residues in contact with GLN 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A SER* 2.8 36.6 + - - +
273A HIS* 4.6 3.6 + - - -
275A GLY* 1.3 74.8 - - - +
277A MET* 1.3 65.7 + - - +
279A ALA* 3.4 7.2 + - - +
280A GLN* 3.1 27.7 + - - +
299A PHE* 3.4 47.1 - - + -
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Residues in contact with MET 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TYR* 3.7 23.6 - - - +
273A HIS 3.2 15.2 + - - +
274A GLN* 3.2 26.0 - - + +
276A GLN* 1.3 78.3 - - - +
278A LEU* 1.3 68.9 + - + +
280A GLN* 3.4 1.9 + - - +
281A TYR* 3.0 46.0 + - + -
296A GLY* 3.2 28.7 - - - +
299A PHE* 3.9 6.2 - - + +
300A TRP* 3.5 41.5 - - + -
303A ASP* 5.0 2.5 - - - +
309A GLU* 5.7 0.4 - - - +
310A SER* 4.1 13.5 - - - +
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Residues in contact with LEU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TYR* 4.2 18.4 - - + +
37A LEU* 4.0 10.3 - - + -
262A LEU* 3.8 39.2 - - + +
265A ALA* 4.2 7.6 - - + -
266A LYS* 3.8 35.0 - - + +
269A ALA* 5.2 0.7 - - + -
274A GLN 3.3 18.8 + - - +
275A GLY 3.9 4.0 - - - +
276A GLN 3.2 0.2 - - - -
277A MET* 1.3 88.6 - - + +
279A ALA* 1.3 59.6 + - - +
280A GLN 3.1 0.2 - - - -
281A TYR* 3.2 18.6 + - + +
282A ILE* 2.9 35.4 + - - +
310A SER* 5.8 0.4 - - - +
312A ILE* 5.8 0.4 - - + -
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Residues in contact with ALA 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A LYS* 4.2 21.2 - - + +
275A GLY 3.3 13.2 + - - +
276A GLN* 3.4 10.7 + - - +
278A LEU* 1.3 79.7 - - - +
280A GLN* 1.3 61.7 + - + +
282A ILE* 3.5 8.7 - - - +
283A GLU* 3.1 28.9 + - - +
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Residues in contact with GLN 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A GLN 3.1 16.0 + - - +
277A MET 3.7 0.2 - - - +
278A LEU 3.1 0.2 - - - -
279A ALA* 1.3 80.2 + - - +
281A TYR* 1.3 59.8 + - - +
282A ILE 3.2 0.2 - - - -
283A GLU* 3.2 12.3 + - - +
284A SER* 2.9 23.7 + - - -
292A ALA* 3.2 29.8 - - - +
295A ARG* 2.9 43.7 + - + +
296A GLY* 3.5 22.7 - - - +
299A PHE* 4.3 11.6 - - + -
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Residues in contact with TYR 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LEU* 4.2 5.6 - - + -
277A MET* 3.0 38.8 + - + -
278A LEU* 3.6 22.0 - - + +
280A GLN* 1.3 76.3 - - - +
282A ILE* 1.3 57.0 + - - +
284A SER* 3.1 5.4 + - - -
285A PHE* 2.9 52.2 + - + -
293A HIS* 3.7 29.8 - + - -
296A GLY* 3.7 25.8 + - - -
297A SER* 3.8 3.6 - - - -
300A TRP* 3.6 20.4 - - - +
310A SER 5.8 0.9 - - - -
311A TYR* 3.3 32.0 - + - -
312A ILE* 4.0 21.8 - - + -
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Residues in contact with ILE 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A VAL* 4.0 20.1 - - + +
262A LEU* 3.9 20.0 - - + -
263A GLU* 3.8 39.3 - - + +
266A LYS* 3.8 21.1 - - - +
278A LEU 2.9 20.2 + - - +
279A ALA* 3.5 8.5 - - - +
281A TYR* 1.3 75.5 - - - +
283A GLU* 1.3 58.2 + - + +
285A PHE 3.4 0.7 + - - -
286A THR* 2.7 47.2 + - - +
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Residues in contact with GLU 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ASP* 4.6 6.6 - - - +
279A ALA 3.1 17.9 + - - +
280A GLN* 3.4 20.2 - - - +
282A ILE* 1.3 76.5 - - + +
284A SER* 1.3 57.8 + - - +
286A THR* 4.7 2.5 - - - -
287A GLN* 2.9 66.4 + - - +
292A ALA* 3.9 14.9 - - + +
295A ARG* 5.3 4.2 + - - +
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Residues in contact with SER 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ASN* 4.9 2.3 + - - -
217A ALA 4.1 1.9 - - - +
280A GLN 2.9 13.6 + - - -
281A TYR* 3.1 10.1 + - - -
283A GLU* 1.3 77.9 - - - +
285A PHE* 1.3 66.6 + - - +
288A GLY* 2.8 30.0 + - - -
289A SER 2.7 29.3 + - - +
290A ILE* 4.6 3.1 - - - +
292A ALA* 3.7 2.9 - - - +
293A HIS* 3.3 26.3 - - - +
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Residues in contact with PHE 285 (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 4.8 1.8 - - - -
218A SER* 3.3 7.1 - - - -
219A VAL* 2.8 27.9 + - - +
255A LEU* 3.8 24.6 - - + +
258A VAL* 4.1 13.9 - - + -
259A VAL* 3.8 14.4 - - + -
262A LEU* 3.7 30.3 - - + -
281A TYR* 2.9 24.7 + - + +
284A SER* 1.3 89.6 - - - +
286A THR* 1.3 59.0 + - - +
293A HIS* 4.2 11.0 - + - -
312A ILE* 3.9 17.0 - - + -
313A GLY* 3.7 32.8 - - - -
314A PHE* 4.6 13.2 - + - -
328A PHE* 4.3 9.6 - + - -
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Residues in contact with THR 286 (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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218A SER* 3.4 4.4 - - - -
219A VAL* 3.9 14.7 - - + +
220A LEU* 3.0 56.3 + - + +
259A VAL* 3.8 15.4 - - - +
282A ILE* 2.7 29.3 + - - +
283A GLU* 4.1 3.1 - - - -
285A PHE* 1.3 79.1 - - - +
287A GLN* 1.3 66.8 + - - +
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Residues in contact with GLN 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A SER* 3.6 2.2 - - - -
220A LEU* 3.4 19.5 - - - +
225A SER* 3.2 13.4 + - - -
226A LEU* 5.0 2.8 - - - +
227A ASP* 3.2 31.5 - - + +
230A VAL* 3.3 25.6 - - + +
248A ARG* 3.1 45.2 + - - +
283A GLU* 2.9 43.3 + - - +
286A THR* 1.3 85.1 - - - +
288A GLY* 1.3 59.9 + - - +
289A SER* 4.4 3.4 - - - +
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Residues in contact with GLY 288 (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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193A LEU* 5.9 0.5 - - - +
197A ASN* 3.1 18.5 + - - +
216A LEU* 3.3 23.5 - - - +
217A ALA 3.5 20.4 - - - -
218A SER* 3.6 4.1 - - - -
230A VAL* 4.0 4.0 - - - +
284A SER 2.8 14.1 + - - -
287A GLN* 1.3 79.9 - - - +
289A SER* 1.3 58.8 + - - +
290A ILE* 3.8 1.7 + - - +
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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
------------------------------------------------------------
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