Contacts of the helix formed by residues 279 - 300 (chain A) in PDB entry 1EXB
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 SER 279 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275A ASP 3.0 17.1 + - - -
276A LYS* 2.6 24.1 + - - -
277A ILE 3.4 0.2 - - - -
278A LEU* 1.3 82.6 - - - +
280A GLU* 1.3 66.5 + - - +
281A GLU* 3.6 8.6 + - - +
282A GLY 3.0 8.0 + - - -
283A ARG* 2.9 21.2 + - - -
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Residues in contact with GLU 280 (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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279A SER* 1.3 74.1 - - - +
281A GLU* 1.3 63.0 + - - +
283A ARG* 3.3 7.6 + - - +
284A ARG* 2.7 54.9 + - + +
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Residues in contact with GLU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A LYS* 5.7 4.7 - - - +
279A SER* 3.2 8.2 + - - +
280A GLU* 1.3 78.6 - - - +
282A GLY* 1.3 64.3 + - - +
284A ARG* 3.1 24.6 + - + +
285A GLN* 3.1 44.5 + - + +
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Residues in contact with GLY 282 (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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250A ILE* 5.9 0.9 - - - +
276A LYS 3.1 21.3 + - - -
277A ILE* 3.5 12.3 - - - -
279A SER* 3.0 10.5 + - - -
281A GLU* 1.3 80.0 - - - +
283A ARG* 1.3 62.8 + - - +
285A GLN* 3.3 17.4 + - - +
286A GLN* 3.1 21.7 + - - +
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Residues in contact with ARG 283 (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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255A TYR 3.7 13.1 + - - -
256A ASP 4.2 15.6 + - - -
257A SER 5.9 0.6 - - - -
258A GLY* 5.7 1.8 - - - +
277A ILE* 2.5 47.5 + - - +
278A LEU* 3.3 32.8 - - - +
279A SER 2.9 8.4 + - - +
280A GLU* 3.7 9.9 - - - +
281A GLU 3.2 0.2 - - - -
282A GLY* 1.3 81.1 + - - +
284A ARG* 1.3 67.2 + - + +
286A GLN* 3.2 17.0 + - - +
287A ALA* 3.0 22.3 + - - +
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Residues in contact with ARG 284 (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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280A GLU* 2.7 54.0 + - + +
281A GLU* 3.1 31.5 + - + +
283A ARG* 1.3 77.2 - - + +
285A GLN* 1.3 62.0 + - + +
287A ALA* 3.3 9.2 + - - +
288A LYS* 3.2 33.0 + - - +
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Residues in contact with GLN 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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218A HIS* 5.7 0.8 - - - -
220A PHE* 3.5 57.7 + - + +
250A ILE* 4.1 28.1 - - + +
276A LYS 5.1 1.6 - - - +
277A ILE* 5.8 0.3 - - - -
281A GLU* 3.1 32.9 + - + +
282A GLY* 3.4 16.6 - - - +
283A ARG 3.1 0.2 - - - -
284A ARG* 1.3 74.3 - - + +
286A GLN* 1.3 65.5 + - - +
288A LYS* 3.1 5.9 + - - +
289A LEU* 3.0 26.7 + - - +
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Residues in contact with GLN 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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250A ILE* 4.2 9.7 - - - +
253A GLY* 3.8 18.2 + - - -
255A TYR* 3.8 19.0 - - - +
256A ASP* 3.6 49.9 - - - +
277A ILE* 5.1 0.9 - - - +
282A GLY 3.1 9.9 + - - +
283A ARG* 3.6 23.8 + - - +
285A GLN* 1.3 78.6 - - - +
287A ALA* 1.3 63.0 + - - +
289A LEU* 3.1 40.3 + - - +
290A LYS* 3.1 12.5 + - - +
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Residues in contact with ALA 287 (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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283A ARG 3.0 12.3 + - - +
284A ARG* 3.5 13.2 - - - +
285A GLN 3.2 0.2 - - - -
286A GLN* 1.3 78.2 - - - +
288A LYS* 1.3 62.2 + - + +
290A LYS* 3.3 19.2 + - - +
291A GLU* 3.7 12.0 + - - +
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Residues in contact with LYS 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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220A PHE* 4.2 24.1 - - + -
284A ARG* 3.2 18.4 + - - +
285A GLN 3.1 8.3 + - - +
287A ALA* 1.3 76.6 - - + +
289A LEU* 1.3 65.0 + - - +
291A GLU* 3.1 20.7 + - - +
292A LEU* 3.1 11.0 + - - +
354A ILE* 3.2 44.6 - - + +
355A LEU* 2.8 26.2 + - - +
356A GLY* 5.0 1.2 - - - -
357A ASN* 5.8 0.6 - - - +
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Residues in contact with LEU 289 (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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220A PHE* 4.0 13.0 - - + -
250A ILE* 3.2 33.4 - - + +
251A VAL* 4.0 26.0 - - + -
253A GLY* 4.7 2.7 - - - -
285A GLN 3.0 19.1 + - - +
286A GLN* 3.1 35.4 + - - +
288A LYS* 1.3 74.4 - - - +
290A LYS* 1.3 61.3 + - - +
292A LEU* 3.1 23.3 + - + +
293A GLN* 2.8 30.0 + - - +
303A LEU* 4.2 18.3 - - + +
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Residues in contact with LYS 290 (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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256A ASP* 5.4 9.0 - - - +
286A GLN 3.1 9.9 + - - +
287A ALA* 3.4 13.9 - - - +
288A LYS 3.2 0.4 - - - -
289A LEU* 1.3 77.0 - - - +
291A GLU* 1.3 61.9 + - + +
293A GLN* 3.4 19.1 + - - +
294A ALA* 3.6 7.3 + - - +
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Residues in contact with GLU 291 (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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287A ALA 3.9 10.0 - - - +
288A LYS* 3.1 22.7 + - - +
290A LYS* 1.3 77.1 - - + +
292A LEU* 1.3 64.0 + - - +
294A ALA* 3.1 20.7 + - - +
295A ILE* 3.5 11.8 + - - +
354A ILE* 3.9 33.0 - - + +
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Residues in contact with LEU 292 (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 MET* 3.8 27.4 - - + -
220A PHE* 5.1 0.7 - - + -
288A LYS 3.1 13.5 + - - +
289A LEU* 3.5 29.6 - - + +
291A GLU* 1.3 73.6 - - - +
293A GLN* 1.3 61.2 + - - +
295A ILE* 2.9 12.4 + - + +
296A ALA* 2.9 26.9 + - - +
303A LEU* 3.9 13.9 - - + -
306A LEU* 3.8 6.4 - - + +
351A ILE* 3.9 32.5 - - + -
354A ILE* 3.5 24.2 - - + -
355A LEU* 4.1 14.6 - - + -
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Residues in contact with GLN 293 (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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252A SER 5.4 0.5 - - - +
289A LEU 2.8 14.1 + - - +
290A LYS* 3.4 16.2 - - - +
292A LEU* 1.3 75.5 - - - +
294A ALA* 1.3 57.3 + - - +
296A ALA* 3.3 13.0 + - - +
297A GLU* 3.0 42.9 + - - +
301A CYS 5.2 2.0 + - - -
302A THR* 5.7 1.4 - - - +
303A LEU* 3.8 28.2 + - + +
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Residues in contact with ALA 294 (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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290A LYS 3.6 5.4 + - - +
291A GLU* 3.1 14.9 + - - +
292A LEU 3.1 0.4 - - - -
293A GLN* 1.3 78.6 - - - +
295A ILE* 1.3 62.7 + - + +
297A GLU* 2.8 35.4 - - - +
298A ARG* 3.1 16.2 + - - +
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Residues in contact with ILE 295 (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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291A GLU 3.5 9.2 + - - +
292A LEU* 2.9 19.6 + - + +
294A ALA* 1.3 76.0 - - + +
296A ALA* 1.3 66.0 + - - +
298A ARG* 3.3 13.1 + - - +
299A LEU* 3.1 39.0 + - + +
306A LEU* 4.3 11.2 - - + -
347A ILE* 4.3 20.6 - - + -
350A GLU* 3.4 37.5 - - + +
351A ILE* 3.9 25.6 - - + +
354A ILE* 4.6 6.5 - - + -
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Residues in contact with ALA 296 (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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292A LEU 2.9 12.1 + - - +
293A GLN* 3.4 15.3 - - - +
294A ALA 3.3 0.2 - - - -
295A ILE* 1.3 74.6 - - - +
297A GLU* 1.3 66.8 + - - +
299A LEU* 3.0 4.4 + - - +
300A GLY 3.0 17.7 + - - -
301A CYS* 3.2 32.3 + - - +
302A THR 4.0 18.2 - - - +
303A LEU* 4.0 6.5 - - - +
306A LEU* 4.1 12.3 - - + +
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Residues in contact with GLU 297 (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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293A GLN* 3.0 28.7 + - - +
294A ALA* 2.8 37.5 - - - +
296A ALA* 1.3 76.4 - - - +
298A ARG* 1.3 61.7 + - - +
300A GLY* 3.1 13.2 + - - +
301A CYS 4.1 4.7 + - - -
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Residues in contact with ARG 298 (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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294A ALA* 3.1 16.9 + - - +
295A ILE* 3.3 21.4 - - - +
296A ALA 3.1 0.4 - - - -
297A GLU* 1.3 80.9 - - - +
299A LEU* 1.3 64.3 + - + +
347A ILE* 4.0 19.3 - - - +
350A GLU* 2.6 44.0 + - - -
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Residues in contact with LEU 299 (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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295A ILE* 3.3 19.5 - - + +
296A ALA 3.0 8.1 + - - +
298A ARG* 1.3 85.7 - - + +
300A GLY* 1.3 62.0 + - - +
301A CYS* 4.3 8.1 - - - +
306A LEU* 4.3 16.8 - - + -
339A VAL* 4.9 3.8 - - + -
342A LYS* 3.4 57.2 + - + +
343A LEU* 4.4 4.0 - - + -
347A ILE* 4.1 41.7 - - + -
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Residues in contact with GLY 300 (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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296A ALA 3.0 3.2 + - - -
297A GLU* 3.1 13.5 + - - -
298A ARG 3.3 0.6 + - - -
299A LEU* 1.3 80.0 - - - +
301A CYS* 1.3 58.6 + - - +
342A LYS* 5.7 1.3 - - - -
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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
------------------------------------------------------------
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