Contacts of the helix formed by residues 273 - 285 (chain A) in PDB entry 1L8A
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 LYS 273 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A TYR* 3.4 35.2 - - + -
269A THR* 4.0 2.0 + - - -
272A GLY* 1.3 79.6 - - - +
274A ILE* 1.3 66.2 + - - +
275A ILE 3.1 1.3 - - - -
276A ASN* 2.9 43.4 + - + +
277A GLU* 3.0 11.9 + - - +
314A MET 3.3 16.2 + - - -
315A ASN* 3.1 21.5 + - - +
316A GLU 5.4 0.4 - - - -
317A THR 2.7 29.9 + - - +
318A VAL* 4.1 6.1 - - + -
319A ASP* 3.3 11.0 - - - +
322A TYR* 3.8 1.0 - - - -
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Residues in contact with ILE 274 (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 ASP* 3.7 16.8 - - + +
259A CYS* 4.9 0.7 - - + -
261A LEU* 3.2 46.9 - - + +
268A VAL* 3.5 37.0 - - + -
269A THR* 3.5 14.8 + - + +
273A LYS* 1.3 71.6 - - - +
275A ILE* 1.3 67.6 + - + +
277A GLU* 3.6 12.5 - - - +
278A LEU* 2.8 45.0 + - + +
319A ASP* 2.9 12.8 + - - +
247B ARG* 4.3 13.2 - - - +
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Residues in contact with ILE 275 (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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59A TYR* 3.7 30.3 - - + +
259A CYS* 3.6 37.7 - - + -
261A LEU* 4.1 3.8 - - + -
273A LYS* 3.1 1.0 - - - +
274A ILE* 1.3 82.2 - - + +
276A ASN* 1.3 62.2 + - - +
278A LEU* 4.4 4.9 - - - -
279A GLU* 3.0 25.8 + - - +
291A LYS* 4.2 9.2 - - + -
293A MET* 3.7 29.4 - - + -
319A ASP* 5.2 0.2 + - - -
387A LEU* 3.6 18.8 - - + +
389A HIS* 3.7 23.3 - - + +
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Residues in contact with ASN 276 (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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56A ILE* 3.3 46.8 - - + +
57A SER 4.5 2.1 + - - +
59A TYR* 3.6 19.3 - - - +
273A LYS* 2.9 42.8 + - + +
275A ILE* 1.3 79.1 - - - +
277A GLU* 1.3 60.2 + - - +
279A GLU* 4.3 4.0 - - - -
280A GLY 2.9 24.8 + - - -
291A LYS* 4.0 9.9 + - - -
315A ASN* 5.1 2.6 + - - +
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Residues in contact with GLU 277 (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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56A ILE* 5.3 1.8 - - - -
239A LYS* 4.5 6.8 + - - -
269A THR* 4.4 5.0 + - - +
273A LYS 3.0 12.0 + - - +
274A ILE* 3.6 15.6 - - - +
276A ASN* 1.3 76.9 - - - +
278A LEU* 1.3 70.4 + - + +
280A GLY* 3.8 1.3 - - - -
281A ILE* 3.1 24.1 + - + +
243B THR* 3.0 34.5 + - + +
247B ARG* 2.8 52.7 + - - +
284B GLY 4.7 1.3 - - - +
285B ALA* 5.8 0.7 - - - -
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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
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230A ASP* 4.4 7.4 - - + +
233A MET* 4.1 23.8 - - + -
239A LYS* 4.3 16.6 - - + +
257A ILE* 4.1 17.3 - - + -
259A CYS* 4.1 24.5 - - - -
274A ILE* 2.8 35.3 + - + +
275A ILE* 3.7 4.3 - - - +
277A GLU* 1.3 88.6 - - - +
279A GLU* 1.3 63.0 + - - +
281A ILE* 3.4 1.5 - - - +
282A PHE* 3.0 36.1 + - + +
387A LEU* 3.9 20.0 - - + -
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Residues in contact with GLU 279 (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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56A ILE* 3.4 16.4 - - - +
57A SER* 2.7 40.5 + - - -
62A THR* 5.3 0.3 + - - -
275A ILE 3.0 18.5 + - - +
276A ASN* 3.8 4.1 - - - +
277A GLU 3.3 0.2 - - - -
278A LEU* 1.3 76.2 - - - +
280A GLY* 1.3 58.1 + - - +
283A GLU* 2.8 45.2 + - + +
289A VAL* 3.8 27.2 - - + +
291A LYS* 3.0 31.7 + - + +
387A LEU* 3.9 8.5 - - + +
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Residues in contact with GLY 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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56A ILE* 3.9 19.2 - - - +
276A ASN 2.9 17.4 + - - -
277A GLU* 3.8 0.9 - - - -
278A LEU 3.3 0.2 - - - -
279A GLU* 1.3 77.9 - - - +
281A ILE* 1.3 56.4 + - - +
283A GLU* 3.9 3.4 - - - +
284A GLY* 3.0 20.3 + - - -
284B GLY* 3.1 27.7 - - - -
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Residues in contact with ILE 281 (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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239A LYS* 4.0 35.4 - - + +
242A ILE* 4.5 3.1 - - + -
277A GLU* 3.1 14.3 + - + +
278A LEU* 3.4 12.1 - - - +
280A GLY* 1.3 72.8 - - - +
282A PHE* 1.3 69.0 + - + +
284A GLY* 3.3 1.2 + - - -
285A ALA* 2.8 26.5 + - - +
239B LYS 4.8 4.3 - - - +
242B ILE* 4.3 8.7 - - + -
243B THR* 3.7 24.5 - - + -
281B ILE* 3.5 34.7 - - + +
284B GLY* 3.3 10.6 + - - +
285B ALA* 4.1 11.7 - - + -
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Residues in contact with PHE 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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233A MET* 3.8 23.1 - - + -
239A LYS* 4.2 14.6 - - + -
242A ILE* 3.8 30.5 - - + -
255A PHE* 3.6 33.0 - + - -
257A ILE* 4.1 11.2 - - + -
278A LEU* 3.0 32.9 + - + +
281A ILE* 1.3 80.1 - - + +
283A GLU* 1.3 63.7 + - - +
285A ALA* 3.2 6.6 + - - +
286A GLY 3.3 0.2 + - - -
287A TRP* 2.9 58.6 + + + +
289A VAL* 4.0 16.2 - - + -
385A VAL* 3.8 13.9 - - + -
387A LEU* 5.7 0.4 - - + -
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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
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56A ILE 5.6 7.2 - - - +
279A GLU* 2.8 30.2 + - + +
280A GLY* 3.9 4.3 - - - +
282A PHE* 1.3 76.0 - - - +
284A GLY* 1.3 59.8 + - - +
286A GLY* 2.9 22.3 + - - -
287A TRP 3.5 15.6 - - - +
288A ASN* 5.4 0.3 - - - -
289A VAL* 3.8 21.6 + - + +
382A LYS* 5.0 3.6 + - - -
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Residues in contact with GLY 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 GLY 3.0 17.5 + - - -
281A ILE 3.6 4.5 - - - -
282A PHE 3.2 0.2 - - - -
283A GLU* 1.3 79.2 - - - +
285A ALA* 1.3 55.6 + - - +
286A GLY 3.1 2.8 + - - -
277B GLU* 4.8 1.6 - - - +
280B GLY* 3.2 42.6 - - - -
281B ILE* 3.5 2.7 + - - -
284B GLY* 4.4 1.8 - - - -
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Residues in contact with ALA 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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242A ILE* 3.5 31.0 - - + -
243A THR* 4.1 22.3 - - + +
246A THR* 2.5 33.3 + - - +
281A ILE 2.8 16.1 + - - +
282A PHE 3.6 4.9 - - - +
283A GLU 3.1 0.8 - - - -
284A GLY* 1.3 75.8 - - - +
286A GLY* 1.3 50.8 + - - +
287A TRP* 3.4 6.5 - - + +
277B GLU 6.0 0.2 - - - -
281B ILE* 4.2 5.4 - - + +
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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
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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