Contacts of the helix formed by residues 273 - 285 (chain A) in PDB entry 1LD8
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 273 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A VAL* 2.9 38.0 + - - +
232A ARG* 3.6 18.9 - - + +
237A TRP* 4.2 0.4 - - - +
266A MET 5.7 1.0 + - - +
267A ILE* 5.5 0.2 - - - +
270A VAL* 3.1 33.9 + - + +
271A PRO 3.4 0.6 - - - -
272A HIS* 1.3 75.2 - - - +
274A GLU* 1.3 62.4 + - - +
275A SER* 3.3 4.5 + - - -
276A ALA* 3.6 25.6 + - + +
277A TRP* 3.4 16.8 + - - -
793B ASN* 3.0 26.2 + - - +
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Residues in contact with GLU 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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272A HIS 3.3 5.8 + - - +
273A ASN* 1.3 71.2 + - - +
275A SER* 1.3 60.2 + - - +
277A TRP* 3.1 8.1 + - + +
278A ASN* 2.9 51.4 + - - +
310A TYR* 3.8 34.7 + - + +
779B SER* 3.6 20.5 + - - +
780B ARG* 2.9 31.9 + - - -
789B GLN* 5.0 1.6 + - - -
792B CYS* 3.7 9.2 - - - -
793B ASN* 4.4 5.7 + - - +
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Residues in contact with SER 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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232A ARG 4.5 1.1 - - - -
234A ASN* 2.9 33.1 + - - +
237A TRP* 3.4 29.6 - - - -
273A ASN* 3.3 7.1 + - - -
274A GLU* 1.3 77.5 - - - +
276A ALA* 1.3 57.9 + - - +
278A ASN* 3.3 4.7 + - - +
279A TYR* 2.9 28.8 + - - +
735B TRP* 4.6 2.4 - - - -
792B CYS* 3.7 4.2 - - - -
793B ASN* 2.8 24.9 + - - +
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Residues in contact with ALA 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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237A TRP* 3.9 29.8 - - + -
263A THR* 3.1 14.9 - - + +
266A MET* 4.4 8.7 - - + -
267A ILE* 3.7 24.0 - - + +
273A ASN* 3.6 18.6 + - + +
274A GLU 3.3 0.4 - - - -
275A SER* 1.3 78.2 - - - +
277A TRP* 1.3 58.2 + - - +
279A TYR* 3.2 1.6 + - - +
280A LEU* 2.9 24.1 + - - +
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Residues in contact with TRP 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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267A ILE* 3.5 44.1 - - + +
270A VAL 5.5 0.2 - - - -
271A PRO* 2.9 24.9 + - + -
273A ASN 3.4 22.0 - - - -
274A GLU* 3.1 8.2 + - - +
276A ALA* 1.3 78.6 - - - +
278A ASN* 1.3 67.2 + - - +
280A LEU* 3.3 7.1 + - + +
281A LYS* 3.1 23.8 + - - +
299A LEU* 3.9 21.1 - - + -
302A LEU* 6.1 1.1 - - + -
306A HIS 5.2 3.4 - - - -
308A SER* 4.5 2.7 - - - -
310A TYR* 3.5 36.0 - + + +
311A LEU* 3.6 47.1 - - + -
314A PHE* 3.8 32.8 - + + -
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Residues in contact with ASN 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ASN* 5.0 1.2 + - - +
274A GLU* 2.9 51.5 + - - +
275A SER* 3.6 5.8 - - - +
277A TRP* 1.3 78.9 - - - +
279A TYR* 1.3 58.1 + - - +
281A LYS* 3.5 21.9 + - - +
282A GLY* 2.8 23.6 + - - -
735B TRP* 3.5 20.7 - - + +
736B GLU* 5.3 8.9 + - + +
776B TRP* 5.7 3.2 - - - -
780B ARG* 4.5 4.4 - - - +
792B CYS* 3.6 17.8 - - - +
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Residues in contact with TYR 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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237A TRP* 3.5 46.4 - + + -
240A ARG* 3.7 8.1 - - - +
241A TYR* 4.1 11.0 - + + -
244A ILE* 3.5 4.3 - - - +
250A TYR* 2.7 30.2 + - - -
259A GLU* 2.6 30.7 + - + -
263A THR* 3.1 27.6 - - - -
275A SER 2.9 17.0 + - - +
276A ALA 3.6 4.3 - - - +
278A ASN* 1.3 74.4 - - - +
280A LEU* 1.3 66.0 + - - +
282A GLY 3.1 0.2 + - - -
283A ILE* 3.0 46.8 + - + +
735B TRP* 3.5 19.7 - + + -
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Residues in contact with LEU 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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260A VAL* 4.2 26.9 - - + +
263A THR* 3.8 18.2 - - + -
264A LEU* 4.1 15.5 - - + -
267A ILE* 3.9 20.6 - - + -
276A ALA 2.9 13.2 + - - +
277A TRP* 3.5 17.3 - - + +
279A TYR* 1.3 80.1 - - - +
281A LYS* 1.3 63.1 + - - +
283A ILE* 3.4 7.4 - - + +
284A LEU* 3.3 41.1 - - + +
295A LEU* 4.5 9.6 - - + -
299A LEU* 5.1 0.7 - - + -
314A PHE* 3.9 24.5 - - + -
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Residues in contact with LYS 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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277A TRP 3.1 9.0 + - - +
278A ASN* 3.8 25.1 + - - +
280A LEU* 1.3 78.9 - - - +
282A GLY* 1.3 59.1 + - - +
284A LEU 3.1 1.0 + - - -
285A GLN* 2.8 55.2 + - + +
289A LEU* 4.3 17.2 - - + +
314A PHE* 3.7 20.6 - - + -
317A ASP* 3.7 26.7 + - + +
736B GLU 5.8 3.2 + - - -
772B SER* 6.5 1.3 - - - +
775B GLN* 3.7 27.9 - - - +
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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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241A TYR* 4.4 1.8 - - - -
278A ASN 2.8 16.9 + - - -
279A TYR 3.1 4.0 + - - -
281A LYS* 1.3 79.8 - - - +
283A ILE* 1.3 60.4 + - - +
284A LEU 3.5 0.3 + - - -
285A GLN* 3.5 30.2 + - - +
286A ASP* 4.6 2.8 - - - +
735B TRP* 3.7 21.1 - - - -
1C GLC 3.7 12.1 + - - -
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Residues in contact with ILE 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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241A TYR* 4.0 9.4 - - + -
250A TYR* 3.5 39.4 - - + +
256A LEU* 3.7 17.1 - - + +
259A GLU* 3.9 27.1 - - + +
260A VAL* 4.0 23.1 - - + +
263A THR* 4.7 0.4 - - - +
279A TYR* 3.0 39.4 + - + +
280A LEU* 3.4 18.2 - - - +
282A GLY* 1.3 75.8 - - - +
284A LEU* 1.3 64.2 + - + +
286A ASP* 5.4 0.7 - - - -
287A ARG* 5.9 1.7 - - - +
292A TYR* 4.9 1.9 + - - -
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Residues in contact with LEU 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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256A LEU* 4.0 7.2 - - + -
260A VAL* 3.9 24.2 - - + -
280A LEU* 3.3 27.6 - - + +
281A LYS 3.1 1.4 + - - -
283A ILE* 1.3 88.2 - - + +
285A GLN* 1.3 64.3 - - - +
286A ASP 3.4 3.4 + - - -
287A ARG* 3.4 4.3 + - - -
288A GLY 3.1 21.7 + - - -
289A LEU* 3.7 18.4 - - + -
292A TYR* 3.7 45.4 - - + -
295A LEU* 3.4 33.0 - - + -
314A PHE* 4.7 0.2 - - + -
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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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281A LYS* 2.8 39.1 + - + +
282A GLY* 3.5 11.8 + - - +
284A LEU* 1.3 78.8 - - - +
286A ASP* 1.3 69.7 + - - +
288A GLY* 3.1 12.7 + - - +
289A LEU* 4.2 11.4 - - + -
735B TRP 3.0 25.9 + - - +
736B GLU 5.8 0.2 - - - -
769B ASN* 5.8 2.0 - - - +
771B LYS* 5.8 4.1 + - - +
772B SER* 4.5 12.1 - - - -
1C GLC 3.0 23.2 + - - +
2C FRU 3.4 17.0 + - - +
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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