Contacts of the helix formed by residues 277 - 292 (chain A) in PDB entry 1LT8
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 THR 277 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A ALA* 1.3 77.3 - - - +
278A ARG* 1.3 64.7 + - - +
279A TRP* 3.2 14.7 + - + +
280A ASP* 3.1 34.0 + - - +
281A ILE* 3.3 12.5 + - - +
306A HIS* 4.4 1.8 - - - -
357A ILE* 3.4 33.2 - - + -
269B PHE 3.8 9.9 - - - -
270B GLY* 3.9 9.9 - - - -
272B GLU* 3.5 27.4 - - + +
361B ARG* 4.1 3.8 - - - +
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Residues in contact with ARG 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A THR* 1.3 73.5 - - - +
279A TRP* 1.3 90.4 + - + +
281A ILE* 3.3 2.3 + - - +
282A GLN* 3.0 34.7 + - - +
305A TYR* 3.6 45.5 - - + +
306A HIS* 4.7 2.2 - - - -
308A ARG* 3.8 6.8 - - - +
309A ALA* 3.5 20.4 - - + +
328A HIS* 3.1 37.7 + - + -
34B GLU* 2.9 42.2 + - - -
35B LYS* 4.2 5.1 - - - +
268B PRO 5.4 1.8 + - - -
269B PHE* 3.3 26.1 + - - +
272B GLU* 4.4 3.0 + - - -
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Residues in contact with TRP 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A THR* 3.1 14.5 - - + +
278A ARG* 1.3 93.5 - - + +
280A ASP* 1.3 65.3 + - - +
282A GLN* 3.3 30.7 + - - +
283A LYS* 3.1 22.5 + - - +
328A HIS* 4.5 8.3 - + - -
331A TRP* 5.2 2.2 - - - -
332A GLY* 4.1 25.8 - - - -
349A LYS* 5.0 13.5 - - + -
352A TRP* 3.3 61.9 - + + +
353A GLU* 4.5 20.9 - - + +
357A ILE* 6.1 2.7 - - + -
269B PHE* 3.4 49.4 + + + +
270B GLY* 5.2 0.7 - - - -
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Residues in contact with ASP 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A PRO* 5.6 1.8 - - + +
252A HIS* 2.8 21.9 + - + +
276A ALA* 3.5 10.9 - - + -
277A THR* 3.1 29.1 + - - +
279A TRP* 1.3 76.7 - - - +
281A ILE* 1.3 60.1 - - + +
283A LYS* 3.4 9.3 + - - +
284A TYR* 3.0 24.4 + - - +
357A ILE* 5.7 1.7 - - - +
361B ARG* 2.7 32.8 + - - -
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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
----------------------------------------------------------
221A PRO* 4.3 15.5 - - + -
250A ALA* 4.8 0.9 - - - -
276A ALA* 3.8 17.3 - - + -
277A THR 3.3 13.0 + - - +
278A ARG 3.7 6.7 - - - +
279A TRP 3.2 0.8 - - - -
280A ASP* 1.3 76.5 - - + +
282A GLN* 1.3 60.1 + - - +
284A TYR* 3.0 10.2 + - + +
285A ALA* 2.8 27.5 + - - +
302A PHE* 3.6 28.3 - - + -
306A HIS* 3.3 43.7 - - + +
309A ALA* 3.9 6.5 - - + -
310A ILE* 3.6 18.2 - - + -
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Residues in contact with GLN 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ARG* 3.0 23.2 + - - +
279A TRP* 3.3 31.9 + - - +
281A ILE* 1.3 75.6 - - - +
283A LYS* 1.3 62.6 + - - +
285A ALA* 3.3 1.1 + - - -
286A ARG* 3.0 20.3 + - - +
309A ALA* 3.4 25.1 - - + +
312A GLU* 4.2 14.8 - - - +
313A GLU* 2.7 59.0 + - + +
328A HIS* 5.2 1.7 - - - -
331A TRP* 4.4 6.2 - - - -
349A LYS* 3.6 20.2 - - - +
353A GLU* 4.5 6.1 - - - +
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Residues in contact with LYS 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A TRP 3.1 12.3 + - - +
280A ASP* 3.5 11.4 - - - +
282A GLN* 1.3 78.8 - - - +
284A TYR* 1.3 62.7 + - - +
286A ARG* 3.3 6.6 + - - +
287A GLU* 2.9 57.5 + - + +
353A GLU* 5.5 1.9 + - - +
701A CIT 5.8 2.4 + - - -
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Residues in contact with TYR 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A PRO* 3.6 29.2 - - + -
224A SER* 6.0 0.2 - - - -
225A LEU* 4.1 20.4 - - + -
246A SER* 2.9 34.2 + - - -
248A PRO* 3.1 16.8 - - + +
280A ASP 3.0 13.6 + - - +
281A ILE* 3.0 24.7 + - + +
283A LYS* 1.3 77.0 - - - +
285A ALA* 1.3 65.4 + - + +
287A GLU* 3.3 11.7 + - - +
288A ALA* 2.8 27.7 + - + +
296A ILE* 3.5 20.4 - - + +
297A GLY 2.8 28.3 + - - -
302A PHE* 4.1 13.7 - + - -
310A ILE* 4.2 4.7 - - + -
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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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281A ILE 2.8 18.8 + - - +
282A GLN 3.7 4.3 - - - +
284A TYR* 1.3 78.3 - - - +
286A ARG* 1.3 57.6 + - - +
288A ALA* 3.3 6.3 + - - +
289A TYR* 2.9 31.2 + - - +
296A ILE* 4.1 3.3 - - - +
310A ILE* 4.0 28.9 - - + -
313A GLU* 4.2 6.5 - - + -
314A LEU* 3.9 22.9 - - + +
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Residues in contact with ARG 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A GLN 3.0 16.8 + - - +
283A LYS* 3.7 7.6 - - + +
285A ALA* 1.3 78.2 - - - +
287A GLU* 1.3 59.2 + - + +
289A TYR* 3.3 18.1 + - - +
290A ASN* 2.9 48.1 + - - +
313A GLU* 2.8 50.6 + - - +
314A LEU* 3.6 9.0 - - - +
316A PRO* 4.9 3.4 - - - +
317A GLU* 2.7 38.6 + - - -
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Residues in contact with GLU 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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221A PRO 5.9 0.3 - - - -
222A THR* 5.0 12.3 + - - +
225A LEU* 3.6 22.4 - - + +
283A LYS* 2.9 53.1 + - + +
284A TYR* 4.4 4.3 - - - -
286A ARG* 1.3 75.7 - - + +
288A ALA* 1.3 60.0 + - - +
290A ASN* 3.4 9.5 + - - +
291A LEU* 3.0 29.1 + - - +
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Residues in contact with ALA 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A LEU* 3.6 25.5 - - + +
246A SER* 4.4 1.6 - - - +
284A TYR* 2.8 28.0 + - + +
285A ALA* 3.5 5.6 - - - +
287A GLU* 1.3 71.8 - - - +
289A TYR* 1.3 66.0 + - - +
291A LEU* 3.1 6.5 + - - -
292A GLY 3.1 0.2 + - - -
293A VAL* 2.9 38.4 + - + +
296A ILE* 4.0 17.5 - - + -
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Residues in contact with TYR 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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22A ILE* 3.9 22.9 - - + -
285A ALA 2.9 17.0 + - - +
286A ARG* 3.4 15.3 - - - +
288A ALA* 1.3 75.3 - - - +
290A ASN* 1.3 71.1 + - - +
292A GLY* 2.7 21.8 + - - -
293A VAL 3.8 4.3 - - - -
294A ARG* 3.0 55.6 + - - +
296A ILE* 4.1 1.9 - - + +
314A LEU* 3.9 15.9 - - + -
317A GLU* 3.5 34.0 - - + +
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Residues in contact with ASN 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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232A LYS* 5.2 1.4 + - - -
286A ARG* 2.9 38.8 + - - +
287A GLU* 3.7 9.5 - - - +
289A TYR* 1.3 95.6 - - - +
291A LEU* 1.3 60.2 + - - +
292A GLY* 3.4 0.5 + - - -
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Residues in contact with LEU 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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225A LEU* 3.5 35.0 - - + +
228A VAL* 3.8 25.4 - - + -
229A LYS* 3.9 32.8 - - + +
232A LYS* 2.7 43.6 + - + +
244A LEU* 4.2 1.3 - - + +
287A GLU 3.0 17.1 + - - +
288A ALA 3.4 5.6 - - - +
289A TYR 3.1 0.4 - - - -
290A ASN* 1.3 76.5 - - - +
292A GLY* 1.3 56.8 + - - +
293A VAL* 4.1 7.9 - - + -
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Residues in contact with GLY 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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232A LYS* 4.7 2.7 - - - -
244A LEU* 4.0 16.3 + - - +
289A TYR 2.7 12.6 + - - -
290A ASN 3.1 1.4 - - - -
291A LEU* 1.3 80.4 - - - +
293A VAL* 1.3 65.0 + - - +
294A ARG* 3.5 23.0 + - - +
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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