Contacts of the helix formed by residues 329 - 351 (chain A) in PDB entry 4LT6
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 329 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A GLY* 5.1 0.4 - - - -
311A LEU* 3.4 6.0 - - - +
327A ASN 3.1 8.6 + - - -
328A VAL* 1.3 90.3 - - - +
330A THR* 1.3 63.1 + - - +
331A SER 3.6 3.1 + - - -
332A THR* 3.3 19.4 + - - +
333A ARG* 3.2 7.6 + - - +
398A ARG* 5.9 4.9 - - - -
401A VAL* 4.1 10.8 - - - +
402A GLY* 6.3 0.4 - - - -
405A GLU* 2.8 33.1 + - - -
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Residues in contact with THR 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A LEU* 3.6 24.0 - - + -
329A SER* 1.3 72.9 - - - +
331A SER* 1.3 64.9 + - - +
333A ARG* 3.1 15.1 + - - +
334A THR* 2.8 34.4 + - - -
405A GLU* 3.7 15.7 + - + +
411A THR 5.8 0.2 + - - -
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Residues in contact with SER 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A SER* 4.1 1.1 - - - -
330A THR* 1.3 81.7 + - - +
332A THR* 1.3 57.0 + - - +
334A THR* 3.1 4.2 + - - -
335A VAL* 2.8 33.1 + - - +
405A GLU* 3.0 24.2 + - - +
411A THR 4.5 1.7 + - - -
412A LEU* 3.5 20.0 - - - +
413A ALA 2.9 45.2 + - - -
414A HIS* 5.3 0.4 - - - -
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Residues in contact with THR 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A LEU 4.1 8.1 - - - +
241A GLY* 2.7 34.8 + - - +
242A PHE* 3.8 35.0 - - + -
328A VAL* 3.4 2.8 - - - +
329A SER* 3.2 28.0 + - - +
331A SER* 1.3 78.7 - - - +
333A ARG* 1.3 62.3 + - - +
335A VAL* 3.9 2.5 - - - +
336A MET* 3.0 30.5 + - - +
401A VAL* 5.7 4.7 - - + -
414A HIS* 6.2 1.8 - - + -
415A VAL* 5.5 4.7 - - + +
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Residues in contact with ARG 333 (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 TRP* 4.0 25.8 + - + +
281A PRO* 5.0 8.5 - - - +
311A LEU* 3.2 54.9 + - + +
312A MET* 3.8 29.6 - - + +
328A VAL* 3.9 8.7 - - + -
329A SER 3.2 14.3 + - - +
330A THR* 3.1 22.9 + - - +
332A THR* 1.3 76.5 + - - +
334A THR* 1.3 63.9 + - - +
336A MET* 3.8 1.8 - - - +
337A VAL* 3.0 36.6 + - - +
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Residues in contact with THR 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A THR* 2.8 19.1 + - - -
331A SER* 3.5 4.5 - - - -
333A ARG* 1.3 84.2 + - - +
335A VAL* 1.3 61.9 + - - +
337A VAL* 3.4 7.2 + - - +
338A GLU* 3.3 41.2 + - - +
412A LEU* 4.0 19.1 - - + -
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Residues in contact with VAL 335 (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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235A ILE* 4.1 11.9 - - + -
242A PHE* 3.9 16.4 - - + -
331A SER 2.8 22.0 + - - +
332A THR* 3.9 4.7 - - - +
334A THR* 1.3 72.2 - - - +
336A MET* 1.3 65.0 + - - +
338A GLU* 3.3 13.5 + - - +
339A GLU* 3.2 25.5 + - + +
370A TYR* 4.2 6.3 - - - +
412A LEU* 4.3 12.1 - - + -
414A HIS* 3.5 52.9 - - + +
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Residues in contact with MET 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ILE* 3.4 31.8 - - + +
241A GLY 5.2 0.7 - - - +
242A PHE* 3.4 21.1 - - + -
243A LEU* 3.1 56.8 - - + +
248A TRP* 3.8 8.7 - - + -
312A MET* 4.0 23.1 - - + +
328A VAL* 5.4 0.9 - - - -
332A THR* 3.0 23.3 + - - +
333A ARG 3.8 3.1 - - - +
335A VAL* 1.3 74.9 - - - +
337A VAL* 1.3 61.8 + - - +
339A GLU* 3.0 8.7 + - - +
340A PHE* 2.9 37.1 + - + -
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Residues in contact with VAL 337 (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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275A PHE 5.4 0.9 - - - +
276A SER* 5.4 4.5 - - - +
280A TRP* 3.8 31.2 - - + +
312A MET* 5.7 0.9 - - + -
333A ARG* 3.0 27.0 + - + +
334A THR* 3.8 7.4 - - - +
335A VAL 3.3 0.2 - - - -
336A MET* 1.3 76.0 - - + +
338A GLU* 1.3 65.1 + - + +
340A PHE* 3.2 17.0 + - + +
341A LYS* 3.1 50.8 + - + +
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Residues in contact with GLU 338 (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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334A THR* 3.3 33.9 + - - +
335A VAL* 3.6 14.8 - - - +
336A MET 3.2 0.4 - - - -
337A VAL* 1.3 81.6 - - + +
339A GLU* 1.3 58.4 + - + +
341A LYS* 3.2 12.7 + - + +
342A GLN* 2.9 29.4 + - - +
412A LEU* 5.7 3.5 - - - +
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Residues in contact with GLU 339 (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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229A TRP* 3.4 26.0 + - + -
233A ARG* 2.3 52.5 + - + +
235A ILE* 4.1 24.9 - - + -
335A VAL* 3.2 18.0 + - + +
336A MET 3.0 8.8 + - - +
338A GLU* 1.3 76.2 - - - +
340A PHE* 1.3 67.5 + - - +
342A GLN* 3.3 5.5 + - - +
343A GLY 2.9 18.5 + - - -
364A PRO* 4.4 9.7 - - - +
414A HIS* 6.1 0.9 - - - -
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Residues in contact with PHE 340 (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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229A TRP* 3.9 16.4 - + - -
248A TRP* 4.2 17.3 - + - -
251A LEU* 4.5 8.3 - - + -
271A PHE* 3.6 31.9 - + - -
272A PHE* 3.6 15.9 - + - +
275A PHE* 3.1 41.7 - + + +
276A SER* 4.0 8.5 - - - -
280A TRP* 4.8 4.3 - + - -
312A MET* 4.0 27.8 - - + -
336A MET* 2.9 23.6 + - + -
337A VAL* 3.3 18.6 - - + +
339A GLU* 1.3 77.5 - - - +
341A LYS* 1.3 62.8 + - - +
343A GLY* 3.1 3.8 + - - -
344A LEU* 3.0 18.2 + - - +
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Residues in contact with LYS 341 (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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276A SER* 3.6 33.2 - - - -
337A VAL* 3.1 36.8 + - + +
338A GLU* 3.6 12.9 - - + +
340A PHE* 1.3 79.0 - - - +
342A GLN* 1.3 65.4 + - - +
344A LEU* 3.1 9.3 + - + +
345A ALA* 3.0 22.6 + - - +
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Residues in contact with GLN 342 (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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229A TRP* 6.3 0.2 - - - +
233A ARG* 4.3 25.0 - - - +
338A GLU 2.9 14.2 + - - +
339A GLU* 3.3 13.7 + - - +
341A LYS* 1.3 75.9 - - - +
343A GLY* 1.3 62.2 + - - +
345A ALA* 3.3 10.6 + - - +
346A VAL* 3.0 50.3 + - - +
359A LYS* 5.8 0.8 + - - +
360A LEU* 5.5 0.4 - - - -
472B ASN* 5.4 2.4 + - - -
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Residues in contact with GLY 343 (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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229A TRP* 5.0 1.3 - - - +
272A PHE* 3.5 28.5 - - - -
339A GLU 2.9 13.8 + - - -
340A PHE 3.1 4.2 + - - -
342A GLN* 1.3 73.4 - - - +
344A LEU* 1.3 55.3 + - - +
346A VAL* 3.9 0.2 - - - -
347A THR* 2.7 41.1 + - - +
360A LEU* 4.1 11.9 - - - -
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Residues in contact with LEU 344 (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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269A HIS* 3.5 26.7 - - + +
272A PHE* 3.4 9.5 - - + +
273A LEU* 3.8 29.6 - - + +
276A SER* 3.8 17.3 - - - +
340A PHE 3.0 12.5 + - - +
341A LYS* 3.3 13.7 - - + +
343A GLY* 1.3 78.0 - - - +
345A ALA* 1.3 55.2 + - - +
347A THR* 3.2 4.6 + - - -
348A ASP* 3.0 33.1 + - - -
468B ARG* 3.5 40.4 - - - +
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Residues in contact with ALA 345 (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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341A LYS 3.0 12.2 + - - +
342A GLN* 3.7 18.4 - - - +
343A GLY 3.2 0.2 - - - -
344A LEU* 1.3 74.1 - - - +
346A VAL* 1.3 67.2 + - + +
348A ASP* 3.2 19.4 + - - +
349A GLU* 3.4 19.4 + - - +
468B ARG* 5.9 1.1 - - - +
469B GLN* 4.8 0.3 + - - -
472B ASN* 3.9 28.9 - - - +
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Residues in contact with VAL 346 (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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342A GLN* 3.0 38.2 + - - +
343A GLY* 4.1 2.5 - - - +
345A ALA* 1.3 75.5 - - + +
347A THR* 1.3 57.7 + - - +
349A GLU* 3.0 14.3 + - - +
350A ILE* 2.8 40.8 + - + +
359A LYS* 3.7 38.1 - - + +
360A LEU* 3.7 34.5 - - + +
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Residues in contact with THR 347 (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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268A VAL* 4.3 0.9 - - + -
269A HIS* 2.9 39.2 + - - -
272A PHE* 3.8 22.3 - - + -
343A GLY 2.7 26.5 + - - +
344A LEU* 3.2 8.1 + - - -
346A VAL* 1.3 74.1 - - - +
348A ASP* 1.3 65.4 + - - +
349A GLU 3.1 0.2 - - - -
350A ILE* 3.6 7.4 - - + +
351A LEU* 3.1 29.3 + - - +
357A TRP* 4.1 25.6 - - + -
360A LEU* 4.4 7.6 - - + -
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Residues in contact with ASP 348 (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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269A HIS* 3.1 15.6 - - - -
344A LEU 3.0 20.4 + - - +
345A ALA* 3.4 12.4 - - - +
346A VAL 3.2 0.4 - - - -
347A THR* 1.3 76.6 + - - +
349A GLU* 1.3 63.2 + - - +
351A LEU* 3.9 2.8 + - - +
352A GLN* 3.5 28.3 + - - +
465B THR* 4.2 9.5 + - + +
468B ARG* 2.7 48.7 + - - +
469B GLN* 3.5 29.4 - - + +
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Residues in contact with GLU 349 (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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345A ALA* 3.7 15.4 - - - +
346A VAL* 3.0 10.2 + - - +
348A ASP* 1.3 78.6 - - - +
350A ILE* 1.3 66.6 + - - +
352A GLN* 3.0 14.0 + - - +
354A LYS* 3.2 28.3 + - + -
355A SER* 2.8 24.5 + - - +
359A LYS* 2.6 38.0 + - - -
469B GLN* 4.0 15.0 - - - +
472B ASN* 4.4 13.0 - - - +
473B ILE* 6.0 1.0 - - - +
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Residues in contact with ILE 350 (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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37A TYR* 3.5 14.8 - - + -
346A VAL* 2.8 35.4 + - + +
347A THR* 3.4 7.4 + - + +
348A ASP 3.4 0.2 - - - -
349A GLU* 1.3 76.7 - - - +
351A LEU* 1.3 59.7 + - + +
352A GLN 2.9 6.2 + - - -
353A GLY* 3.0 13.5 + - - -
355A SER* 3.4 28.4 - - - +
356A ASP* 3.6 19.1 - - - +
357A TRP* 3.6 62.8 - - + +
360A LEU* 4.1 7.0 - - + -
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Residues in contact with LEU 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASP* 5.6 4.3 - - - +
37A TYR* 3.4 42.9 + - + -
265A SER* 4.1 22.9 - - - +
266A THR* 4.4 16.8 - - + +
269A HIS* 3.5 38.4 - - + +
347A THR* 3.1 19.3 + - - +
348A ASP* 3.9 2.9 + - - +
350A ILE* 1.3 73.7 - - - +
352A GLN* 1.3 61.4 + - - +
357A TRP* 4.5 10.5 - - + -
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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
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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