Contacts of the helix formed by residues 329 - 352 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LYS* 5.8 1.1 - - - -
311B LEU* 3.4 7.9 - - - -
327B ASN 3.4 6.1 + - - -
328B VAL* 1.3 77.9 - - - +
330B THR* 1.3 63.9 + - - +
331B SER* 3.4 5.0 + - - -
332B THR* 3.4 17.1 + - - +
333B ARG* 3.1 18.2 + - - +
401B VAL* 5.0 3.2 - - - +
405B GLU* 2.7 39.1 + - - -
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Residues in contact with THR 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LYS* 3.0 29.5 + - - +
32A GLU* 3.4 29.6 + - - +
311B LEU* 3.2 21.9 - - + +
329B SER* 1.3 75.3 - - - +
331B SER* 1.3 68.9 + - - +
333B ARG* 3.8 14.3 + - - +
334B THR* 3.0 26.4 + - - -
405B GLU* 4.1 0.9 + - - -
411B THR 4.8 5.4 + - - -
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Residues in contact with SER 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B SER* 3.1 2.1 + - - -
330B THR* 1.3 80.3 + - - +
332B THR* 1.3 67.0 + - - +
334B THR* 2.9 15.6 + - - -
335B VAL* 3.0 15.3 + - - +
401B VAL* 5.1 0.2 - - - -
405B GLU* 3.1 21.0 + - - +
411B THR 4.1 2.5 + - - -
412B LEU* 3.3 21.7 - - - +
413B ALA 2.8 45.4 + - - -
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Residues in contact with THR 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B LEU 4.3 6.3 - - - +
241B GLY* 2.5 34.4 + - - +
242B PHE* 3.5 35.2 - - + -
328B VAL* 3.6 3.1 - - - +
329B SER* 3.4 24.1 + - - +
331B SER* 1.3 84.4 - - - +
333B ARG* 1.3 63.0 + - - +
335B VAL* 3.5 4.8 + - - +
336B MET* 3.0 29.8 + - - +
401B VAL* 5.6 3.4 - - + -
413B ALA 4.9 5.6 - - - +
414B HIS* 5.7 0.9 - - + -
415B VAL* 5.1 6.1 - - + +
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Residues in contact with ARG 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B TRP* 4.1 18.7 + - + +
281B PRO* 4.3 11.7 - - - +
311B LEU* 3.3 55.1 + - + +
312B MET* 4.2 18.4 - - + -
328B VAL* 3.8 14.6 - - + -
329B SER 3.1 19.1 + - - +
330B THR* 3.8 14.3 + - - +
331B SER 3.0 0.2 + - - -
332B THR* 1.3 76.8 + - - +
334B THR* 1.3 63.3 + - - +
336B MET* 3.1 6.4 + - - +
337B VAL* 2.8 47.8 + - + +
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Residues in contact with THR 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B THR* 3.0 15.6 + - - -
331B SER 2.9 9.0 + - - -
333B ARG* 1.3 81.4 + - - +
335B VAL* 1.3 63.4 + - + +
337B VAL* 3.2 8.2 + - - +
338B GLU* 3.2 26.3 + - + +
412B LEU* 3.6 23.5 - - + +
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Residues in contact with VAL 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ILE* 4.2 9.2 - - + -
242B PHE* 4.1 13.5 - - + -
331B SER 3.0 16.4 + - - +
332B THR* 3.7 10.5 - - - +
334B THR* 1.3 76.8 - - + +
336B MET* 1.3 62.0 + - - +
338B GLU* 3.5 7.9 + - - +
339B GLU* 3.2 28.0 + - + +
370B TYR* 4.0 6.5 - - - +
412B LEU* 4.4 11.4 - - + -
414B HIS* 3.4 53.8 - - + +
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Residues in contact with MET 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ILE* 3.6 35.8 - - + +
241B GLY 5.2 0.9 - - - +
242B PHE* 3.5 18.6 - - + -
243B LEU* 3.2 57.0 - - + +
248B TRP* 3.9 8.5 - - + -
312B MET* 3.8 21.1 - - + +
328B VAL* 5.4 1.3 - - - -
332B THR 3.0 21.5 + - - +
333B ARG* 3.6 3.8 - - - +
335B VAL* 1.3 74.7 - - - +
337B VAL* 1.3 65.8 + - + +
338B GLU 3.1 2.0 - - - -
339B GLU* 3.1 8.1 + - - +
340B PHE* 3.0 31.3 + - + -
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Residues in contact with VAL 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B PHE 5.7 0.7 - - - +
276B SER* 4.7 7.9 - - - +
280B TRP* 4.0 30.7 - - + +
312B MET* 6.0 1.1 - - - -
333B ARG* 2.8 35.7 + - + +
334B THR* 3.2 7.6 + - - +
336B MET* 1.3 72.2 - - + +
338B GLU* 1.3 61.5 + - - +
340B PHE* 3.4 12.8 + - + +
341B LYS* 3.2 46.6 + - - +
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Residues in contact with GLU 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B THR* 3.2 15.2 + - + +
335B VAL* 3.6 11.9 - - - +
337B VAL* 1.3 79.9 - - - +
339B GLU* 1.3 60.8 + - + +
341B LYS* 3.3 18.2 + - - +
342B GLN* 2.9 67.5 + - - +
369B LYS* 5.1 6.3 + - - +
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Residues in contact with GLU 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B TRP* 3.5 25.0 + - + -
233B ARG* 3.1 49.2 + - + +
235B ILE* 4.5 19.3 - - + -
335B VAL* 3.2 22.4 - - + +
336B MET* 3.1 9.9 + - - +
338B GLU* 1.3 78.6 - - - +
340B PHE* 1.3 60.3 + - - +
342B GLN* 3.8 7.5 + - - +
343B GLY 2.9 22.0 + - - -
364B PRO* 4.3 8.1 - - - +
369B LYS* 3.5 23.2 + - - -
414B HIS* 5.9 1.2 - - - -
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Residues in contact with PHE 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B TRP* 3.7 15.5 - + - -
235B ILE* 5.3 0.2 - - + -
248B TRP* 3.8 35.9 - + - -
251B LEU* 4.0 13.5 - - + -
271B PHE* 3.8 15.7 - + - -
272B PHE* 3.5 22.9 - + + +
275B PHE* 3.5 29.8 - - + -
276B SER* 3.8 18.4 - - - +
280B TRP* 4.6 7.4 - + - -
312B MET* 4.3 20.4 - - + -
336B MET* 3.0 23.7 + - + -
337B VAL* 3.6 15.0 - - + +
338B GLU 3.3 0.2 - - - -
339B GLU* 1.3 76.3 - - - +
341B LYS* 1.3 57.4 + - - +
343B GLY 3.3 0.9 + - - -
344B LEU* 3.0 22.7 + - - +
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Residues in contact with LYS 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B SER* 3.8 33.4 - - - +
277B LYS* 6.0 2.5 - - - +
337B VAL* 3.2 27.9 + - - +
338B GLU* 3.7 22.5 + - - +
339B GLU 3.2 0.2 - - - -
340B PHE* 1.3 77.1 - - - +
342B GLN* 1.3 67.7 + - - +
343B GLY 3.0 1.3 - - - -
344B LEU* 3.0 9.1 + - + +
345B ALA* 3.0 21.7 + - - +
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Residues in contact with GLN 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ARG* 4.8 13.3 - - - +
338B GLU* 2.9 53.2 + - - +
339B GLU* 4.0 14.4 + - - +
341B LYS* 1.3 77.6 - - - +
343B GLY* 1.3 60.2 + - - +
345B ALA* 3.5 9.1 + - + +
346B VAL* 3.3 30.0 + - + +
369B LYS* 4.5 15.2 - - - +
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Residues in contact with GLY 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B TRP* 4.8 2.2 - - - -
233B ARG* 5.2 1.5 - - - +
272B PHE* 3.7 22.7 - - - -
339B GLU 2.9 18.7 + - - -
340B PHE 3.6 2.2 - - - -
341B LYS 3.0 0.2 - - - -
342B GLN* 1.3 75.2 - - - +
344B LEU* 1.3 59.7 + - - +
346B VAL* 3.2 2.6 + - - +
347B THR* 2.9 34.3 + - - +
360B LEU* 4.4 10.3 - - - -
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Residues in contact with LEU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B HIS* 3.8 23.1 - - + +
272B PHE* 3.5 17.2 - - + +
273B LEU* 3.7 37.7 - - + +
276B SER* 3.9 16.2 - - - +
277B LYS* 4.0 17.0 - - - +
340B PHE 3.0 10.5 + - - +
341B LYS* 3.0 10.5 + - + +
343B GLY* 1.3 71.5 - - - +
345B ALA* 1.3 66.3 + - - +
347B THR* 4.0 2.5 - - - -
348B ASP* 3.1 25.5 + - + +
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Residues in contact with ALA 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B LYS 3.0 11.7 + - - +
342B GLN* 3.6 13.7 - - + +
343B GLY 3.1 0.2 - - - -
344B LEU* 1.3 81.5 - - - +
346B VAL* 1.3 64.1 + - + +
348B ASP* 3.4 5.6 - - - +
349B GLU* 3.4 27.9 + - - +
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Residues in contact with VAL 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ARG* 6.2 1.8 - - - +
342B GLN* 3.3 16.2 - - + +
343B GLY* 3.2 8.6 + - - +
344B LEU 3.2 0.2 - - - -
345B ALA* 1.3 75.6 - - + +
347B THR* 1.3 67.6 + - - +
348B ASP 3.1 1.3 - - - -
349B GLU* 2.9 22.6 + - - +
350B ILE* 3.1 19.8 + - + +
355B SER* 5.3 0.2 - - - -
359B LYS* 4.0 36.3 - - + +
360B LEU* 3.7 35.2 - - + +
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Residues in contact with THR 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B VAL* 4.4 2.7 - - + -
269B HIS* 2.7 39.2 + - - -
272B PHE* 3.6 25.6 - - + -
343B GLY 2.9 17.2 + - - +
344B LEU* 3.7 5.9 + - - -
346B VAL* 1.3 75.1 - - - +
348B ASP* 1.3 62.5 + - - +
350B ILE* 3.2 10.8 + - - +
351B LEU* 3.0 26.9 + - - +
357B TRP* 4.3 13.0 - - + -
360B LEU* 3.9 20.9 - - + -
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Residues in contact with ASP 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B HIS* 3.7 21.3 + - + -
344B LEU* 3.1 24.0 + - + +
345B ALA* 3.4 7.4 - - - +
346B VAL 3.1 0.2 - - - -
347B THR* 1.3 80.0 + - - +
349B GLU* 1.3 64.7 + - - +
351B LEU* 3.5 3.7 + - - +
352B GLN* 3.4 37.4 + - - +
354B LYS* 5.5 1.9 + - - -
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Residues in contact with GLU 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B ALA* 3.4 19.0 - - - +
346B VAL* 2.9 11.1 + - - +
348B ASP* 1.3 79.1 - - + +
350B ILE* 1.3 62.4 + - - +
352B GLN* 3.0 13.5 + - - -
354B LYS* 3.0 46.0 + - + +
355B SER* 3.3 30.8 + - - +
359B LYS* 3.4 26.4 + - - +
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Residues in contact with ILE 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B TYR* 3.2 21.8 - - + -
346B VAL* 3.1 18.5 + - + +
347B THR* 3.2 19.3 + - - +
349B GLU* 1.3 75.5 - - - +
351B LEU* 1.3 58.4 + - + +
353B GLY* 3.1 15.9 + - - -
355B SER* 3.2 27.7 - - - +
356B ASP* 3.7 10.5 - - - +
357B TRP* 3.5 72.7 - - + +
360B LEU* 4.7 2.5 - - + -
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Residues in contact with LEU 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ASP* 5.3 1.6 - - - +
37B TYR* 3.8 46.8 + - + -
265B SER* 4.3 8.3 - - - +
266B THR* 3.9 24.9 - - + -
269B HIS* 3.7 37.2 - - + -
347B THR 3.0 18.8 + - - +
348B ASP* 4.2 4.7 - - - +
350B ILE* 1.3 78.1 - - + +
352B GLN* 1.3 59.9 + - + +
353B GLY 3.3 1.6 - - - -
357B TRP* 4.4 17.9 - - + -
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Residues in contact with GLN 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B TYR* 4.2 0.9 - - - -
348B ASP* 3.4 30.6 + - - +
349B GLU 3.0 7.3 + - - +
351B LEU* 1.3 79.7 - - + +
353B GLY* 1.3 56.2 + - - +
354B LYS* 2.9 45.8 + - + +
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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