Contacts of the helix formed by residues 316 - 340 (chain B) in PDB entry 5TQB
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 GLU 316 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B GLU* 3.1 1.4 - - + -
315B PRO* 1.3 99.2 - - + +
317B ALA* 1.3 64.6 + - - +
318B TRP* 3.1 5.3 + - - +
319B LYS* 3.1 56.0 + - + +
320B ASP* 3.8 8.4 + - - +
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Residues in contact with ALA 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B GLU* 4.0 12.3 - - + +
314B GLU* 3.4 31.2 + - + +
315B PRO 3.5 0.2 - - - -
316B GLU* 1.3 78.4 - - - +
318B TRP* 1.3 61.9 + - - +
320B ASP* 3.2 13.1 + - - +
321B THR* 3.1 21.7 + - - +
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Residues in contact with TRP 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B GLY 3.6 18.6 - - - +
305B GLU* 3.6 18.7 + - + +
306B ARG* 3.7 61.0 - - + +
309B SER* 4.2 7.6 + - - -
314B GLU 5.0 0.4 + - - -
315B PRO 3.1 29.4 + - - -
316B GLU* 4.2 1.5 + - - -
317B ALA* 1.3 79.5 - - - +
319B LYS* 1.3 100.3 + - + +
321B THR* 3.2 4.2 + - - -
322B TRP* 2.9 63.2 + + - +
360B GLU 4.1 17.0 - - - -
361B LEU 4.8 3.4 - - - -
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Residues in contact with LYS 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B GLU* 3.1 38.3 + - + +
318B TRP* 1.3 122.0 - - + +
320B ASP* 1.3 57.2 + - - +
322B TRP* 3.3 4.8 + - - +
323B ARG* 2.9 54.3 + - - +
360B GLU 5.4 0.7 - - - -
361B LEU* 3.9 36.2 - - + +
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Residues in contact with ASP 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B GLU* 3.8 8.7 + - - +
317B ALA* 3.2 13.1 + - - +
319B LYS* 1.3 78.0 - - - +
321B THR* 1.3 62.0 + - - +
323B ARG* 3.3 28.6 + - - +
324B SER* 3.2 22.7 + - - -
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Residues in contact with THR 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B LEU* 5.8 1.3 - - + -
298B ARG* 3.4 25.4 - - + +
301B LEU* 4.1 19.1 - - + -
302B GLY* 3.9 12.1 - - - +
305B GLU* 2.7 27.0 + - - +
317B ALA 3.1 7.6 + - - -
318B TRP* 3.2 8.9 + - - -
320B ASP* 1.3 79.3 - - - +
322B TRP* 1.3 56.1 + - - +
324B SER* 2.9 19.1 + - - +
325B SER* 3.2 14.2 + - - -
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Residues in contact with TRP 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B ARG 3.9 0.9 - - - -
299B TYR* 2.8 68.2 + + - +
302B GLY* 3.6 24.7 - - - -
303B GLU* 3.9 17.5 - - + -
306B ARG* 3.7 22.9 - - - -
318B TRP* 2.9 31.8 + + - +
319B LYS* 3.8 6.7 - - - +
321B THR* 1.3 74.7 - - - +
323B ARG* 1.3 65.6 + - - +
325B SER* 3.3 4.0 + - - -
326B ARG* 3.0 22.5 + - - +
356B SER* 4.5 2.5 - - - -
357B ILE* 3.7 40.1 - - + +
360B GLU* 3.5 33.0 - - + -
361B LEU 4.8 3.6 - - - +
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Residues in contact with ARG 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LYS* 2.9 52.8 + - - +
320B ASP* 3.3 31.2 + - - +
322B TRP* 1.3 77.4 - - - +
324B SER* 1.3 59.2 - - - +
326B ARG* 3.1 33.0 + - - +
327B LYS* 3.1 39.8 + - - +
357B ILE* 5.4 0.9 - - + -
361B LEU* 4.8 23.3 - - - +
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Residues in contact with SER 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B ARG* 4.3 16.3 + - - +
320B ASP 3.2 10.0 + - - -
321B THR* 2.9 20.4 + - - +
323B ARG* 1.3 74.5 - - - +
325B SER* 1.3 63.4 + - - +
327B LYS* 3.2 16.5 + - - +
328B TRP* 3.0 36.5 + - - -
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Residues in contact with SER 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B GLY* 2.6 27.6 + - - -
298B ARG* 3.8 10.5 - - - +
299B TYR* 3.3 23.5 + - - +
321B THR 3.2 15.2 + - - -
322B TRP* 3.4 13.9 - - - -
323B ARG 3.2 0.2 - - - -
324B SER* 1.3 75.8 - - - +
326B ARG* 1.3 62.8 + - - +
328B TRP* 3.3 2.3 + - - +
329B LEU* 3.0 29.6 + - - +
357B ILE* 3.6 9.3 - - - +
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Residues in contact with ARG 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B TRP 3.0 12.0 + - - +
323B ARG* 3.1 36.1 + - - +
325B SER* 1.3 77.2 - - - +
327B LYS* 1.3 61.9 + - - +
329B LEU* 3.9 4.4 - - - +
330B ARG* 2.8 75.5 + - - +
354B ILE* 4.1 22.4 - - + +
357B ILE* 3.9 24.2 - - + +
358B ILE* 5.2 7.6 - - + +
361B LEU 5.9 0.8 + - - -
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Residues in contact with LYS 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B TRP* 5.5 0.7 - - - -
323B ARG* 3.1 31.4 + - - +
324B SER* 3.2 17.3 + - - +
326B ARG* 1.3 81.8 - - + +
328B TRP* 1.3 67.1 + - + +
330B ARG* 3.6 6.7 + - - +
331B GLN* 3.1 24.1 + - - +
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Residues in contact with TRP 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ARG* 4.6 18.4 - - - +
277B THR* 3.6 27.1 - - - -
278B GLU* 4.2 7.9 - - + -
281B ILE* 3.5 26.2 - - + -
290B VAL 3.7 11.7 - - - -
291B TRP* 3.3 53.6 - + - +
294B GLY* 3.6 12.1 - - - -
295B GLY* 3.6 20.6 - - - +
298B ARG* 3.2 43.9 - - - +
324B SER* 3.0 32.0 + - - +
327B LYS* 1.3 82.1 - - + +
329B LEU* 1.3 57.1 + - - +
331B GLN* 3.3 4.0 + - - +
332B CYS* 2.8 27.0 + - - +
402B EDO 6.3 0.2 - - - -
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Residues in contact with LEU 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B TYR* 4.1 25.1 - - + +
295B GLY* 4.0 19.7 - - - +
299B TYR* 5.4 0.4 - - + -
325B SER* 3.0 32.6 + - - +
326B ARG 3.3 0.9 + - - +
328B TRP* 1.3 73.2 - - - +
330B ARG* 1.3 66.8 + - - +
332B CYS* 3.2 4.0 + - + +
333B LEU* 3.0 30.0 + - - +
350B ALA* 4.2 19.5 - - + +
353B LEU* 3.5 37.5 - - + -
354B ILE* 3.6 25.6 - - + +
357B ILE* 4.5 4.5 - - + -
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Residues in contact with ARG 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ARG* 2.8 63.7 + - + +
327B LYS* 3.8 7.4 - - - +
329B LEU* 1.3 75.3 - - - +
331B GLN* 1.3 57.4 + - - +
333B LEU* 3.2 6.2 + - - +
334B LYS* 3.0 27.7 + - - +
354B ILE* 3.7 22.2 - - + +
358B ILE* 3.9 23.8 - - - +
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Residues in contact with GLN 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B TRP* 3.5 36.6 - - + +
327B LYS 3.1 18.7 + - - +
328B TRP 3.5 4.9 - - - +
329B LEU 3.2 0.2 - - - -
330B ARG* 1.3 73.8 - - - +
332B CYS* 1.3 65.2 + - - +
334B LYS* 3.5 30.2 + - - +
335B VAL* 3.0 37.6 + - - +
403B EDO 3.0 35.6 + - - -
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Residues in contact with CYS 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B VAL* 3.7 32.8 - - - +
291B TRP* 3.6 19.3 - - + -
292B TYR* 4.0 19.3 - - - +
328B TRP 2.8 14.2 + - - +
329B LEU* 3.2 14.8 + - + +
331B GLN* 1.3 76.9 - - - +
333B LEU* 1.3 58.6 + - - +
335B VAL* 3.4 2.3 + - - +
336B PHE* 2.8 31.2 + - - +
346B LEU* 4.0 9.2 - - - -
350B ALA* 4.6 11.0 - - - -
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Residues in contact with LEU 333 (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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329B LEU 3.0 24.7 + - - +
330B ARG* 3.7 6.7 - - - +
332B CYS* 1.3 77.2 - - - +
334B LYS* 1.3 65.4 + - - +
336B PHE* 3.2 15.0 - - + +
337B GLU* 3.0 37.3 + - + +
347B GLY* 3.6 31.2 - - - +
350B ALA* 3.3 27.6 - - + -
351B LYS* 4.3 20.9 - - + +
354B ILE* 3.9 16.4 - - + -
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Residues in contact with LYS 334 (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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330B ARG 3.0 14.5 + - - +
331B GLN* 3.5 35.1 + - - +
333B LEU* 1.3 78.2 - - - +
335B VAL* 1.3 63.5 + - + +
337B GLU* 3.2 13.5 + - - +
338B ALA* 3.1 21.9 + - + +
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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
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285B ASP 3.9 15.3 - - - +
286B LEU* 3.7 39.9 - - + +
287B SER 4.7 0.2 - - - +
288B VAL* 3.9 10.5 - - + +
291B TRP* 4.0 9.0 - - + +
331B GLN* 3.0 34.6 + - - +
332B CYS 3.9 2.9 - - - +
334B LYS* 1.3 73.6 - - + +
336B PHE* 1.3 59.6 + - - +
338B ALA* 4.3 6.3 - - + -
339B GLU* 2.9 41.0 + - + +
403B EDO 4.1 2.0 - - - +
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Residues in contact with PHE 336 (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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288B VAL* 3.8 26.4 - - + +
332B CYS* 2.8 19.0 + - - +
333B LEU* 3.2 19.5 - - + +
335B VAL* 1.3 76.6 - - - +
337B GLU* 1.3 67.3 + - + +
340B GLU* 3.1 3.5 + - - -
341B TYR* 3.0 63.7 + + + +
343B ASP 3.4 31.0 - - - -
344B GLU* 4.5 6.1 - - + -
346B LEU* 4.6 4.7 - - + -
347B GLY* 3.7 24.0 - - - -
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Residues in contact with GLU 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B LEU* 3.0 31.0 + - + +
334B LYS* 3.2 10.4 + - - +
336B PHE* 1.3 81.4 - - + +
338B ALA* 1.3 63.1 + - - +
340B GLU* 3.1 20.6 + - - +
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Residues in contact with ALA 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B LEU* 6.1 2.9 - - + -
334B LYS* 3.1 14.4 + - + +
335B VAL* 3.4 8.7 + - + +
337B GLU* 1.3 80.3 - - - +
339B GLU* 1.3 69.3 + - + +
340B GLU* 3.6 6.4 + - - +
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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
----------------------------------------------------------
37A LYS* 3.3 25.9 + - - -
47A LYS* 2.9 39.3 + - - -
286B LEU* 4.3 26.5 - - + +
288B VAL* 4.8 7.4 - - + -
335B VAL* 2.9 36.1 + - + +
336B PHE 4.3 1.1 - - - +
338B ALA* 1.3 82.6 - - + +
340B GLU* 1.3 71.8 + - - +
341B TYR* 4.5 5.8 - - + +
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Residues in contact with GLU 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LYS* 3.5 10.7 - - - +
336B PHE 3.1 3.5 + - - -
337B GLU* 3.1 17.8 + - - +
338B ALA 4.4 5.2 - - - +
339B GLU* 1.3 81.5 - - - +
341B TYR* 1.3 67.4 + - - +
342B GLU* 3.8 7.8 - - - +
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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