Contacts of the helix formed by residues 324 - 347 (chain B) in PDB entry 3K5N
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 ASP 324 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B ASN* 4.7 0.4 - - - -
186B GLY* 4.3 12.9 - - - -
187B ASP 4.7 1.9 + - - -
319B ARG* 5.8 3.1 - - - +
320B ARG* 2.8 23.5 + - + +
323B GLU* 1.3 80.4 - - + +
325B LYS* 1.3 66.0 + - - +
326B PRO* 3.1 8.9 - - - +
327B ALA* 2.8 34.0 + - + +
328B LEU 3.2 7.3 + - - -
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Residues in contact with LYS 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B MET* 3.3 15.1 - - + +
181B LEU 2.0 34.4 + - - +
182B GLY 3.2 9.7 + - - -
183B PRO* 2.4 27.5 + - - +
185B ASN* 3.6 18.9 - - + +
197B TYR* 3.3 22.0 - - + +
320B ARG 3.2 4.3 + - - -
321B PHE* 2.8 55.6 - - + +
322B ALA* 5.5 1.1 - - - +
324B ASP* 1.3 74.5 - - - +
326B PRO* 1.3 74.9 - - + +
328B LEU* 2.9 15.3 + - - +
329B ALA 3.2 7.6 + - - -
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Residues in contact with PRO 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ASN 3.3 27.4 - - - +
186B GLY* 4.3 0.4 - - - -
187B ASP 3.6 33.0 - - - +
188B ALA* 4.2 8.1 - - + +
191B LEU* 4.4 13.2 - - + +
193B PHE* 4.2 1.9 - - - -
195B LEU* 4.2 11.4 - - + -
197B TYR* 3.5 8.1 - - - +
324B ASP* 3.5 8.7 - - - +
325B LYS* 1.3 96.1 - - + +
327B ALA* 1.3 57.0 + - - +
329B ALA* 3.2 6.4 - - - +
330B THR* 3.1 25.7 + - - -
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Residues in contact with ALA 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B ARG* 3.9 23.6 + - - +
324B ASP* 2.8 30.7 + - - +
326B PRO* 1.3 75.4 - - - +
328B LEU* 1.3 66.8 + - - +
329B ALA 2.9 0.9 - - - -
330B THR* 3.6 13.0 - - - +
331B TYR* 3.0 23.6 + - - +
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Residues in contact with LEU 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B GLU* 4.5 7.9 - - + -
166B TYR* 4.2 17.3 - - + -
167B CYS* 4.2 20.6 - - - -
180B MET* 3.9 7.0 - - + -
317B ILE* 4.2 21.1 - - + +
320B ARG* 4.2 9.8 - - + +
321B PHE* 3.8 39.5 - - + +
324B ASP 3.2 5.5 + - - +
325B LYS* 2.9 16.0 + - - +
327B ALA* 1.3 78.4 - - - +
329B ALA* 1.3 57.8 + - - +
331B TYR* 3.3 17.2 - - + +
332B ASN* 3.0 27.9 + - - +
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Residues in contact with ALA 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B VAL* 4.0 10.6 - - + +
180B MET* 3.7 9.8 - - + +
193B PHE* 3.5 16.4 - - + -
195B LEU* 3.5 31.6 - - + -
325B LYS 3.2 1.2 + - - +
326B PRO* 3.2 12.1 - - + +
328B LEU* 1.3 79.0 - - - +
330B THR* 1.3 67.0 - - - +
331B TYR 3.0 0.7 + - - -
332B ASN* 3.1 3.5 + - - +
333B LEU* 3.1 25.6 + - - +
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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
----------------------------------------------------------
191B LEU* 4.4 6.2 - - - +
193B PHE* 3.4 25.8 - - + -
326B PRO 3.1 14.5 + - - -
327B ALA* 3.9 13.6 - - + +
329B ALA* 1.3 79.3 - - - +
331B TYR* 1.3 63.3 + - - +
333B LEU* 3.8 2.1 + - - +
334B LYS* 3.4 19.1 + - - +
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Residues in contact with TYR 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B GLU* 3.3 27.9 + - - -
317B ILE* 4.7 19.7 - - + +
320B ARG* 4.5 23.6 - - - +
327B ALA 3.0 17.7 + - - +
328B LEU* 3.3 19.1 - - + +
330B THR* 1.3 78.2 - - - +
332B ASN* 1.3 76.4 + - + +
334B LYS* 3.3 14.8 + - - +
335B ASN* 3.4 32.4 + - - +
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Residues in contact with ASN 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ASP* 3.3 32.2 + - - +
158B GLU* 4.2 13.7 - - + +
167B CYS* 3.5 20.5 - - - -
168B ILE 4.0 0.4 - - - -
169B GLY* 3.4 32.1 - - - +
178B VAL* 4.3 4.4 - - - +
328B LEU 3.0 13.8 + - - +
329B ALA* 3.5 5.8 - - - +
331B TYR* 1.3 85.1 - - + +
333B LEU* 1.3 57.4 + - - +
334B LYS 2.9 1.8 - - - -
335B ASN* 2.3 40.2 + - - +
336B CYS* 3.1 2.4 + - - -
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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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170B LEU 4.4 0.2 - - - +
171B GLU* 4.0 26.9 - - + -
176B ARG* 3.8 27.4 - - + +
177B ILE 3.9 18.6 - - - +
178B VAL* 4.2 6.7 - - + +
193B PHE* 3.3 46.0 - - + -
329B ALA 3.1 12.7 + - - +
330B THR 4.2 3.4 - - - +
332B ASN* 1.3 79.6 - - - +
334B LYS* 1.3 50.9 + - - +
336B CYS* 3.2 13.1 + - + +
337B GLU* 2.6 46.8 + - - +
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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
----------------------------------------------------------
303B GLU* 3.1 33.7 + - - -
330B THR 3.4 11.0 + - - +
331B TYR* 3.3 12.7 + - - +
332B ASN 2.8 1.2 + - - -
333B LEU* 1.3 79.6 - - - +
335B ASN* 1.3 57.6 + - - +
337B GLU* 4.0 13.4 + - + +
338B LEU* 2.3 56.6 + - + +
341B GLN* 4.5 8.7 + - - +
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Residues in contact with ASN 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ASP* 3.3 25.2 + - - +
158B GLU* 3.7 10.5 + - - -
293B LEU* 4.0 24.4 - - + +
331B TYR* 3.4 40.4 + - - +
332B ASN* 2.3 31.9 + - - +
334B LYS* 1.3 68.3 - - - +
336B CYS* 1.3 63.0 + - - +
338B LEU* 3.3 15.1 + - - +
339B VAL* 3.5 16.6 + - - +
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Residues in contact with CYS 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B SER* 3.0 31.6 + - - +
156B ASP* 3.7 19.3 - - - -
169B GLY 2.8 36.1 - - - -
171B GLU* 3.2 26.8 - - + +
332B ASN* 3.1 11.1 + - - -
333B LEU* 3.5 15.5 - - + +
335B ASN* 1.3 79.2 - - - +
337B GLU* 1.3 62.9 + - - +
339B VAL* 3.4 1.4 + - - -
340B THR 3.2 11.1 + - - -
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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
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171B GLU* 3.5 22.5 - - - +
176B ARG* 2.8 43.1 + - - +
333B LEU* 2.6 34.2 + - + +
334B LYS* 3.8 13.2 + - - +
335B ASN 3.2 0.4 - - - -
336B CYS* 1.3 77.7 - - - +
338B LEU* 1.3 56.0 + - + +
340B THR* 3.5 1.7 - - - +
341B GLN* 2.4 53.9 + - + +
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Residues in contact with LEU 338 (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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293B LEU* 3.9 16.8 - - + -
297B ALA* 3.9 24.7 - - + -
301B LEU* 4.1 12.2 - - + +
303B GLU* 4.0 23.8 - - + +
334B LYS* 2.3 56.0 + - + +
335B ASN* 3.3 9.4 + - - +
337B GLU* 1.3 78.4 - - + +
339B VAL* 1.3 57.5 + - - +
341B GLN* 3.6 12.3 - - - +
342B ILE* 2.7 41.4 + - + +
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Residues in contact with VAL 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B SER* 3.9 7.9 - - - +
221B ILE* 4.3 4.5 - - + -
222B GLY* 4.0 22.2 - - - +
223B TRP* 4.1 24.7 - - + +
293B LEU* 3.7 19.1 - - + -
335B ASN 3.5 15.0 - - - +
336B CYS* 3.4 5.6 + - - +
337B GLU 3.3 0.2 - - - -
338B LEU* 1.3 74.6 - - - +
340B THR* 1.3 67.4 + - - +
342B ILE* 3.4 6.2 - - - +
343B PHE* 2.7 56.9 + - + -
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Residues in contact with THR 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B TRP* 4.7 5.2 - - + -
154B SER* 3.6 10.2 - - - -
171B GLU* 2.6 40.7 + - - +
221B ILE* 4.1 13.5 - - - +
336B CYS 3.2 4.1 + - - -
337B GLU 3.5 5.6 - - - +
339B VAL* 1.3 83.6 - - - +
341B GLN* 1.3 68.7 + - + +
343B PHE* 3.0 9.6 + - - +
344B HIS* 3.0 38.0 + - + +
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Residues in contact with GLN 341 (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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301B LEU* 4.1 29.4 - - + +
303B GLU* 5.5 3.2 + - - -
334B LYS* 4.5 8.2 + - - +
337B GLU* 2.4 51.2 + - + +
338B LEU* 3.6 16.4 - - - +
340B THR* 1.3 80.7 - - + +
342B ILE* 1.3 64.9 + - - +
344B HIS* 3.3 8.7 + - - +
345B LYS* 3.0 22.2 + - - +
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Residues in contact with ILE 342 (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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223B TRP* 4.0 35.2 - - + -
281B LEU* 4.5 9.0 - - + -
293B LEU* 4.5 10.3 - - + -
296B VAL* 4.3 13.9 - - + -
297B ALA* 4.9 3.6 - - - +
300B LEU* 4.2 11.0 - - + -
301B LEU* 3.6 21.5 - - + -
338B LEU* 2.7 30.2 + - + +
339B VAL* 3.4 5.8 - - - +
341B GLN* 1.3 71.2 - - - +
343B PHE* 1.3 67.2 + - + +
345B LYS* 4.4 4.7 - - - +
346B THR* 2.7 54.7 + - + +
348B ILE* 5.7 0.4 - - + -
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Residues in contact with PHE 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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152B TRP* 3.4 32.4 - + + -
221B ILE* 3.5 32.1 - - + -
222B GLY 4.6 0.7 - - - -
223B TRP* 5.0 1.1 - + - -
275B ILE* 3.7 27.6 - - + -
277B GLY* 4.1 21.5 - - - -
339B VAL* 2.7 49.1 + - + +
340B THR 3.0 9.2 + - - +
342B ILE* 1.3 79.9 - - + +
344B HIS* 1.3 54.9 + - - +
346B THR* 3.0 5.5 + - - -
347B GLU* 2.8 30.3 + - - -
348B ILE* 3.6 25.3 + - + +
349B MET* 4.5 16.6 + - + +
350B PRO* 5.5 0.7 - - - +
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Residues in contact with HIS 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B TRP* 3.6 30.7 - + - -
340B THR* 3.0 36.2 + - + +
341B GLN* 3.5 8.4 - - - +
342B ILE 3.0 0.4 - - - -
343B PHE* 1.3 78.5 - - - +
345B LYS* 1.3 67.7 + - - +
347B GLU* 3.3 22.2 + - - +
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Residues in contact with LYS 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B TRP* 5.1 2.8 - - - -
300B LEU* 4.1 40.3 - - + +
301B LEU* 4.6 13.5 - - + +
341B GLN 3.0 13.7 + - - +
342B ILE 3.9 2.5 - - - +
344B HIS* 1.3 81.4 - - - +
346B THR* 1.3 62.6 + - - +
347B GLU* 4.0 4.3 - - - +
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Residues in contact with THR 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B LEU* 3.7 25.3 - - + +
286B TRP* 3.6 34.6 + - + -
300B LEU* 3.5 19.7 - - + -
342B ILE* 2.7 37.0 + - + +
343B PHE* 3.0 6.2 + - - -
345B LYS* 1.3 69.3 - - - +
347B GLU* 1.3 83.3 + - - +
348B ILE* 3.2 15.6 - - - +
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Residues in contact with GLU 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B PHE 2.8 12.5 + - - -
344B HIS* 3.6 14.9 - - - +
345B LYS 3.2 4.5 - - - +
346B THR* 1.3 92.0 + - - +
348B ILE* 1.3 60.9 + - - +
349B MET 3.4 2.6 + - - -
350B PRO* 3.8 20.4 - - + +
351B PHE* 3.5 15.6 + - - +
487B PRO* 5.9 4.9 - - + +
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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