Contacts of the helix formed by residues 325 - 346 (chain B) in PDB entry 4ZG9
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 MET 325 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B TYR* 3.9 16.4 - - + +
311B PRO* 4.5 12.1 - - - +
314B SER* 3.1 52.7 - - - +
315B GLY* 3.2 13.9 - - - +
318B TYR* 4.2 7.9 - - + -
319B GLY 3.2 22.4 - - - +
320B PRO 3.5 17.3 - - - +
322B GLY 3.2 11.7 + - - +
323B PRO 3.1 0.8 - - - -
324B GLU* 1.3 77.7 - - - +
326B THR* 1.3 60.7 - - - +
328B PRO* 2.9 17.9 - - + +
329B LEU* 3.3 27.7 + - + +
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Residues in contact with THR 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778A PHE* 3.4 41.8 - - + -
779A THR* 3.6 22.6 - - + +
185B VAL* 3.7 18.5 - - + +
322B GLY 5.0 0.3 + - - -
323B PRO* 3.1 18.9 + - - +
324B GLU 3.3 1.0 - - - -
325B MET* 1.3 78.0 - - - +
327B ASN* 1.3 66.3 + - - +
329B LEU* 3.5 6.5 + - - +
330B ARG* 3.3 15.8 + - - +
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Residues in contact with ASN 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779A THR* 4.0 19.9 - - - +
323B PRO 5.0 0.2 + - - -
324B GLU* 3.9 5.6 + - - +
326B THR* 1.3 77.8 - - - +
328B PRO* 1.4 65.2 - - + +
330B ARG* 2.8 26.0 + - - +
331B GLU* 3.0 22.1 + - + +
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Residues in contact with PRO 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B GLN* 4.1 32.5 - - + +
311B PRO* 5.0 7.9 - - + +
314B SER* 3.6 24.9 - - - +
324B GLU 3.0 23.3 - - - +
325B MET* 2.9 22.2 - - + +
327B ASN* 1.4 81.9 - - + +
329B LEU* 1.3 60.5 + - - +
331B GLU* 3.9 9.1 - - + +
332B ILE* 3.3 23.0 + - - +
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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
----------------------------------------------------------
174B PHE* 3.8 30.3 - - + -
178B TYR* 4.0 34.1 - - + -
181B LYS 5.1 6.5 - - - +
182B GLY* 6.0 0.9 - - - -
185B VAL* 4.5 5.4 - - + -
186B MET* 3.7 21.7 - - + +
311B PRO* 3.9 24.7 - - + -
325B MET* 3.3 26.3 + - + +
326B THR* 3.9 7.9 - - - +
327B ASN 3.1 1.0 - - - -
328B PRO* 1.3 74.8 - - - +
330B ARG* 1.3 61.3 + - - +
332B ILE* 3.0 20.5 - - + +
333B ASP* 3.0 13.9 + - - +
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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
----------------------------------------------------------
777A ASP* 3.9 14.3 + - - +
779A THR* 3.6 30.3 - - + +
780A GLN* 5.3 4.2 - - - +
185B VAL* 3.0 35.3 + - + +
187B PRO* 3.6 15.0 - - - +
188B ASN* 4.0 6.3 - - - +
326B THR 3.3 5.9 + - - +
327B ASN* 2.8 14.6 + - - +
329B LEU* 1.3 72.8 - - - +
331B GLU* 1.3 63.8 + - + +
333B ASP* 3.0 36.3 + - - +
334B LYS* 2.8 58.7 + - - +
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Residues in contact with GLU 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B GLU* 5.8 0.5 - - - +
327B ASN* 3.0 25.3 + - + +
328B PRO* 4.0 8.5 - - + +
329B LEU 3.3 0.4 - - - -
330B ARG* 1.3 78.0 - - - +
332B ILE* 1.3 62.0 + - - +
334B LYS* 3.1 35.9 + - - +
335B ILE* 3.4 24.6 + - - +
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Residues in contact with ILE 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B PHE* 4.1 16.4 - - + -
171B VAL* 3.8 20.2 - - + -
174B PHE* 4.6 6.7 - - + -
186B MET* 5.1 0.2 - - - -
189B ILE* 4.5 10.8 - - + -
282B HIS* 4.6 12.1 - - + +
306B PHE* 4.7 0.4 - - + -
308B SER* 3.3 37.2 - - - +
310B GLN* 4.0 7.2 - - + +
311B PRO* 5.3 3.1 - - + -
328B PRO 3.3 15.5 + - - +
329B LEU* 3.0 35.9 - - + +
331B GLU* 1.3 75.8 - - - +
333B ASP* 1.3 60.1 + - - +
334B LYS 3.0 1.3 - - - -
335B ILE* 2.7 23.1 + - + +
336B VAL* 3.0 13.8 + - + +
356B PHE* 5.1 0.2 - - + -
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Residues in contact with ASP 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B VAL 4.2 1.3 - - - +
186B MET* 3.1 27.3 - - + -
187B PRO* 3.2 1.6 - - - +
188B ASN* 2.6 37.3 + - - -
189B ILE* 2.7 44.0 + - + +
329B LEU 3.0 16.1 + - - +
330B ARG* 3.0 22.3 + - - +
332B ILE* 1.3 77.1 - - - +
334B LYS* 1.3 62.1 + - - +
336B VAL* 3.6 2.6 + - - +
337B GLY 3.0 16.6 + - - -
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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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102B GLU* 5.2 10.3 - - - +
188B ASN* 5.1 0.9 - - - +
330B ARG* 2.8 48.2 + - - +
331B GLU* 3.1 44.2 + - - +
332B ILE 3.0 0.2 - - - -
333B ASP* 1.3 77.4 - - - +
335B ILE* 1.3 59.4 + - + +
337B GLY* 2.9 3.8 + - - -
338B GLN* 2.8 43.2 + - + +
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Residues in contact with ILE 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B PHE* 3.9 10.7 - - + -
282B HIS* 3.6 32.8 - - + +
283B GLU* 3.8 21.3 - - + +
286B ILE* 3.4 25.2 - - + +
306B PHE* 3.9 20.6 - - + -
331B GLU 3.4 14.8 + - - +
332B ILE* 2.7 14.9 + - + +
334B LYS* 1.3 72.8 - - + +
336B VAL* 1.3 62.5 + - - +
338B GLN* 3.4 24.9 + - - +
339B LEU* 3.0 21.1 + - - +
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Residues in contact with VAL 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B PHE* 3.9 26.9 - - + -
188B ASN* 3.8 15.9 - - + -
189B ILE* 3.6 25.8 - - + -
192B LEU* 3.8 28.5 - - + -
332B ILE 3.0 12.6 + - - +
333B ASP 3.6 6.7 - - - +
335B ILE* 1.3 77.4 - - - +
337B GLY* 1.3 58.3 + - - +
339B LEU* 2.9 24.5 + - + +
340B MET* 2.9 19.6 + - + +
356B PHE* 4.1 6.1 - - + -
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Residues in contact with GLY 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B VAL* 5.7 0.2 - - - -
188B ASN* 2.9 31.1 - - - +
333B ASP 3.0 4.9 + - - -
334B LYS* 2.9 8.4 + - - -
336B VAL* 1.3 78.9 - - - +
338B GLN* 1.3 56.5 + - - +
340B MET* 3.4 2.5 + - - +
341B ASP* 2.9 41.2 + - - +
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Residues in contact with GLN 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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101B TRP* 4.6 13.4 - - - +
102B GLU* 6.2 2.0 - - - +
132B THR* 3.3 37.4 + - + +
283B GLU* 3.4 43.8 + - - +
286B ILE* 4.3 8.4 - - + +
287B LEU* 6.0 1.0 - - - +
334B LYS* 2.8 29.4 + - + +
335B ILE* 3.7 22.3 - - - +
336B VAL 3.2 0.2 - - - -
337B GLY* 1.3 72.7 - - - +
339B LEU* 1.3 62.0 + - - +
341B ASP* 4.3 3.4 - - - +
342B GLY* 3.2 17.5 + - - -
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Residues in contact with LEU 339 (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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167B ILE* 4.3 34.3 - - + -
169B PHE* 4.2 22.9 - - + -
286B ILE* 3.9 30.5 - - + -
289B ILE* 5.0 5.6 - - + -
290B LEU* 4.2 15.7 - - + +
335B ILE 3.0 12.9 + - - +
336B VAL* 2.9 12.4 + - + +
338B GLN* 1.3 77.6 - - - +
340B MET* 1.3 68.4 + - - +
342B GLY* 3.3 3.3 + - - -
343B LEU* 3.1 28.8 + - + +
354B VAL* 4.7 20.0 - - + -
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Residues in contact with MET 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B TRP* 3.4 66.7 - - + +
192B LEU* 4.3 10.3 - - + -
336B VAL* 2.9 26.1 + - + +
337B GLY 4.1 2.0 - - - +
339B LEU* 1.3 79.8 - - - +
341B ASP* 1.3 65.8 + - - +
343B LEU* 3.3 22.3 + - + +
344B LYS* 3.1 22.9 + - - +
349B HIS* 4.6 11.9 - - + +
352B VAL 6.0 0.7 - - - +
354B VAL* 4.3 15.3 - - + -
491B TYR* 3.8 23.6 - - + -
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Residues in contact with ASP 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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132B THR* 3.3 22.4 + - - +
133B ASN* 4.7 5.9 - - - +
136B VAL* 5.2 4.5 - - + -
143B HIS* 3.3 30.5 + - - +
144B TRP* 3.1 29.5 + - - +
145B VAL* 4.6 2.8 + - - +
188B ASN* 5.4 0.4 - - - +
337B GLY* 2.9 30.4 + - - +
338B GLN* 4.0 5.6 - - - +
340B MET* 1.3 76.2 - - - +
342B GLY* 1.3 59.9 + - - +
344B LYS* 3.1 5.6 + - - +
345B GLN* 2.8 27.4 + - - +
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Residues in contact with GLY 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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132B THR* 3.8 10.7 + - - -
290B LEU* 3.8 20.1 - - - +
338B GLN 3.2 12.4 + - - -
339B LEU 3.8 3.6 - - - -
341B ASP* 1.3 78.3 - - - +
343B LEU* 1.3 58.3 - - - +
345B GLN* 3.5 12.7 - - - +
346B LEU* 3.2 31.9 + - - +
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Residues in contact with LEU 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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167B ILE* 4.4 9.0 - - + -
290B LEU* 3.6 20.2 - - + -
293B LEU* 3.6 23.3 - - + -
339B LEU* 3.1 32.1 + - + +
340B MET* 3.8 25.6 - - + +
341B ASP 3.1 0.2 - - - -
342B GLY* 1.3 74.5 - - - +
344B LYS* 1.3 63.2 + - - +
346B LEU* 3.1 3.7 + - + -
347B LYS 3.1 4.2 + - - -
348B LEU* 2.7 43.4 + - + +
349B HIS* 3.5 16.6 - - + +
352B VAL* 4.5 13.0 - - + +
354B VAL* 4.4 13.5 - - + -
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Residues in contact with LYS 344 (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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135B GLN* 4.5 9.9 + - - +
136B VAL* 6.2 0.7 - - + -
141B GLU* 4.5 11.9 + - + +
142B SER* 2.6 43.6 + - - +
144B TRP* 4.5 11.4 - - + +
147B ASP* 3.1 26.4 + - - +
340B MET 3.1 13.0 + - - +
341B ASP* 3.2 9.9 - - - +
343B LEU* 1.3 72.7 - - - +
345B GLN* 1.3 57.8 + - - +
347B LYS* 2.6 26.7 + - - -
349B HIS* 3.4 41.1 + - + +
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Residues in contact with GLN 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU* 4.5 19.5 - - + +
130B CYS* 3.5 20.3 - - - +
131B CYS 3.0 21.6 + - - -
132B THR* 3.2 21.4 + - - +
133B ASN 4.0 0.2 - - - -
134B TYR* 3.5 6.6 + - + -
135B GLN* 3.1 65.4 + - + +
136B VAL* 6.1 0.2 - - - +
341B ASP 2.8 14.3 + - - +
342B GLY* 3.5 13.4 + - - +
344B LYS* 1.3 73.4 - - - +
346B LEU* 1.3 61.8 + - + +
347B LYS* 3.4 2.9 + - - +
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Residues in contact with LEU 346 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU* 4.8 16.2 - - + +
158B PRO* 4.9 4.9 - - - +
290B LEU* 3.9 39.9 - - + +
293B LEU* 4.6 2.9 - - + -
294B THR* 4.0 23.6 - - + -
342B GLY 3.2 17.7 - - - +
343B LEU* 3.1 6.1 + - - +
344B LYS 3.1 1.0 - - - -
345B GLN* 1.3 79.5 - - + +
347B LYS* 1.3 69.7 + - - +
348B LEU* 3.2 28.8 + - + +
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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