Contacts of the helix formed by residues 330 - 351 (chain B) in PDB entry 2Q4E
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 GLY 330 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B PRO 3.4 6.0 + - - -
329B ASP* 1.3 73.3 + - - +
331B TYR* 1.3 61.6 + - - +
332B TRP 3.3 1.6 - - - -
333B PRO* 3.3 11.0 - - - +
334B SER* 2.9 31.0 + - - -
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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
----------------------------------------------------------
132B VAL* 6.1 1.0 - - - +
141B LYS* 5.2 3.6 + - - -
198B LEU* 4.1 3.1 - - - +
202B PHE* 3.3 46.6 - + + -
329B ASP* 3.0 17.1 + - - +
330B GLY* 1.3 76.9 - - - +
332B TRP* 1.3 88.7 + + + +
334B SER* 3.4 5.5 - - - -
335B ILE* 2.5 70.2 + - + +
338B LYS* 6.2 0.7 - - - -
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Residues in contact with TRP 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B GLN* 3.8 5.4 - - - +
125B ILE 3.7 14.6 - - - +
126B MSE 3.4 36.7 - - + +
127B ASP* 5.8 2.7 - - - -
129B THR 5.7 0.2 - - - -
132B VAL* 4.3 17.9 - - + -
133B HIS* 3.3 36.6 - + - -
194B ARG* 5.5 1.8 - - - -
313B GLU* 4.4 16.3 + - + +
329B ASP* 3.5 37.0 + - + +
331B TYR* 1.3 95.4 - + - +
333B PRO* 1.3 74.2 - - + +
334B SER 2.9 1.1 - - - -
335B ILE* 2.8 19.6 + - + +
336B SER* 2.7 29.9 + - - +
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Residues in contact with PRO 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B PHE* 3.5 6.5 - - + -
115B VAL* 4.2 23.3 - - + -
124B GLN* 4.1 0.7 - - - +
125B ILE* 3.6 32.7 - - + +
328B PRO* 6.6 0.2 - - + -
329B ASP 2.9 27.6 - - - +
330B GLY* 3.3 17.0 - - - +
332B TRP* 1.3 85.6 - - + +
334B SER* 1.3 53.4 + - - +
336B SER* 3.4 8.4 + - - +
337B ARG* 2.8 32.7 + - - +
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Residues in contact with SER 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B GLY 2.9 21.6 + - - -
331B TYR* 3.5 5.8 - - - -
332B TRP 2.9 0.6 - - - -
333B PRO* 1.3 77.0 - - - +
335B ILE* 1.3 56.3 + - - +
336B SER 2.9 7.4 + - - -
337B ARG* 4.1 10.4 - - - +
338B LYS* 3.0 47.8 + - - +
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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
----------------------------------------------------------
127B ASP* 5.2 0.2 - - - +
194B ARG* 2.8 40.6 + - - +
197B LEU* 5.3 6.1 - - + -
198B LEU* 3.7 11.0 - - + -
202B PHE* 3.6 25.8 - - + -
331B TYR* 2.5 66.4 + - + +
332B TRP* 2.8 27.8 + - + +
334B SER* 1.3 72.9 - - - +
336B SER* 1.3 59.2 + - - +
338B LYS* 4.3 11.4 - - + +
339B THR* 3.2 7.2 + - - +
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Residues in contact with SER 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B VAL* 4.6 6.1 - - - -
111B PHE* 3.6 20.1 - - - -
126B MSE 4.8 1.0 - - - -
127B ASP* 2.8 30.4 + - - +
190B TRP* 4.2 0.3 - - - -
332B TRP* 2.7 21.1 + - - +
333B PRO* 3.4 7.2 - - - +
335B ILE* 1.3 83.6 - - - +
337B ARG* 1.3 60.7 + - - +
338B LYS 3.3 1.3 - - - -
339B THR* 3.1 7.5 - - - +
340B GLN* 2.9 32.7 + - - +
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Residues in contact with ARG 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B VAL* 3.6 19.7 - - + -
111B PHE* 3.7 11.2 - - + -
112B ASP* 2.5 32.1 + - - +
115B VAL* 3.2 41.8 - - - +
116B ASP* 4.8 4.0 + - - -
119B GLU* 5.1 1.4 + - - -
333B PRO* 2.8 24.0 + - - +
334B SER* 3.5 9.1 + - - +
336B SER* 1.3 76.3 - - - +
338B LYS* 1.3 53.3 + - + +
340B GLN* 3.5 1.2 - - - -
341B LEU* 2.5 48.9 + - + +
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Residues in contact with LYS 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B LEU* 3.6 10.6 - - + +
201B ASN 4.9 0.2 + - - -
202B PHE* 2.6 50.0 + - + +
204B LEU* 3.5 26.3 - - + +
331B TYR* 6.2 1.0 - - - -
334B SER* 3.0 36.8 + - - +
335B ILE* 4.7 10.7 - - + +
337B ARG* 1.3 77.6 - - + +
339B THR* 1.3 62.1 + - - +
341B LEU* 3.2 8.1 + - - +
342B VAL* 3.2 28.4 + - - +
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Residues in contact with THR 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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190B TRP* 3.2 42.8 + - + -
193B ILE* 4.3 4.2 - - - +
194B ARG* 2.9 45.3 + - - +
197B LEU* 3.5 16.0 - - - +
335B ILE 3.2 5.5 + - - +
336B SER* 3.1 12.8 - - - +
338B LYS* 1.3 77.4 - - - +
340B GLN* 1.3 66.3 + - - +
341B LEU 3.1 0.4 - - - -
342B VAL* 3.4 2.1 + - - +
343B VAL* 3.1 29.5 + - - +
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Residues in contact with GLN 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B PRO* 3.5 5.7 - - - +
104B VAL* 3.2 33.4 + - + +
105B ALA 3.0 24.4 + - - +
107B ASN 4.1 1.2 - - - +
108B VAL* 4.4 8.3 + - - +
111B PHE* 4.5 12.3 - - + -
182B LEU* 4.2 0.4 - - - +
190B TRP* 2.7 32.3 - - + -
336B SER 2.9 20.5 + - - +
337B ARG* 3.5 3.8 - - - +
339B THR* 1.3 76.8 - - - +
341B LEU* 1.3 60.2 + - - +
342B VAL 3.4 0.2 - - - -
343B VAL* 3.7 10.8 - - - +
344B ASP* 2.5 51.8 + - - +
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Residues in contact with LEU 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B VAL* 3.3 41.8 - - + +
204B LEU* 3.5 30.7 - - + -
337B ARG* 2.5 29.1 + - + +
338B LYS* 3.5 6.5 - - - +
339B THR 3.1 0.4 - - - -
340B GLN* 1.3 77.0 - - - +
342B VAL* 1.3 60.3 + - - +
344B ASP* 3.9 9.9 + - - +
345B ALA* 3.9 8.3 + - - +
359B LEU* 4.7 19.1 - - + +
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Residues in contact with VAL 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ILE* 4.0 26.9 - - + -
197B LEU* 4.7 6.7 - - + -
204B LEU* 4.6 8.1 - - + -
205B PRO* 4.0 13.9 - - + -
208B VAL* 4.2 14.4 - - + -
229B LEU* 4.6 12.3 - - + -
338B LYS 3.2 15.9 + - - +
339B THR 3.4 0.4 + - - +
341B LEU* 1.3 76.3 - - + +
343B VAL* 1.3 57.4 + - - +
344B ASP 2.9 2.2 - - - -
345B ALA* 2.5 36.2 + - + +
346B VAL* 3.2 7.7 + - + +
359B LEU* 3.7 22.4 - - + -
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Residues in contact with VAL 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B LEU* 3.9 21.7 - - + +
185B LEU* 3.1 51.8 - - + +
186B GLY* 4.8 0.9 - - - -
190B TRP* 4.0 23.1 - - + -
193B ILE* 3.4 25.5 - - + +
339B THR 3.1 14.0 + - - +
340B GLN* 3.7 25.6 - - - +
341B LEU 3.6 0.4 - - - -
342B VAL* 1.3 77.0 - - - +
344B ASP* 1.3 61.4 + - - +
345B ALA 3.4 2.3 + - - -
346B VAL* 3.8 3.9 + - - +
347B LYS* 4.0 1.6 + - - +
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Residues in contact with ASP 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B MSE 3.0 18.4 - - - +
107B ASN* 3.2 22.9 - - + -
108B VAL* 3.7 4.4 + - + +
182B LEU* 4.1 10.4 - - - +
340B GLN* 2.5 42.7 + - - +
341B LEU* 3.9 8.2 + - - +
342B VAL 2.9 1.0 - - - -
343B VAL* 1.3 82.3 - - - +
345B ALA* 1.3 58.1 + - - +
346B VAL 3.6 0.2 - - - -
347B LYS* 5.0 5.7 - - - +
348B GLU* 3.2 29.8 + - - +
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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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208B VAL* 3.8 30.0 - - + +
341B LEU 4.2 0.9 - - - +
342B VAL* 2.5 30.0 + - - +
344B ASP* 1.3 73.6 - - - +
346B VAL* 1.3 66.9 + - - +
348B GLU* 3.2 8.1 - - - +
349B SER* 3.9 1.4 - - - -
357B ILE* 3.2 27.5 - - + +
359B LEU* 3.8 18.8 - - + -
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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
----------------------------------------------------------
185B LEU* 3.8 30.1 - - + -
193B ILE* 5.1 5.2 - - + -
208B VAL* 4.2 12.1 - - + -
210B ALA* 4.4 6.7 - - + -
225B CYS* 3.8 23.1 - - - -
226B GLY 4.7 3.1 - - - +
227B ALA* 4.2 20.9 - - + -
229B LEU* 5.9 1.3 - - + -
239B ILE* 4.6 13.2 - - + -
342B VAL* 3.2 8.6 + - + +
343B VAL 4.0 1.3 - - - +
345B ALA* 1.3 74.5 - - - +
347B LYS* 1.3 56.0 + - - +
348B GLU 2.7 2.9 + - - -
349B SER* 2.4 31.7 + - - -
350B VAL* 3.0 19.9 + - + +
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Residues in contact with LYS 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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181B GLY 5.6 4.7 - - - -
182B LEU* 4.4 22.9 - - + -
185B LEU* 4.0 15.9 - - + +
220B GLY 4.6 13.7 - - - -
222B ILE* 4.2 17.9 - - + -
343B VAL 4.0 3.5 + - - +
344B ASP* 5.2 6.5 - - - +
346B VAL* 1.3 81.4 - - - +
348B GLU* 1.3 60.0 + - - +
349B SER 3.0 1.7 + - - -
350B VAL* 3.7 11.4 - - - -
351B ASP* 3.3 44.3 + - - +
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Residues in contact with GLU 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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344B ASP 3.2 22.7 + - - +
345B ALA* 3.2 13.0 - - - +
346B VAL 2.7 1.0 + - - -
347B LYS* 1.3 79.0 - - - +
349B SER* 1.3 56.4 + - - +
351B ASP 4.8 1.1 - - - -
352B LYS* 2.9 35.1 + - + +
357B ILE* 3.0 40.7 - - + +
359B LEU* 5.4 1.0 - - - +
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Residues in contact with SER 349 (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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208B VAL 4.7 0.2 - - - -
209B THR* 4.6 0.9 - - - -
210B ALA* 3.1 26.9 + - - -
345B ALA 3.4 2.0 + - - -
346B VAL 2.4 23.8 + - - -
348B GLU* 1.3 73.4 - - - +
350B VAL* 1.3 58.3 + - - -
351B ASP 3.0 6.0 + - - -
352B LYS* 3.4 6.7 + - - -
354B TYR* 2.9 34.7 + - - -
355B GLN 2.6 35.6 + - - +
357B ILE* 3.8 7.6 - - - -
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Residues in contact with VAL 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ALA* 3.4 24.0 - - + -
211B PHE 5.3 0.4 - - - +
214B ALA* 3.4 34.8 - - + -
216B LEU* 4.1 22.8 - - + +
222B ILE* 5.1 6.1 - - + -
225B CYS* 4.8 7.6 - - + -
346B VAL* 3.0 22.3 + - + +
347B LYS* 3.4 10.5 + - + +
349B SER* 1.3 76.6 - - - +
351B ASP* 1.3 64.2 + - - +
352B LYS 3.7 0.2 - - - -
353B ASN 5.2 1.0 + - - -
354B TYR* 4.9 18.3 + - + +
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Residues in contact with ASP 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B LEU* 3.6 26.6 - - - +
220B GLY 5.2 0.3 - - - +
347B LYS* 3.3 43.7 + - - +
348B GLU 4.4 0.5 - - - +
349B SER 3.0 0.2 - - - -
350B VAL* 1.3 85.1 - - - +
352B LYS* 1.3 67.0 + - - +
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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
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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