Contacts of the helix formed by residues 333 - 349 (chain B) in PDB entry 2VQQ
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 333 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293B GLU 5.0 0.5 - - - +
294B GLY* 3.7 28.0 - - - +
295B HIS* 3.2 20.3 + - + +
332B HIS* 1.3 78.9 + - - +
334B LEU* 1.3 64.4 + - - +
335B THR* 3.5 11.0 + - - +
336B ALA* 3.0 29.7 + - + +
337B ILE* 3.0 24.6 + - - +
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Residues in contact with LEU 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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36B GLY* 4.0 9.9 - - - +
37B ARG* 3.8 35.2 - - + +
40B SER* 3.8 22.2 - - - +
332B HIS 3.2 13.2 + - - +
333B ASP* 1.3 73.6 - - - +
335B THR* 1.3 63.7 + - - +
337B ILE* 3.9 6.1 - - + -
338B CYS* 3.0 31.8 + - - -
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Residues in contact with THR 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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44B ARG* 4.8 7.0 + - - +
333B ASP* 3.4 8.1 + - - +
334B LEU* 1.3 78.0 - - - +
336B ALA* 1.3 59.8 + - - +
338B CYS* 3.8 3.8 - - - +
339B ASP* 2.8 54.4 + - - +
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Residues in contact with ALA 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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292B VAL* 3.5 29.8 - - + +
293B GLU 4.0 7.4 - - - +
295B HIS* 3.7 17.5 - - + -
306B ALA* 4.3 2.3 - - - +
333B ASP* 3.0 22.5 + - + +
335B THR* 1.3 78.2 - - - +
337B ILE* 1.3 56.4 + - - +
339B ASP* 3.5 6.6 + - - +
340B ALA* 2.9 31.6 + - - +
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Residues in contact with ILE 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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37B ARG* 3.5 52.3 - - + +
41B ILE* 4.1 17.9 - - + -
289B PHE* 4.0 25.0 - - + -
295B HIS* 4.2 4.3 - - - +
328B LEU* 5.4 1.1 - - + -
330B GLY 4.8 1.1 - - - +
331B GLY* 3.7 30.5 - - - +
332B HIS* 3.7 2.7 - - - +
333B ASP 3.0 21.6 + - - +
334B LEU* 3.5 13.9 - - + +
336B ALA* 1.3 76.2 - - - +
338B CYS* 1.3 61.4 + - - +
340B ALA* 4.0 0.5 - - - +
341B SER* 2.8 34.9 + - - -
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Residues in contact with CYS 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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40B SER* 3.5 45.3 - - - -
41B ILE* 3.7 12.1 - - - -
44B ARG* 3.5 37.6 + - + +
334B LEU* 3.0 25.8 + - - +
335B THR* 4.7 0.2 - - - -
337B ILE* 1.3 75.5 - - - +
339B ASP* 1.3 66.0 + - - +
341B SER* 3.9 1.6 - - - -
342B GLU* 3.0 26.3 + - - +
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Residues in contact with ASP 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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44B ARG* 2.9 31.0 + - - +
306B ALA* 3.4 20.8 - - + +
335B THR* 2.8 38.4 + - - +
336B ALA* 3.6 5.0 - - - +
338B CYS* 1.3 72.3 - - - +
340B ALA* 1.3 57.4 + - - +
342B GLU* 3.5 4.9 + - - +
343B ALA* 3.1 26.3 + - - +
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Residues in contact with ALA 340 (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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289B PHE* 3.4 39.5 - - + -
292B VAL* 4.4 4.5 - - + -
306B ALA* 3.5 22.2 - - + +
309B PHE* 4.7 2.5 - - + -
336B ALA 2.9 19.7 + - - +
339B ASP* 1.3 73.6 - - - +
341B SER* 1.3 66.7 + - - +
343B ALA* 3.3 2.4 + - - +
344B CYS* 3.0 28.8 + - - -
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Residues in contact with SER 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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41B ILE* 3.4 40.7 - - - +
44B ARG* 6.2 0.4 - - - -
45B LEU* 4.4 6.3 - - - -
150B PHE* 3.8 13.1 - - - -
289B PHE* 3.5 17.4 - - - -
337B ILE 2.8 24.2 + - - -
338B CYS* 3.9 3.6 - - - -
340B ALA* 1.3 75.6 - - - +
342B GLU* 1.3 62.6 + - - +
344B CYS* 3.4 1.9 + - - +
345B VAL* 3.1 30.0 + - - +
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Residues in contact with GLU 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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44B ARG* 3.0 33.9 + - + -
45B LEU* 4.2 4.6 - - - +
48B THR* 3.7 21.9 - - + +
50B LEU* 3.6 23.7 - - + +
338B CYS 3.0 17.4 + - - +
339B ASP* 3.5 5.8 - - - +
341B SER* 1.3 77.6 - - - +
343B ALA* 1.3 57.6 + - - +
346B SER* 2.9 34.6 + - - -
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Residues in contact with ALA 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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306B ALA 3.6 25.1 - - - +
307B ARG* 4.4 6.1 - - - +
310B GLY* 3.7 15.7 - - - +
339B ASP 3.1 12.8 + - - +
340B ALA 3.3 8.0 + - - +
342B GLU* 1.3 77.4 - - - +
344B CYS* 1.3 56.9 + - - +
346B SER* 3.6 5.3 + - - -
347B ALA* 3.0 28.6 + - - +
353B LEU* 3.9 6.5 - - + +
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Residues in contact with CYS 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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150B PHE* 4.1 9.0 - - + -
195B TRP* 4.3 1.8 - - - -
289B PHE* 3.8 20.4 - - - -
309B PHE* 3.7 20.0 - - - -
310B GLY* 4.5 0.7 - - - -
313B THR* 3.3 26.9 - - - +
326B LEU* 3.8 19.3 - - + -
340B ALA 3.0 20.5 + - - +
341B SER 3.9 3.8 - - - +
342B GLU 3.4 0.2 - - - -
343B ALA* 1.3 74.5 - - - +
345B VAL* 1.3 58.2 + - - +
347B ALA* 3.2 5.9 + - - +
348B LEU* 2.9 33.0 + - - +
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Residues in contact with VAL 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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10B THR* 4.6 3.8 - - + -
12B LEU* 4.1 10.5 - - + -
45B LEU* 4.0 20.4 - - + -
50B LEU* 4.2 12.1 - - + -
54B CYS* 3.9 27.6 - - - -
150B PHE* 3.8 34.5 - - + -
341B SER 3.1 17.2 + - - +
342B GLU 4.2 0.9 - - - +
344B CYS* 1.3 71.9 - - - +
346B SER* 1.3 67.1 + - - +
348B LEU* 3.2 6.4 + - - +
349B LEU* 2.9 30.0 + - + +
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Residues in contact with SER 346 (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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50B LEU* 4.1 11.8 - - - +
342B GLU* 2.9 22.8 + - - -
343B ALA* 3.7 6.5 - - - -
345B VAL* 1.3 76.3 - - - +
347B ALA* 1.3 58.6 + - - +
349B LEU* 3.4 2.8 + - - +
350B GLY 3.4 2.9 + - - -
351B ASN* 3.0 60.4 + - - +
352B GLU 4.9 2.8 + - - -
353B LEU* 4.7 8.4 - - - +
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Residues in contact with ALA 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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310B GLY 3.5 23.1 - - - +
313B THR* 4.1 10.8 - - + -
314B LYS* 2.7 40.7 + - - +
317B MET* 3.4 5.6 - - - +
343B ALA 3.0 15.8 + - - +
344B CYS 3.2 9.4 + - - +
346B SER* 1.3 72.6 - - - +
348B LEU* 1.3 59.3 + - - +
350B GLY 2.9 8.5 + - - -
351B ASN 4.9 0.2 - - - -
353B LEU* 3.9 10.7 - - + +
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Residues in contact with LEU 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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10B THR* 3.2 22.6 + - + +
147B LYS* 4.8 6.4 + - - -
148B ASN* 2.7 38.1 - - + +
149B GLY 3.6 29.6 - - - +
150B PHE* 4.0 18.4 - - + -
313B THR* 3.8 20.6 - - + -
317B MET* 3.9 9.2 - - - +
324B ILE* 3.9 18.8 - - + -
326B LEU* 4.4 8.7 - - + -
344B CYS 2.9 23.7 + - - +
345B VAL* 3.2 11.2 + - - +
347B ALA* 1.3 72.8 - - - +
349B LEU* 1.3 59.3 + - - +
350B GLY* 3.3 1.0 + - - -
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Residues in contact with LEU 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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9B THR* 5.0 7.0 - - + -
10B THR* 3.7 23.6 - - - +
50B LEU* 3.6 38.6 - - + +
53B LYS* 3.8 41.7 - - + +
54B CYS* 4.1 4.9 - - - -
147B LYS* 5.1 8.3 + - - +
345B VAL* 2.9 22.6 + - + +
346B SER 3.7 5.2 - - - +
347B ALA 3.2 0.4 - - - -
348B LEU* 1.3 75.8 - - - +
350B GLY* 1.3 59.5 + - - +
351B ASN* 3.6 15.5 + - - +
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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
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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