Contacts of the helix formed by residues 333 - 349 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293A GLU 5.0 0.5 - - - +
294A GLY* 3.9 26.2 - - - +
295A HIS* 3.2 16.1 + - + +
332A HIS* 1.3 80.8 + - + +
334A LEU* 1.3 64.4 + - - +
335A THR* 3.5 9.9 + - - -
336A ALA* 3.0 33.7 + - + +
337A ILE* 2.9 24.6 + - - +
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Residues in contact with LEU 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ALA 3.9 17.5 - - - +
36A GLY* 3.8 22.2 - - - +
37A ARG* 3.8 20.6 - - + +
40A SER* 3.9 16.4 - - - +
332A HIS 3.1 15.3 + - - +
333A ASP* 1.3 73.0 - - - +
335A THR* 1.3 63.1 + - - +
337A ILE* 4.0 4.7 - - + -
338A CYS* 3.0 32.5 + - - -
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Residues in contact with THR 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ARG* 4.8 6.9 + - - +
333A ASP* 3.4 9.0 + - - -
334A LEU* 1.3 78.6 - - - +
336A ALA* 1.3 58.3 + - - +
338A CYS* 3.9 3.4 - - - +
339A ASP* 3.0 53.6 + - - +
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Residues in contact with ALA 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A VAL* 3.5 30.6 - - + +
293A GLU 3.8 8.5 - - - +
295A HIS* 3.7 17.7 - - + -
306A ALA* 4.2 2.6 - - - +
333A ASP* 3.0 21.9 + - - +
335A THR* 1.3 78.5 - - - +
337A ILE* 1.3 56.6 + - - +
339A ASP* 3.6 5.7 - - - +
340A ALA* 3.0 29.3 + - - +
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Residues in contact with ILE 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ARG* 3.6 50.7 - - + +
41A ILE* 4.1 18.6 - - + -
289A PHE* 4.0 18.9 - - + -
295A HIS* 4.2 4.7 - - + +
328A LEU* 5.4 1.1 - - + -
330A GLY 5.0 0.9 - - - +
331A GLY* 3.7 30.1 - - - +
332A HIS 3.7 2.7 - - - +
333A ASP 2.9 18.0 + - - +
334A LEU* 3.5 13.9 - - + +
336A ALA* 1.3 72.9 - - - +
338A CYS* 1.3 64.6 + - - +
340A ALA* 3.9 5.9 - - - +
341A SER* 2.9 34.2 + - - -
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Residues in contact with CYS 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A SER* 3.3 46.7 - - - -
41A ILE* 3.7 9.0 - - - -
44A ARG* 3.6 36.8 + - + +
334A LEU* 3.0 25.7 + - - +
335A THR 3.9 0.2 - - - +
337A ILE* 1.3 76.7 - - - +
339A ASP* 1.3 58.7 + - - +
341A SER* 3.4 5.7 + - - -
342A GLU* 2.9 30.7 + - - +
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Residues in contact with ASP 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ARG* 2.8 38.7 + - - +
306A ALA* 3.4 21.5 - - + +
335A THR* 3.0 35.8 + - - +
336A ALA* 3.6 4.0 - - - +
338A CYS* 1.3 74.6 - - - +
340A ALA* 1.3 57.8 + - - +
342A GLU* 3.4 5.0 + - - +
343A ALA* 3.0 27.5 + - - +
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Residues in contact with ALA 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A PHE* 3.5 39.0 - - + -
292A VAL* 4.4 4.9 - - + -
306A ALA* 3.6 21.4 - - + +
309A PHE* 4.7 2.7 - - + -
336A ALA 3.0 18.6 + - - +
337A ILE 3.9 0.2 - - - +
339A ASP* 1.3 74.8 - - - +
341A SER* 1.3 66.4 + - - +
343A ALA* 3.2 2.9 + - - +
344A CYS* 3.0 28.4 + - - -
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Residues in contact with SER 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ILE* 3.4 38.4 - - - +
44A ARG* 6.3 0.4 - - - -
45A LEU* 4.6 5.2 - - - -
150A PHE* 3.8 12.5 - - - -
289A PHE* 3.4 20.9 - - - -
337A ILE 2.9 22.9 + - - -
338A CYS 3.7 4.0 - - - -
340A ALA* 1.3 75.3 - - - +
342A GLU* 1.3 62.8 + - - +
344A CYS* 3.4 1.0 + - - +
345A VAL* 3.0 31.9 + - - +
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Residues in contact with GLU 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ARG* 2.9 35.7 + - + -
45A LEU* 4.4 4.9 - - + +
48A THR* 3.7 20.9 - - + +
50A LEU* 3.6 24.4 - - + +
338A CYS 2.9 16.9 + - - +
339A ASP* 3.5 5.9 - - - +
341A SER* 1.3 75.8 - - - +
343A ALA* 1.3 56.9 + - - +
346A SER* 2.9 33.8 + - - -
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Residues in contact with ALA 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A ALA 3.5 28.5 - - - +
307A ARG* 4.3 6.3 - - - +
310A GLY* 3.7 16.6 - - - +
339A ASP 3.0 12.3 + - - +
340A ALA 3.2 6.0 + - - +
342A GLU* 1.3 75.9 - - - +
344A CYS* 1.3 59.0 + - - +
346A SER* 3.7 5.9 - - - -
347A ALA* 3.1 28.1 + - - +
353A LEU* 3.9 6.6 - - + +
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Residues in contact with CYS 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A PHE* 4.0 9.6 - - + -
195A TRP* 4.4 1.8 - - - -
289A PHE* 3.8 24.2 - - - -
309A PHE* 3.8 15.9 - - - -
310A GLY* 4.5 0.9 - - - -
313A THR* 3.4 26.0 - - - +
326A LEU* 3.9 17.9 - - + -
340A ALA 3.0 20.3 + - - +
341A SER 3.8 3.6 - - - +
343A ALA* 1.3 74.9 - - - +
345A VAL* 1.3 60.2 + - - +
347A ALA* 3.3 5.3 + - - +
348A LEU* 2.9 33.1 + - - +
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Residues in contact with VAL 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A THR* 4.8 3.1 - - + -
12A LEU* 4.3 4.0 - - + -
45A LEU* 3.8 26.2 - - + -
50A LEU* 4.2 13.7 - - + -
54A CYS* 3.9 27.8 - - - -
150A PHE* 4.0 30.7 - - + -
341A SER* 3.0 22.1 + - - +
342A GLU 4.1 1.3 - - - +
344A CYS* 1.3 72.9 - - - +
346A SER* 1.3 66.6 + - - +
348A LEU* 3.2 8.7 + - + +
349A LEU* 3.0 30.4 + - + +
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Residues in contact with SER 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU* 4.1 12.6 - - - +
342A GLU* 2.9 20.2 + - - -
343A ALA* 3.7 6.7 - - - -
345A VAL* 1.3 77.3 - - - +
347A ALA* 1.3 59.8 + - - +
349A LEU* 3.4 2.5 + - - +
350A GLY 3.3 3.3 + - - -
351A ASN* 3.1 59.9 + - - +
352A GLU 5.0 2.3 + - - -
353A LEU* 4.7 8.0 - - - +
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Residues in contact with ALA 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A GLY 3.5 23.6 - - - +
313A THR* 4.1 10.5 - - + -
314A LYS* 2.6 38.7 + - - +
317A MET* 3.4 4.6 - - - +
343A ALA 3.1 14.9 + - - +
344A CYS 3.4 8.3 - - - +
346A SER* 1.3 73.4 - - - +
348A LEU* 1.3 59.5 + - - +
350A GLY 2.9 9.7 + - - -
353A LEU* 3.9 13.1 - - + +
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Residues in contact with LEU 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A THR* 3.1 15.8 + - + +
147A LYS* 4.8 6.2 + - - +
148A ASN* 3.0 37.0 + - + +
149A GLY 3.6 31.0 - - - +
150A PHE* 4.1 13.5 - - + -
313A THR* 3.7 20.2 - - + -
317A MET* 3.8 9.7 - - - +
324A ILE* 3.8 27.8 - - + -
326A LEU* 4.5 11.2 - - + -
344A CYS 2.9 19.9 + - - +
345A VAL* 3.2 11.2 + - - +
347A ALA* 1.3 75.0 - - - +
349A LEU* 1.3 59.3 + - - +
350A GLY 3.2 0.9 + - - -
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Residues in contact with LEU 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A THR* 3.9 8.7 - - - +
10A THR* 3.6 25.1 - - - +
50A LEU* 3.7 30.7 - - + +
53A LYS* 3.4 50.6 - - + +
54A CYS* 4.0 14.1 - - - -
147A LYS* 5.2 7.8 + - - +
345A VAL* 3.0 20.8 + - + +
346A SER 3.7 5.4 - - - +
347A ALA 3.2 0.4 - - - -
348A LEU* 1.3 75.3 - - - +
350A GLY* 1.3 61.2 + - - +
351A ASN* 3.3 13.2 + - - +
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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