Contacts of the helix formed by residues 340 - 347 (chain B) in PDB entry 2VGO
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 HIS 340 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315B GLY* 3.5 26.2 - - - -
318B ASP* 2.7 28.6 + - + -
319B LEU* 3.6 31.4 + - + +
322B LYS* 4.5 7.4 + - + -
332B LEU* 4.3 10.5 - - + -
336B GLY 3.0 12.1 + - - +
337B VAL 3.1 16.3 + - - +
339B GLU* 1.3 77.7 - - - +
341B PRO* 1.4 81.6 - - + +
342B TRP* 3.0 32.6 + - + +
343B VAL* 3.0 11.2 + - + -
344B LYS* 2.9 20.3 + - - +
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Residues in contact with PRO 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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318B ASP* 5.5 1.6 - - - +
322B LYS* 6.2 0.7 - - - +
339B GLU 3.4 5.6 - - - +
340B HIS* 1.4 100.2 - - + +
342B TRP* 1.3 55.7 + - - +
344B LYS* 3.5 8.1 + - + +
345B ALA* 3.0 31.7 + - - +
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Residues in contact with TRP 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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190B GLU* 2.7 46.0 + - + -
193B SER* 4.1 4.9 - - - -
194B ALA* 3.7 29.6 - - + -
197B MET* 4.5 1.3 - - + -
279B CYS* 4.1 8.3 - - - -
283B LEU* 3.9 21.5 - - + -
313B SER* 3.6 2.5 + - - -
315B GLY* 3.7 16.6 - - - -
316B SER* 3.6 28.5 - - - -
319B LEU* 3.6 32.5 - - + -
340B HIS* 3.0 21.5 + - + +
341B PRO* 1.3 75.1 - - - +
343B VAL* 1.3 71.6 + - + +
345B ALA* 3.6 1.3 + - - -
346B ASN* 3.0 55.4 + - - +
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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
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194B ALA* 3.8 22.7 - - - +
197B MET* 4.6 4.7 - - + -
198B GLU* 3.8 24.5 - - + +
319B LEU* 3.8 15.9 - - + -
337B VAL* 3.3 32.5 - - + +
338B MET 4.1 9.2 - - - +
340B HIS* 3.0 7.9 + - + +
342B TRP* 1.3 94.8 - - + +
344B LYS* 1.3 57.1 + - - +
347B SER* 2.8 36.7 + - - -
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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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338B MET 3.9 12.5 + - - +
339B GLU* 3.7 42.5 + - - +
340B HIS 2.9 17.7 + - - +
341B PRO* 3.8 7.4 - - + +
343B VAL* 1.3 78.1 - - - +
345B ALA* 1.3 61.7 + - - +
347B SER* 4.2 7.8 + - - +
348B ARG* 4.9 0.7 + - - -
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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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341B PRO 3.0 19.0 + - - +
342B TRP* 4.7 1.1 - - - -
344B LYS* 1.3 77.2 - - - +
346B ASN* 1.3 71.4 + - - +
348B ARG* 3.0 21.6 + - - -
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Residues in contact with ASN 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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190B GLU* 3.8 16.5 + - - +
191B GLN* 2.9 46.6 + - - +
194B ALA* 3.6 15.5 - - + -
342B TRP* 3.0 51.0 + - - +
345B ALA* 1.3 89.5 - - - +
347B SER* 1.3 64.2 + - - +
348B ARG* 3.2 13.9 + - - +
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Residues in contact with SER 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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194B ALA* 3.7 12.7 - - - +
195B THR* 3.6 16.2 - - - +
198B GLU* 2.6 28.9 + - - +
343B VAL* 2.8 25.4 + - - -
344B LYS* 4.2 6.6 + - - +
346B ASN* 1.3 72.0 - - - +
348B ARG* 1.3 73.9 + - - +
349B ARG* 3.3 12.9 + - - +
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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
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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