Contacts of the helix formed by residues 340 - 347 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315A GLY* 3.5 25.4 - - - -
318A ASP* 2.8 29.2 + - + -
319A LEU* 3.6 29.6 + - + +
322A LYS* 4.4 8.0 + - + -
332A LEU* 4.3 9.6 - - + -
336A GLY 2.9 11.9 + - - +
337A VAL 3.2 16.8 + - - +
338A MET 3.4 0.2 - - - -
339A GLU* 1.3 77.7 - - - +
341A PRO* 1.4 81.4 - - + +
342A TRP* 3.0 32.5 + - + +
343A VAL* 3.0 11.1 + - + +
344A LYS* 2.9 19.4 + - - +
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Residues in contact with PRO 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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322A LYS* 6.2 0.4 - - - +
339A GLU 3.4 5.3 - - - +
340A HIS* 1.4 100.2 - - + +
342A TRP* 1.3 55.9 + - - +
344A LYS* 3.7 8.6 - - + +
345A ALA* 2.8 32.2 + - - +
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Residues in contact with TRP 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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190A GLU* 2.8 46.6 + - + -
193A SER* 4.1 4.7 - - - -
194A ALA* 3.7 30.1 - - + -
197A MET* 4.5 2.0 - - + -
279A CYS* 4.0 8.7 - - - -
283A LEU* 4.1 19.5 - - + -
313A SER* 3.6 4.2 + - - -
315A GLY* 3.7 15.7 - - - +
316A SER* 3.6 28.9 - - - -
319A LEU* 3.6 31.4 - - + -
340A HIS* 3.0 21.4 + - + +
341A PRO* 1.3 74.3 - - - +
343A VAL* 1.3 68.2 + - + +
345A ALA* 4.6 1.3 - - - -
346A ASN* 2.9 55.3 + - - +
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Residues in contact with VAL 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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194A ALA* 4.1 11.9 - - - +
197A MET* 4.6 6.5 - - + -
198A GLU* 3.9 32.1 - - + +
319A LEU* 3.8 27.8 - - + -
337A VAL* 3.3 29.4 - - + +
338A MET 3.9 11.2 - - - +
340A HIS* 3.0 11.5 + - + +
342A TRP* 1.3 82.1 - - + +
344A LYS* 1.3 64.8 + - + +
347A SER* 2.9 32.1 + - - -
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Residues in contact with LYS 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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198A GLU* 5.5 5.5 + - - -
338A MET 3.7 19.1 + - - +
339A GLU* 4.1 21.0 - - - +
340A HIS 2.9 15.6 + - - +
341A PRO* 3.7 9.6 - - + +
343A VAL* 1.3 78.4 - - + +
345A ALA* 1.3 61.3 + - - +
346A ASN 3.4 0.2 + - - -
347A SER* 4.3 7.7 + - - +
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Residues in contact with ALA 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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341A PRO 2.8 21.5 + - - +
342A TRP* 4.6 0.7 - - - -
344A LYS* 1.3 73.5 - - - +
346A ASN* 1.3 73.4 + - - +
347A SER 5.2 0.2 - - - -
348A ARG* 5.4 6.6 + - - -
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Residues in contact with ASN 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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190A GLU* 3.9 24.6 + - - +
191A GLN* 3.5 27.2 + - - +
194A ALA* 3.6 15.3 - - + -
342A TRP* 2.9 52.5 + - - +
345A ALA* 1.3 89.4 - - - +
347A SER* 1.3 65.4 + - - +
348A ARG* 3.6 5.9 + - - +
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Residues in contact with SER 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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194A ALA* 3.7 14.0 - - - +
195A THR* 3.5 19.8 - - - +
198A GLU* 2.7 28.9 + - - -
343A VAL* 2.9 20.5 + - - -
344A LYS* 4.3 6.9 + - - +
345A ALA 5.2 0.2 - - - -
346A ASN* 1.3 79.3 - - - +
348A ARG* 1.3 67.1 + - - +
349A ARG* 3.3 9.6 + - - +
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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