Contacts of the helix formed by residues 45 - 50 (chain A) in PDB entry 2VZE
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 ASN 45 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A PHE* 1.3 80.6 - - - +
46A PHE* 1.3 61.5 + - - +
47A ALA* 3.1 26.0 + - - +
48A SER* 3.3 13.1 + - - +
49A ASP* 3.0 34.6 + - - +
127A ILE* 2.9 31.7 + - - +
207A CYS* 3.2 25.0 - - - -
208A VAL 3.9 6.5 + - - +
209A GLU* 6.1 0.4 - - - -
210A THR* 2.8 26.3 + - - +
235A TYR* 3.7 5.7 - - - -
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Residues in contact with PHE 46 (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 PHE* 3.6 14.4 - - + -
45A ASN* 1.3 73.9 + - - +
47A ALA* 1.3 65.2 + - - +
50A VAL* 3.2 36.1 + - + -
51A LEU* 3.2 19.9 + - + -
124A LEU* 4.9 6.7 - - + -
127A ILE* 4.2 12.8 - - + +
235A TYR* 5.1 3.0 + - - +
239A GLY* 3.6 29.6 - - - -
242A ALA* 4.6 1.8 - - + -
243A LYS 5.2 0.2 - - - -
273A LEU* 4.0 16.6 - - + -
274A MET* 3.6 64.2 - - + -
277A TRP* 4.2 13.2 - + + -
278A ALA* 4.0 8.1 - - + -
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Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ASN* 3.1 12.3 + - - +
46A PHE* 1.3 80.1 - - - +
48A SER* 1.3 57.7 + - - +
51A LEU* 3.3 13.6 + - - +
52A ASP* 2.9 33.0 + - - +
124A LEU* 4.7 10.3 - - + +
127A ILE* 3.9 11.6 - - + +
128A ARG* 3.6 39.3 - - + +
207A CYS* 4.5 0.4 - - - -
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Residues in contact with SER 48 (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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45A ASN* 3.3 16.1 + - - +
47A ALA* 1.3 78.8 - - - +
49A ASP* 1.3 83.3 + - - +
50A VAL 3.5 0.2 - - - -
52A ASP* 3.7 24.0 - - - +
53A HIS* 4.3 3.1 + - - +
207A CYS* 3.7 26.8 - - - -
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Residues in contact with ASP 49 (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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43A LYS 4.4 2.8 - - - +
44A PHE* 3.6 28.8 - - + -
45A ASN 3.0 33.0 + - - +
48A SER* 1.3 95.8 + - - +
50A VAL* 1.3 62.7 + - + +
53A HIS* 4.3 10.1 - - - +
243A LYS* 5.6 4.4 - - + +
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Residues in contact with VAL 50 (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 PHE* 4.4 11.2 - - + -
46A PHE* 3.2 36.5 + - + +
49A ASP* 1.3 84.1 - - + +
51A LEU* 1.3 70.5 + - - +
52A ASP 3.2 1.3 - - - -
53A HIS* 3.2 15.1 + - - +
54A TRP* 3.3 20.8 + - - +
243A LYS* 4.2 26.0 - - + -
277A TRP 3.4 25.8 - - - +
278A ALA* 3.7 17.0 - - - +
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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
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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