Contacts of the helix formed by residues 50 - 60 (chain B) 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 VAL 50 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B PHE* 4.3 10.3 - - + -
46B PHE* 3.1 44.6 + - + +
49B ASP* 1.3 82.6 - - - +
51B LEU* 1.3 70.6 + - - +
52B ASP 3.3 1.1 - - - -
53B HIS* 3.3 14.1 - - - +
54B TRP* 3.2 21.4 + - - +
243B LYS* 4.2 27.8 - - + -
277B TRP 3.3 24.7 - - - +
278B ALA* 3.8 10.8 - - - +
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Residues in contact with LEU 51 (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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46B PHE* 3.1 13.4 + - + +
47B ALA* 3.3 11.2 - - - +
50B VAL* 1.3 81.2 - - - +
52B ASP* 1.3 59.2 + - - +
54B TRP* 3.1 21.7 + - - +
55B ALA* 3.3 9.9 + - - +
83B PHE* 4.0 18.5 - - + +
86B LEU* 3.8 26.7 - - + -
87B SER* 4.9 5.4 - - - -
90B SER* 4.4 0.9 - - - +
124B LEU* 3.3 39.7 - - + -
128B ARG* 3.9 19.5 - - - +
277B TRP* 4.0 24.9 - - + +
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Residues in contact with ASP 52 (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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47B ALA 3.0 17.5 + - - +
48B SER* 3.8 19.4 + - - +
50B VAL 3.3 0.2 - - - -
51B LEU* 1.3 72.3 - - - +
53B HIS* 1.3 66.1 + - - +
55B ALA* 3.8 6.7 - - + +
56B ASP* 2.9 36.2 + - - +
87B SER* 3.0 16.0 + - - -
91B GLN* 4.8 2.8 + - - -
128B ARG* 2.9 40.7 + - - -
207B CYS* 5.5 0.7 - - - +
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Residues in contact with HIS 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B SER 4.5 4.0 + - - -
49B ASP 4.3 9.9 - - - +
50B VAL* 3.3 15.9 + - - +
52B ASP* 1.3 79.2 - - - +
54B TRP* 1.3 98.7 + + - +
56B ASP* 3.2 7.2 + - - +
57B MET* 3.1 51.0 + - + +
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Residues in contact with TRP 54 (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 VAL* 3.2 23.4 + - - +
51B LEU* 3.1 9.3 + - - +
53B HIS* 1.3 100.5 - + - +
55B ALA* 1.3 63.3 + - - +
57B MET* 3.3 23.7 + - + +
58B GLU* 3.3 16.1 + - - +
63B ARG* 3.6 36.4 + - - +
83B PHE* 3.7 28.0 - + + -
253B ALA* 5.4 3.6 - - + -
277B TRP 2.9 28.1 + - - -
278B ALA 3.4 12.6 + - - -
279B LEU* 3.5 25.4 - - - -
280B GLY* 3.5 12.3 - - - +
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Residues in contact with ALA 55 (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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51B LEU 3.3 7.6 + - - +
52B ASP* 3.8 8.3 - - + +
54B TRP* 1.3 77.6 - - - +
56B ASP* 1.3 63.2 + - - +
58B GLU* 3.0 14.5 + - - +
59B LYS* 3.0 25.5 + - - +
83B PHE* 3.5 30.1 - - - +
84B ARG* 3.9 9.3 - - - +
87B SER* 3.6 20.9 - - - +
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Residues in contact with ASP 56 (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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75A LYS* 5.9 5.4 - - + +
52B ASP* 2.9 30.6 + - - +
53B HIS* 3.6 6.8 - - - +
55B ALA* 1.3 73.7 - - - +
57B MET* 1.3 56.5 + - - +
59B LYS* 3.9 22.8 + - - +
60B ALA* 3.0 33.7 + - + +
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Residues in contact with MET 57 (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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53B HIS* 3.1 48.7 + - + +
54B TRP* 3.4 23.1 - - + +
56B ASP* 1.3 77.8 - - + +
58B GLU* 1.3 60.1 + - - +
60B ALA* 4.8 0.7 - - - -
61B GLY 3.4 1.6 + - - -
62B LYS* 2.9 66.3 + - + +
63B ARG* 3.2 22.5 + - + -
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Residues in contact with GLU 58 (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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54B TRP 3.6 7.8 - - - +
55B ALA 3.0 7.2 + - - +
57B MET* 1.3 74.2 - - - +
59B LYS* 1.3 66.7 + - - +
61B GLY* 3.0 15.2 + - - -
63B ARG* 3.5 17.0 + - + +
64B PRO 3.8 14.1 - - - +
65B PRO* 3.7 10.8 - - + +
66B SER* 3.1 29.3 + - - +
82B ASN* 3.5 15.4 + - - +
83B PHE* 3.3 34.4 + - - +
84B ARG* 3.3 25.3 + - + +
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Residues in contact with LYS 59 (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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55B ALA* 3.0 23.7 + - - +
56B ASP* 3.9 25.6 + - - +
58B GLU* 1.3 76.5 - - - +
60B ALA* 1.3 61.0 + - - +
61B GLY 3.4 0.7 + - - -
84B ARG* 3.4 55.4 + - - +
87B SER* 5.2 6.5 + - - -
88B GLU* 5.4 8.4 + - - +
91B GLN* 5.3 6.1 - - - +
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Residues in contact with ALA 60 (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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75A LYS* 5.6 11.0 - - + +
56B ASP 3.0 20.5 + - - +
57B MET 4.3 2.5 - - - +
59B LYS* 1.3 76.6 - - + +
61B GLY* 1.3 60.1 + - - +
62B LYS* 3.4 25.2 + - + +
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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