Contacts of the helix formed by residues 55 - 66 (chain B) in PDB entry 1VBF
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 ALA 55 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B THR 3.7 2.5 - - - +
42B HIS* 3.5 34.8 - - - +
43B GLU 3.4 15.2 + - - +
44B ALA* 4.2 4.5 - - + +
53B THR 3.5 1.2 + - - -
54B THR* 1.3 76.2 - - - +
56B LEU* 1.3 55.0 - - - +
57B ASN* 5.2 0.2 - - + -
58B LEU* 2.9 18.8 + - + +
59B GLY 2.7 31.5 + - - -
84B TYR* 3.3 0.7 + - - -
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Residues in contact with LEU 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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7B ILE* 3.8 18.8 - - + -
20B PHE* 3.9 15.7 - - + -
25B ARG* 3.5 28.9 - - - +
37B ALA 3.7 21.1 - - - +
38B TYR* 4.1 9.2 - - + -
41B THR* 3.3 22.6 + - - +
43B GLU 4.6 1.0 + - - -
54B THR 3.4 2.6 + - - -
55B ALA* 1.3 71.6 - - - +
57B ASN* 1.3 63.5 + - - +
60B ILE* 3.0 60.6 + - + +
83B TYR* 4.0 13.9 - - + -
84B TYR* 3.5 9.0 - - - +
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Residues in contact with ASN 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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3B GLU* 5.0 0.6 + - - -
6B GLU* 6.2 2.0 - - - +
7B ILE* 4.1 17.6 - - - +
10B LYS* 3.6 25.8 + - - +
41B THR* 3.0 37.6 + - + +
42B HIS* 3.1 37.3 + - + +
55B ALA* 5.2 0.4 - - + -
56B LEU* 1.3 76.5 - - - +
58B LEU* 1.3 64.2 + - - +
60B ILE* 4.3 2.4 - - - +
61B PHE* 3.3 21.7 + - - +
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Residues in contact with LEU 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 THR* 3.6 6.3 - - + -
55B ALA* 2.9 19.8 + - + +
57B ASN* 1.3 79.8 - - - +
59B GLY* 1.3 58.9 + - - +
61B PHE* 3.1 18.5 + - + +
62B MSE 2.9 66.2 + - + +
173B LEU* 4.9 2.0 - - + -
191B VAL* 4.1 23.1 - - + -
192B MSE 5.5 2.0 - - - +
193B PHE* 3.6 22.2 - - + -
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Residues in contact with GLY 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 2.7 16.4 + - - -
58B LEU* 1.3 73.1 - - - +
60B ILE* 1.3 55.3 + - - +
62B MSE 3.2 3.8 + - - +
63B LEU* 2.9 34.1 + - - +
84B TYR* 3.5 27.8 - - - -
141B TRP* 3.7 19.2 - - - -
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Residues in contact with ILE 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 3.8 22.2 - - + -
11B ILE* 3.6 36.6 - - + -
16B LEU* 3.8 7.0 - - + +
20B PHE* 3.6 19.5 - - + -
56B LEU* 3.0 41.7 + - + +
57B ASN 4.3 1.3 - - - +
59B GLY* 1.3 78.6 - - - +
61B PHE* 1.3 57.6 + - - +
63B LEU* 3.5 4.4 + - + +
64B ASP* 2.8 32.3 + - + +
84B TYR* 4.3 2.9 - - + -
87B LEU* 3.8 21.5 - - + -
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Residues in contact with PHE 61 (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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57B ASN* 3.3 13.4 + - - +
58B LEU* 3.1 23.2 + - + +
60B ILE* 1.3 80.4 - - - +
62B MSE 1.3 62.4 + - + +
64B ASP* 3.3 7.3 + - + +
65B GLU* 2.9 69.4 + - + +
173B LEU* 4.4 7.0 - - + -
188B LEU* 4.2 33.0 - - + -
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Residues in contact with MSE 62 (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 THR* 3.2 24.9 - - + -
58B LEU* 2.9 36.2 + - + +
59B GLY 3.6 5.8 - - - +
61B PHE* 1.3 78.8 - - + +
63B LEU* 1.3 63.5 + - - +
65B GLU* 3.1 5.7 + - - -
66B LEU* 3.0 19.9 + - - +
139B VAL* 4.9 4.7 - - + -
140B VAL 5.1 5.2 - - - +
141B TRP* 3.2 27.4 - - + -
162B ILE* 3.4 24.4 - - + +
173B LEU* 3.9 28.9 - - + -
193B PHE* 3.2 36.3 - - + -
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Residues in contact with LEU 63 (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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13B THR* 5.4 0.5 + - - -
16B LEU* 4.1 15.9 - - + +
59B GLY 2.9 19.2 + - - +
60B ILE* 4.0 4.0 - - + +
62B MSE 1.3 76.3 - - - +
64B ASP* 1.3 63.7 + - - +
66B LEU* 3.0 31.7 + - + +
67B ASP 3.8 2.6 + - - -
68B LEU* 4.1 15.7 + - + +
84B TYR* 3.9 27.6 - - + +
87B LEU* 4.0 28.5 - - + -
88B ILE* 4.0 25.1 - - + -
139B VAL* 4.4 4.5 - - + -
141B TRP* 3.8 23.6 - - + -
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Residues in contact with ASP 64 (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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10B LYS 3.8 4.0 - - - +
11B ILE* 3.5 14.9 - - - +
12B LYS* 2.8 32.1 + - - +
13B THR* 2.9 43.6 + - - -
16B LEU* 3.6 9.1 - - + +
60B ILE* 2.8 20.6 + - + +
61B PHE* 3.6 8.9 - - + +
62B MSE 3.2 0.2 - - - -
63B LEU* 1.3 77.2 - - - +
65B GLU* 1.3 64.6 + - + +
66B LEU 3.4 0.5 + - - -
67B ASP* 3.6 8.1 + - - +
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Residues in contact with GLU 65 (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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61B PHE* 2.9 55.0 + - + +
62B MSE 3.1 6.2 + - - +
64B ASP* 1.3 76.1 - - + +
66B LEU* 1.3 59.7 + - - +
67B ASP* 3.2 5.7 + - - +
160B ILE* 4.6 0.3 - - - +
162B ILE* 3.5 16.0 - - + +
175B LYS* 3.1 52.4 + - - +
186B GLU* 5.0 1.7 - - - +
188B LEU* 4.0 15.9 - - + +
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Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B MSE 3.0 11.3 + - - +
63B LEU* 3.0 19.4 + - + +
65B GLU* 1.3 76.3 - - - +
67B ASP* 1.3 54.3 + - - +
68B LEU* 3.7 28.7 - - + -
74B VAL* 4.7 2.7 - - + -
88B ILE* 5.0 0.7 - - + -
137B ARG* 2.7 69.2 + - + -
138B VAL 4.0 10.3 - - - +
139B VAL* 3.1 33.7 - - + -
160B ILE* 3.8 19.9 - - + +
162B ILE* 3.9 10.3 - - + -
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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