Contacts of the helix formed by residues 45 - 56 (chain E) in PDB entry 6WNX
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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8E SER* 3.8 2.5 - - - -
9E SER* 3.2 17.9 + - - +
10E ASP* 3.5 11.9 - - - +
43E ASN 4.4 0.6 + - - -
44E VAL* 1.3 75.0 - - - +
46E ALA* 1.3 58.8 + - - +
47E ALA* 3.4 12.9 + - - +
48E ILE* 2.9 36.5 + - - +
49E LEU* 2.9 26.7 + - - +
84E GLU* 5.5 5.3 + - - +
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Residues in contact with ALA 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E SER* 3.6 9.8 - - - +
10E ASP* 3.4 21.8 + - - +
12E GLU* 2.9 29.8 - - - +
14E PHE* 4.2 10.9 - - + -
45E ASN* 1.3 71.0 - - - +
47E ALA* 1.3 68.8 + - - +
49E LEU* 2.8 6.3 + - - +
50E LYS* 2.8 27.1 + - - +
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Residues in contact with ALA 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E ASN* 3.5 14.5 - - - +
46E ALA* 1.3 80.4 - - - +
48E ILE* 1.3 65.4 + - + +
50E LYS* 3.3 21.6 - - - +
51E LYS* 3.4 17.1 - - - +
81E THR* 6.5 0.4 - - + -
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Residues in contact with ILE 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E VAL* 4.0 9.4 - - + -
45E ASN* 2.9 29.7 + - - +
47E ALA* 1.3 74.6 - - + +
49E LEU* 1.3 65.9 + - - +
51E LYS* 3.1 13.2 + - + +
52E VAL* 3.0 22.4 + - + +
81E THR* 4.1 22.7 - - + +
84E GLU* 3.6 35.4 - - + +
85E LEU* 4.0 21.1 - - + -
88E ALA* 3.8 28.9 - - + -
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Residues in contact with LEU 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E LEU* 4.4 30.7 - - + +
7E GLN 4.7 0.4 - - - -
8E SER* 4.1 28.5 - - - +
14E PHE* 3.3 32.3 - - + -
27E ILE* 6.2 0.2 - - + -
41E LEU* 4.8 15.7 - - + -
44E VAL* 4.2 11.2 - - + +
45E ASN 2.9 17.1 + - - +
46E ALA 2.8 5.1 + - - +
48E ILE* 1.3 78.4 - - - +
50E LYS* 1.3 62.1 + - - +
52E VAL* 3.2 26.9 + - + +
53E ILE* 3.2 17.7 + - + +
92E LEU* 5.6 3.4 - - + -
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Residues in contact with LYS 50 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14E PHE* 4.1 17.6 - - + -
46E ALA* 2.8 11.1 + - + +
47E ALA* 3.3 16.4 - - - +
49E LEU* 1.3 74.5 - - - +
51E LYS* 1.3 64.1 + - + +
52E VAL 3.1 1.4 + - - -
53E ILE* 3.1 24.6 + - + +
54E GLN* 3.3 18.5 + - + +
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Residues in contact with LYS 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E ALA* 3.4 18.6 - - - +
48E ILE* 3.1 15.7 + - + +
50E LYS* 1.3 79.8 - - + +
52E VAL* 1.3 57.0 + - - +
54E GLN* 3.3 16.9 - - - +
55E TRP* 3.0 23.6 + - - +
74E PHE* 3.6 25.8 - - + -
76E LYS 4.9 5.3 + - - -
77E VAL* 4.0 22.3 - - + +
81E THR* 4.9 12.1 - - - +
85E LEU* 4.0 27.4 - - + -
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Residues in contact with VAL 52 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44E VAL* 5.4 0.7 - - + -
48E ILE* 3.0 28.0 + - + +
49E LEU* 3.4 18.6 - - + +
50E LYS 3.1 0.4 - - - -
51E LYS* 1.3 74.0 - - - +
53E ILE* 1.3 67.2 + - + +
55E TRP* 3.0 8.0 + - - +
56E CYS* 2.9 38.5 + - - -
85E LEU* 4.8 4.3 - - + -
88E ALA* 5.0 3.8 - - + -
92E LEU* 4.3 19.7 - - + -
94E ILE* 4.3 15.7 - - + -
97E LEU* 4.7 14.6 - - + -
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Residues in contact with ILE 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E LEU* 6.0 1.8 - - + -
14E PHE* 3.9 32.8 - - + -
16E VAL* 4.2 27.1 - - + -
20E ILE* 4.7 5.6 - - + +
49E LEU* 3.2 20.8 + - + +
50E LYS* 3.1 12.7 + - + +
52E VAL* 1.3 76.1 - - + +
54E GLN* 1.3 67.1 + - + +
56E CYS* 2.9 29.8 + - - +
57E THR* 4.5 1.0 - - - +
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Residues in contact with GLN 54 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50E LYS* 3.3 11.8 + - - +
51E LYS* 3.3 19.1 - - - +
53E ILE* 1.3 80.7 - - + +
55E TRP* 1.3 64.0 + - - +
57E THR* 3.3 21.6 + - - +
70E TRP* 4.1 11.4 - - + -
74E PHE* 3.9 20.8 - - + -
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Residues in contact with TRP 55 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23E GLN* 4.8 10.5 - - + -
51E LYS 3.0 16.1 + - - +
52E VAL* 3.0 8.7 + - - +
54E GLN* 1.3 76.0 - - - +
56E CYS* 1.3 75.7 + - - +
57E THR* 3.0 17.3 + - - -
58E HIS* 3.9 23.5 + + - -
59E HIS* 6.5 0.2 - - - -
61E ASP* 3.8 19.3 - - - -
70E TRP* 4.9 3.4 - - - -
71E ASP* 4.2 17.3 + - + -
74E PHE* 3.6 36.5 - + + -
94E ILE* 3.7 19.7 - - + -
95E LYS 4.3 2.0 - - - -
96E GLY* 3.6 12.8 - - - -
97E LEU* 3.4 54.0 - - + +
100E VAL* 4.0 11.6 - - + +
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Residues in contact with CYS 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E ILE* 3.5 42.0 - - + +
21E ALA* 6.0 1.1 - - - -
23E GLN* 4.5 17.9 - - + -
24E SER 5.6 0.7 - - - -
52E VAL* 2.9 31.1 + - - +
53E ILE* 2.9 17.3 + - - +
55E TRP* 1.3 93.9 - - - +
57E THR* 1.3 61.8 + - - +
58E HIS 5.0 0.9 - - - -
94E ILE* 4.5 10.5 - - - -
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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