Contacts of the helix formed by residues 46 - 55 (chain E) in PDB entry 6MUO
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 GLY 46 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45E GLN* 1.3 77.7 - - - +
47E TRP* 1.3 63.9 + - - +
48E LEU 3.5 0.7 - - - -
49E LYS* 4.4 1.1 - - - +
50E GLU* 3.5 26.7 + - - +
9I A 3.2 38.0 + - - -
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Residues in contact with TRP 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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111C ILE* 5.4 4.5 - - + -
115C LEU* 3.2 26.7 - - + -
116C LEU* 3.7 21.5 - - + -
45E GLN* 3.0 25.9 - - - +
46E GLY* 1.3 76.3 - - - +
48E LEU* 1.3 98.5 + - + +
50E GLU* 3.5 2.4 + - - +
51E ILE* 3.2 45.5 + - + +
39F ARG* 3.5 28.0 - - - +
44F LYS* 3.5 51.2 - - + +
8I A 5.3 5.6 - - - +
9I A 3.7 15.0 + - - +
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Residues in contact with LEU 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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111C ILE* 5.1 7.2 - - + -
116C LEU* 4.5 11.4 - - + -
45E GLN* 3.9 21.1 - - + +
46E GLY 3.5 0.2 - - - -
47E TRP* 1.3 115.2 - - + +
49E LYS* 1.3 73.7 + - + +
50E GLU 3.5 0.2 + - - -
51E ILE* 4.3 5.3 - - + +
52E ARG* 3.2 66.6 + - + +
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Residues in contact with LYS 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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45E GLN* 4.4 30.5 - - + +
46E GLY 4.0 2.5 + - - +
47E TRP 3.4 0.2 - - - -
48E LEU* 1.3 88.8 - - + +
50E GLU* 1.3 62.4 + - - +
52E ARG* 4.4 10.0 - - - +
53E LYS* 3.5 21.7 + - - +
-67I T 4.6 8.9 + - - -
-66I A 3.8 20.9 + - - +
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Residues in contact with GLU 50 (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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46E GLY 3.5 19.5 + - - +
47E TRP* 3.5 3.9 + - - +
48E LEU 3.2 0.6 - - - -
49E LYS* 1.3 78.9 - - - +
51E ILE* 1.3 64.3 + - + +
53E LYS* 3.4 10.2 + - + +
54E LEU* 3.2 33.4 + - + +
35F ARG* 5.4 4.7 - - - -
36F ARG* 3.8 26.8 - - - +
39F ARG* 4.3 24.8 + - + -
9I A 5.4 1.6 + - - -
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Residues in contact with ILE 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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110C ASN 5.4 2.0 - - - +
111C ILE* 5.8 10.1 - - + -
47E TRP* 3.2 38.9 + - + +
48E LEU* 4.3 7.0 - - + +
49E LYS 3.5 0.2 - - - -
50E GLU* 1.3 77.7 - - - +
52E ARG* 1.3 60.8 + - + +
54E LEU* 2.9 17.4 + - - +
55E GLN* 3.0 28.8 + - - +
39F ARG* 3.5 48.4 - - - +
42F GLY* 4.9 6.5 - - - -
43F VAL 3.8 27.1 - - - +
44F LYS* 4.6 0.4 - - - -
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Residues in contact with ARG 52 (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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111C ILE* 3.4 34.5 - - + +
48E LEU* 3.2 52.0 + - + +
49E LYS* 5.0 10.0 - - - +
51E ILE* 1.3 81.3 - - + +
53E LYS* 1.3 59.2 - - - +
55E GLN* 4.3 8.0 - - + +
56E LYS* 3.3 24.5 + - + +
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Residues in contact with LYS 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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49E LYS 3.5 19.0 + - - +
50E GLU* 3.4 11.9 + - + +
51E ILE 3.1 0.4 - - - -
52E ARG* 1.3 79.7 - - - +
54E LEU* 1.3 69.0 + - + +
56E LYS* 3.4 19.9 + - + +
57E SER* 3.6 11.4 + - - -
59E HIS* 6.4 0.4 - - - -
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Residues in contact with LEU 54 (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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50E GLU* 3.2 20.3 + - + +
51E ILE* 2.9 8.4 + - - +
53E LYS* 1.3 83.3 - - + +
55E GLN* 1.3 65.0 + - - +
56E LYS 3.1 1.5 + - - -
57E SER* 3.3 21.2 + - - +
59E HIS* 4.7 19.1 - - + +
61E LEU* 4.8 12.8 - - + -
36F ARG* 3.7 46.2 - - + +
39F ARG* 3.8 20.6 - - + -
40F ARG* 3.9 23.7 + - + +
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Residues in contact with GLN 55 (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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81C ARG* 3.9 16.5 + - - -
107C VAL* 4.0 18.5 + - + +
108C LEU 4.0 7.1 + - - +
109C PRO* 3.8 9.9 - - + +
110C ASN* 2.9 47.6 + - - +
111C ILE* 5.4 1.9 - - - +
51E ILE* 3.0 26.1 + - - +
52E ARG* 4.9 5.5 - - + +
54E LEU* 1.3 76.5 - - - +
56E LYS* 1.3 59.4 - - - +
57E SER 3.9 4.7 - - - +
107E GLU* 6.3 0.8 - - - -
39F ARG 4.3 1.8 + - - +
40F ARG* 2.5 47.7 + - + +
41F GLY 4.5 0.6 - - - -
42F GLY 4.3 5.7 - - - +
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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