Contacts of the helix formed by residues 44 - 58 (chain B) in PDB entry 3LWE
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 CYS 44 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0A GLY* 2.8 42.4 - - - +
2A ASP* 4.9 4.3 - - - -
3A VAL* 3.8 21.1 - - - -
6B VAL* 5.3 0.4 - - - -
40B HIS 4.5 1.3 - - - -
41B LEU* 2.8 26.7 + - + +
42B GLU 3.4 0.6 - - - -
43B ASP* 1.3 76.9 - - - +
45B LYS* 1.3 64.6 + - - +
46B GLU 3.4 2.2 - - - -
47B VAL* 3.2 16.6 + - + -
48B LEU* 2.9 25.6 + - - +
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Residues in contact with LYS 45 (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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42B GLU 5.6 0.2 - - - -
43B ASP 3.2 8.3 + - - +
44B CYS* 1.3 74.3 - - - +
46B GLU* 1.3 66.6 + - + +
48B LEU* 3.4 9.9 + - - +
49B LEU* 3.0 28.5 + - - +
52B ARG* 5.2 1.2 + - - -
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Residues in contact with GLU 46 (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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44B CYS 3.4 0.2 - - - -
45B LYS* 1.3 83.7 - - - +
47B VAL* 1.3 63.9 + - + +
49B LEU* 3.6 23.7 - - - +
50B GLU* 2.9 36.8 + - + +
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Residues in contact with VAL 47 (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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0A GLY* 4.0 26.2 - - - +
6B VAL* 4.1 28.9 - - + +
7B GLU 4.5 7.4 - - - +
8B LYS* 4.5 2.9 - - - +
9B ILE* 3.8 33.1 + - + +
41B LEU* 4.5 6.5 - - + -
44B CYS* 3.2 14.9 + - + +
46B GLU* 1.3 79.2 - - + +
48B LEU* 1.3 63.3 - - + +
50B GLU* 3.3 8.3 + - - +
51B PHE* 3.1 21.1 + - - +
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Residues in contact with LEU 48 (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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9B ILE* 4.0 13.2 - - + -
21B TYR* 3.7 36.8 - - + +
41B LEU* 3.4 26.5 - - + +
42B GLU* 3.7 18.8 - - - +
44B CYS* 2.9 20.5 + - + +
45B LYS* 3.6 7.9 - - - +
47B VAL* 1.3 76.3 - - + +
49B LEU* 1.3 61.9 + - - +
51B PHE* 3.0 5.9 + - + +
52B ARG* 2.9 43.0 + - - +
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Residues in contact with LEU 49 (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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45B LYS 3.0 17.6 + - - +
46B GLU* 3.6 27.8 - - - +
47B VAL 3.4 0.2 - - - -
48B LEU* 1.3 73.5 - - - +
50B GLU* 1.3 66.5 + - - +
52B ARG* 3.2 30.7 + - + +
53B LYS* 2.9 45.2 + - + +
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Residues in contact with GLU 50 (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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8B LYS* 6.0 7.2 - - + -
46B GLU* 2.9 24.3 + - + +
47B VAL* 3.6 7.6 - - - +
49B LEU* 1.3 78.4 - - - +
51B PHE* 1.3 57.1 + - - +
53B LYS* 3.4 23.0 + - - +
54B LYS* 2.9 27.0 + - - +
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Residues in contact with PHE 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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9B ILE* 3.6 40.2 - - + +
10B LEU 4.1 4.7 - - - -
11B ASP* 3.9 38.8 - - - -
12B MET* 3.8 26.9 - - + -
21B TYR* 4.0 14.6 - + - -
47B VAL 3.1 12.4 + - - +
48B LEU* 3.0 10.9 + - + +
50B GLU* 1.3 75.0 - - - +
52B ARG* 1.3 67.6 + - + +
54B LYS* 3.1 17.7 + - + -
55B ILE* 3.0 51.7 + - + +
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Residues in contact with ARG 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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45B LYS 5.2 1.0 + - - -
48B LEU* 2.9 32.0 + - - +
49B LEU* 3.6 41.4 - - + +
51B PHE* 1.3 77.0 - - + +
53B LYS* 1.3 53.3 + - + +
55B ILE* 3.2 13.6 + - + +
56B ALA* 2.7 36.9 + - - +
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Residues in contact with LYS 53 (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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49B LEU* 2.9 31.0 + - + +
50B GLU* 3.6 30.3 - - - +
52B ARG* 1.3 75.7 - - + +
54B LYS* 1.3 59.4 + - - +
56B ALA* 3.8 6.4 - - - +
57B GLU* 2.9 38.4 + - + +
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Residues in contact with LYS 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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8B LYS* 6.1 2.2 - - - +
9B ILE 4.6 4.9 + - - +
10B LEU* 2.8 37.1 + - - +
11B ASP* 4.8 3.7 + - - -
50B GLU 2.9 14.5 + - - +
51B PHE* 3.1 29.4 + - + +
53B LYS* 1.3 73.1 - - - +
55B ILE* 1.3 53.8 + - + +
57B GLU* 3.2 6.9 + - - +
58B ASN* 2.8 55.9 + - - +
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Residues in contact with ILE 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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12B MET* 4.4 12.8 - - + -
51B PHE* 3.0 51.3 + - + +
52B ARG* 3.4 13.9 - - + +
54B LYS* 1.3 75.4 - - + +
56B ALA* 1.3 64.4 + - - +
58B ASN* 3.0 28.3 + - - +
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Residues in contact with ALA 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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52B ARG 2.7 20.8 + - - +
53B LYS* 3.8 8.3 - - + +
55B ILE* 1.3 75.0 - - - +
57B GLU* 1.3 64.0 + - + +
58B ASN 4.3 2.3 - - - -
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Residues in contact with GLU 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 LYS* 2.9 32.4 + - + +
54B LYS* 3.5 7.0 - - - +
56B ALA* 1.3 75.9 - - + +
58B ASN* 1.3 62.2 + - - +
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Residues in contact with ASN 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 LYS* 2.8 54.6 + - - +
55B ILE* 3.3 17.6 - - - +
56B ALA 4.3 2.2 - - - -
57B GLU* 1.3 79.7 - - - +
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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