Contacts of the helix formed by residues 56 - 65 (chain F) in PDB entry 3LUE
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 ASP 56 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54F VAL 3.4 1.9 + - - +
55F GLY* 1.3 68.9 - - - -
57F GLU* 1.3 62.9 + - - +
58F ALA 2.9 4.9 - - - -
59F GLN* 2.9 26.6 + - + +
60F SER* 3.1 19.8 + - - +
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Residues in contact with GLU 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F LYS* 3.6 1.6 + - - -
54F VAL 3.3 20.4 + - - +
56F ASP* 1.3 81.0 + - - +
58F ALA* 1.3 47.2 - - - +
60F SER* 4.4 2.9 - - - -
61F LYS* 4.4 0.4 + - - +
149H THR* 5.2 7.6 + - + +
166H TYR* 2.1 36.3 + - - -
167H GLU* 2.7 24.4 - - - +
289H ILE* 5.5 0.2 - - - -
292H ASP* 4.7 17.7 - - - +
127Q GLU* 5.2 3.1 - - - +
128Q GLU* 2.7 35.8 - - - +
136Q MET* 6.2 0.2 - - - -
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Residues in contact with ALA 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F ILE* 4.9 2.5 - - - +
36F GLY 4.5 0.9 - - - +
53F TYR* 3.6 31.9 - - + +
54F VAL* 4.0 2.2 - - - +
55F GLY 3.5 12.5 + - - +
56F ASP 2.9 0.8 - - - -
57F GLU* 1.3 67.8 - - - +
59F GLN* 1.3 64.9 + - - +
62F ARG* 3.3 17.0 + - - +
65F LEU* 4.5 1.8 - - + -
67F LEU* 3.7 22.7 - - + +
166H TYR* 1.5 43.6 + - + +
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Residues in contact with GLN 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F SER 5.1 6.6 - - - +
34F ILE* 4.4 12.3 - - + +
55F GLY 3.5 4.1 + - - +
56F ASP* 2.9 23.8 + - + +
58F ALA* 1.3 79.2 - - - +
60F SER* 1.3 57.3 + - - +
61F LYS 3.1 0.2 - - - -
62F ARG* 2.8 69.8 + - - +
70F PRO* 5.8 3.1 - - - +
203F THR* 3.4 9.5 - - - +
207F GLU* 4.9 12.8 - - + +
288H ASP* 3.8 22.4 - - + +
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Residues in contact with SER 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F ASP* 3.1 14.8 + - - +
57F GLU 5.1 0.4 - - - -
58F ALA 3.3 0.4 - - - +
59F GLN* 1.3 73.0 - - - +
61F LYS* 1.3 46.2 - - - +
204F ALA* 3.6 2.3 - - - +
286H ASP* 3.8 5.4 - - - -
288H ASP* 1.6 62.1 + - - +
289H ILE* 1.2 99.0 - - - +
291H LYS* 4.8 0.2 - - - +
292H ASP* 4.6 3.1 + - - -
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Residues in contact with LYS 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F GLU 4.4 0.2 + - - -
59F GLN 3.1 0.4 - - - -
60F SER* 1.3 73.8 - - - +
62F ARG* 1.4 56.5 + - - +
63F GLY 3.2 3.1 - - - -
64F ILE* 2.8 25.2 + - + -
65F LEU 2.9 8.7 + - - -
149H THR* 1.5 46.2 - - - +
165H ILE 3.1 2.7 + - - -
166H TYR* 0.8 329.2 - - + +
286H ASP* 3.8 4.0 + - - -
289H ILE* 2.9 28.5 - - + +
293H LEU* 5.2 0.6 - - - +
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Residues in contact with ARG 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F ILE* 4.8 5.1 - - - +
58F ALA 3.3 13.5 + - - +
59F GLN* 2.8 53.1 + - - +
61F LYS* 1.4 72.1 - - - +
63F GLY* 1.3 63.6 + - - +
65F LEU* 2.9 27.6 - - - +
67F LEU* 3.9 27.8 - - + +
69F TYR* 3.9 14.6 + - - -
70F PRO* 4.9 13.5 - - - +
77F THR* 5.7 1.4 + - - -
78F ASN* 4.4 25.1 - - - +
203F THR* 4.2 13.0 - - + -
166H TYR* 4.5 0.4 - - - -
286H ASP* 3.5 1.0 + - - +
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Residues in contact with GLY 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F LYS 3.2 0.6 - - - -
62F ARG* 1.3 85.0 - - - +
64F ILE* 1.3 60.0 + - - +
65F LEU 3.6 0.7 + - - +
286H ASP* 3.2 13.9 + - - -
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Residues in contact with ILE 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F PRO 4.1 9.0 - - - +
61F LYS* 2.8 27.0 + - + +
63F GLY* 1.3 73.2 - - - +
65F LEU* 1.4 59.8 + - + +
166H TYR* 3.0 28.9 - - + +
169H TYR* 5.6 1.9 - - - +
171H LEU* 1.5 92.7 - - + -
172H PRO* 5.9 0.9 - - + -
173H HIS* 3.5 27.1 - - + +
286H ASP* 4.8 4.7 + - + +
289H ILE* 4.1 0.2 - - + -
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Residues in contact with LEU 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F GLY* 3.9 15.9 - - - +
37F ARG 4.2 3.1 - - - +
38F PRO* 3.6 38.1 - - + -
53F TYR* 3.8 12.1 - - + -
58F ALA* 4.4 2.2 - - + +
61F LYS 2.9 6.1 + - - +
62F ARG* 2.9 18.7 + - - +
63F GLY 3.4 0.7 - - - +
64F ILE* 1.4 85.3 - - + +
66F THR* 1.3 66.4 + - - +
67F LEU* 3.8 4.7 + - + +
166H TYR* 2.3 65.5 - - + +
169H TYR* 3.8 5.2 - - + -
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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