Contacts of the helix formed by residues 56 - 65 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54J VAL 4.6 1.7 - - - +
55J GLY* 1.3 68.9 - - - -
57J GLU* 1.3 62.6 + - - +
58J ALA 2.9 4.9 - - - -
59J GLN* 2.9 26.4 + - + +
60J SER* 3.1 20.0 + - - +
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Residues in contact with GLU 57 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50J LYS* 3.6 6.1 + - - -
53J TYR* 3.6 23.3 - - + +
54J VAL 3.3 24.1 + - - +
56J ASP* 1.3 81.7 + - - +
58J ALA* 1.3 55.1 + - - +
60J SER* 4.4 7.6 - - - +
61J LYS* 4.3 18.8 + - - +
127T GLU* 5.1 3.3 - - - +
128T GLU* 2.7 36.8 - - - +
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Residues in contact with ALA 58 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34J ILE* 4.9 2.2 - - + +
36J GLY 4.5 0.4 - - - +
53J TYR* 3.6 35.4 - - + +
54J VAL* 4.0 2.2 - - - +
55J GLY 3.5 12.9 + - - +
56J ASP 2.9 0.6 - - - -
57J GLU* 1.3 77.2 - - - +
59J GLN* 1.3 65.7 + - - +
60J SER 3.3 1.1 - - - +
61J LYS 3.9 2.5 - - - +
62J ARG* 3.3 19.1 + - - +
65J LEU* 4.4 8.6 - - + +
67J LEU* 3.7 23.6 - - + +
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Residues in contact with GLN 59 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33J SER 5.1 6.9 - - - +
34J ILE* 4.4 11.9 - - - +
55J GLY 3.5 4.9 + - - +
56J ASP* 2.9 23.7 + - + +
58J ALA* 1.3 79.0 - - - +
60J SER* 1.3 59.3 + - - +
61J LYS 2.9 0.4 + - - -
62J ARG* 2.8 70.3 + - - +
70J PRO* 5.8 2.9 - - - +
203J THR* 3.4 13.8 - - + +
204J ALA* 5.2 9.2 - - - -
207J GLU* 4.9 15.8 - - + +
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Residues in contact with SER 60 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56J ASP 3.1 15.3 + - - -
57J GLU* 5.1 4.3 - - - -
58J ALA 3.3 0.6 - - - +
59J GLN* 1.3 75.1 - - - +
61J LYS* 1.3 68.8 + - - +
202J THR* 5.8 4.3 - - - +
203J THR* 4.1 18.2 + - - -
204J ALA* 3.6 28.3 - - - +
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Residues in contact with LYS 61 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44J MET* 5.3 7.7 - - - +
47J MET* 4.5 22.6 - - - +
53J TYR* 4.4 24.7 - - + -
57J GLU* 4.3 21.0 + - - +
58J ALA 3.9 2.2 + - - +
59J GLN 3.1 0.2 - - - -
60J SER* 1.3 87.4 + - - +
62J ARG* 1.4 56.3 + - - +
63J GLY 3.2 3.1 - - - -
64J ILE* 2.8 51.6 + - + +
65J LEU* 2.9 27.0 + - + +
203J THR* 4.7 1.3 + - - -
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Residues in contact with ARG 62 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34J ILE* 4.8 4.0 - - - +
58J ALA 3.3 14.2 + - - +
59J GLN* 2.8 54.1 + - - +
61J LYS* 1.4 73.0 - - - +
63J GLY* 1.3 64.2 + - - +
65J LEU* 2.9 28.0 - - - +
67J LEU* 3.9 29.2 - - + +
69J TYR* 3.9 15.0 + - - -
70J PRO* 4.9 13.3 - - - +
77J THR* 5.7 1.4 + - - -
78J ASN* 4.4 24.9 - - - +
203J THR* 4.2 14.3 - - + +
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Residues in contact with GLY 63 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61J LYS 3.2 0.4 - - - -
62J ARG* 1.3 85.6 - - - +
64J ILE* 1.3 60.6 + - - +
65J LEU 3.6 0.5 + - - +
203J THR* 4.9 6.6 + - - +
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Residues in contact with ILE 64 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38J PRO 4.1 9.0 - - - +
61J LYS* 2.8 56.2 + - + +
63J GLY* 1.3 74.0 - - - +
65J LEU* 1.4 64.1 + - + +
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Residues in contact with LEU 65 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36J GLY* 3.9 15.3 - - - +
37J ARG 4.2 3.1 - - - +
38J PRO* 3.6 39.3 - - + -
39J ARG* 5.7 0.2 - - - -
53J TYR* 3.8 29.8 - - + -
58J ALA* 4.4 9.4 - - + +
61J LYS* 2.9 40.0 + - + +
62J ARG* 2.9 19.8 + - - +
63J GLY 3.4 0.7 - - - +
64J ILE* 1.4 91.1 - - + +
66J THR* 1.3 65.7 + - - +
67J LEU* 3.8 4.9 + - + +
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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