Contacts of the helix formed by residues 56 - 65 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54H VAL 3.4 2.1 + - - +
55H GLY* 1.3 68.6 - - - -
57H GLU* 1.3 63.8 + - - +
58H ALA 2.9 5.2 - - - -
59H GLN* 2.9 25.5 + - + +
60H SER* 3.1 19.2 + - - -
292J ASP* 5.5 0.2 - - - +
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Residues in contact with GLU 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H LYS* 3.6 1.3 + - - -
53H TYR* 3.8 0.2 - - - -
54H VAL 3.3 20.5 + - - +
56H ASP* 1.3 81.7 + - - +
58H ALA* 1.3 47.4 - - - +
60H SER* 4.4 2.9 - - - +
61H LYS* 4.4 0.7 + - - -
149J THR* 5.2 7.3 + - + +
166J TYR* 2.1 37.0 - - - -
167J GLU* 2.7 24.2 - - - +
289J ILE* 5.5 0.2 - - - -
292J ASP* 4.7 17.7 - - - +
127S GLU* 5.1 2.3 - - - +
128S GLU* 2.7 35.9 - - - +
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Residues in contact with ALA 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H ILE* 4.9 2.9 - - + +
36H GLY 4.5 0.7 - - - +
53H TYR* 3.6 32.5 - - + +
54H VAL 4.0 1.6 - - - +
55H GLY 3.5 11.6 + - - +
56H ASP 2.9 0.6 - - - -
57H GLU* 1.3 68.2 - - - +
59H GLN* 1.3 67.0 + - - +
62H ARG* 3.3 17.0 + - - +
65H LEU* 4.5 1.8 - - + -
67H LEU* 3.7 22.1 - - + +
166J TYR* 1.5 43.1 + - - +
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Residues in contact with GLN 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H SER 5.1 6.9 - - - +
34H ILE* 4.4 12.3 - - + +
55H GLY 3.5 4.5 + - - +
56H ASP* 2.9 23.2 + - + +
58H ALA* 1.3 79.6 - - - +
60H SER* 1.3 56.3 + - - +
61H LYS 2.9 0.2 + - - -
62H ARG* 2.8 70.7 + - - +
67H LEU* 5.4 0.6 - - - +
70H PRO* 5.8 2.8 - - - +
203H THR* 3.4 9.5 - - - +
207H GLU* 4.9 14.2 - - + +
288J ASP* 3.8 22.0 - - + +
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Residues in contact with SER 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56H ASP 3.1 15.3 + - - -
57H GLU 5.1 0.2 - - - -
58H ALA 3.3 0.2 - - - -
59H GLN* 1.3 72.6 - - - +
61H LYS* 1.3 45.3 - - - +
204H ALA* 3.6 1.7 - - - +
166J TYR* 4.2 0.2 - - - -
286J ASP* 3.8 5.2 - - - -
288J ASP* 1.6 63.0 + - - +
289J ILE* 1.2 100.2 - - - +
292J ASP* 4.6 3.3 + - - -
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Residues in contact with LYS 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59H GLN 2.9 0.6 + - - -
60H SER* 1.3 73.5 - - - +
62H ARG* 1.4 55.6 + - - +
63H GLY 3.2 2.7 - - - -
64H ILE* 2.8 24.3 + - - -
65H LEU 2.9 8.1 + - - -
149J THR* 1.5 45.8 - - - +
165J ILE 3.1 2.0 - - - -
166J TYR* 0.8 331.5 - - + +
286J ASP* 3.8 4.0 + - - -
289J ILE* 2.9 29.5 - - + +
293J LEU* 5.2 0.9 - - - +
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Residues in contact with ARG 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34H ILE* 4.8 4.2 - - - +
58H ALA 3.3 13.7 + - - +
59H GLN* 2.8 53.3 + - - +
61H LYS* 1.4 73.4 - - - +
63H GLY* 1.3 65.2 + - - +
65H LEU* 2.9 26.7 - - - +
67H LEU* 3.9 28.3 - - + +
69H TYR* 3.9 14.7 + - - -
70H PRO* 4.9 13.7 - - - +
77H THR* 5.7 1.4 + - - -
78H ASN* 4.4 25.6 - - - +
203H THR* 4.2 13.7 - - + -
166J TYR* 4.5 0.2 - - - -
286J ASP* 3.5 0.8 + - - +
288J ASP* 5.1 0.2 - - - -
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Residues in contact with GLY 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61H LYS 3.2 0.8 - - - -
62H ARG* 1.3 84.7 - - - +
64H ILE* 1.3 59.9 + - - +
65H LEU 3.6 0.9 + - - +
203H THR* 5.7 0.2 - - - -
286J ASP* 3.2 14.3 + - - -
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Residues in contact with ILE 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H PRO 4.1 9.2 - - - +
61H LYS* 2.8 26.8 + - + +
63H GLY* 1.3 73.2 - - - +
65H LEU* 1.4 60.0 + - + +
166J TYR* 3.0 27.1 - - + +
169J TYR* 4.4 1.8 - - - +
171J LEU* 1.5 92.4 - - + +
172J PRO* 5.9 0.9 - - + -
173J HIS* 3.5 27.8 - - + +
286J ASP* 4.8 4.0 + - + +
289J ILE* 4.1 0.9 - - + -
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Residues in contact with LEU 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H GLY* 3.9 16.4 - - - +
37H ARG 4.2 2.9 - - - +
38H PRO* 3.6 38.1 - - + -
39H ARG* 6.1 0.2 - - - -
53H TYR* 3.8 12.6 - - + -
58H ALA* 4.4 2.7 - - + +
61H LYS 2.9 5.7 + - - +
62H ARG* 2.9 18.8 + - - +
63H GLY 3.4 1.3 - - - +
64H ILE* 1.4 84.6 - - + +
66H THR* 1.3 65.1 + - - +
67H LEU* 3.8 5.1 + - + +
166J TYR* 2.3 63.9 - - + +
169J TYR* 3.8 6.3 - - + -
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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