Contacts of the helix formed by residues 56 - 65 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54E VAL 3.4 2.1 + - - +
55E GLY* 1.3 69.7 - - - -
57E GLU* 1.3 63.4 + - - +
58E ALA 2.9 5.2 - - - -
59E GLN* 2.9 26.2 + - + +
60E SER* 3.1 19.6 + - - -
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Residues in contact with GLU 57 (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 LYS* 3.6 1.7 + - - -
53E TYR* 3.8 0.2 - - - -
54E VAL 3.3 20.8 + - - +
56E ASP* 1.3 81.7 + - - +
58E ALA* 1.3 48.5 - - - +
60E SER* 4.4 2.0 - - - -
149G THR* 5.2 7.6 + - + +
166G TYR* 2.1 36.7 + - - -
167G GLU* 2.7 24.8 - - - +
289G ILE* 5.5 0.4 - - - -
292G ASP* 4.7 17.7 - - - +
127N GLU* 5.2 2.7 - - - +
128N GLU* 2.7 35.3 - - - +
136N MET* 6.2 0.2 - - - -
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Residues in contact with ALA 58 (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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34E ILE* 4.9 2.5 - - + +
36E GLY 4.5 0.4 - - - +
53E TYR* 3.6 32.8 - - + +
54E VAL* 4.0 1.8 - - - +
55E GLY 3.5 12.3 + - - +
56E ASP 2.9 0.8 - - - -
57E GLU* 1.3 66.8 - - - +
59E GLN* 1.3 65.2 + - - +
62E ARG* 3.3 17.3 + - - +
65E LEU* 4.5 2.0 - - + -
67E LEU* 3.7 22.8 - - + +
166G TYR* 1.5 43.4 + - + +
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Residues in contact with GLN 59 (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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33E SER 5.1 6.8 - - - +
34E ILE* 4.4 12.4 - - + +
55E GLY 3.5 4.3 + - - +
56E ASP* 2.9 23.4 + - + +
58E ALA* 1.3 80.3 - - - +
60E SER* 1.3 57.0 + - - +
61E LYS 2.9 0.4 + - - -
62E ARG* 2.8 70.4 + - - +
67E LEU* 5.4 0.2 - - - +
70E PRO* 5.8 3.1 - - - +
203E THR* 3.4 9.4 - - - +
207E GLU* 4.9 13.5 - - + +
288G ASP* 3.8 23.1 - - + +
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Residues in contact with SER 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E ASP* 3.1 15.2 + - - +
57E GLU 5.1 0.7 - - - -
58E ALA 3.3 0.2 - - - -
59E GLN* 1.3 73.6 - - - +
61E LYS* 1.3 46.2 - - - +
204E ALA* 3.6 1.9 - - - +
166G TYR* 4.2 0.2 - - - -
286G ASP* 3.8 5.2 - - - -
288G ASP* 1.6 63.3 + - - +
289G ILE* 1.2 99.7 - - - +
291G LYS* 4.8 0.2 - - - +
292G ASP* 4.6 3.3 + - - -
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Residues in contact with LYS 61 (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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57E GLU 4.4 0.2 + - - -
59E GLN 2.9 0.4 + - - -
60E SER* 1.3 73.4 - - - +
62E ARG* 1.4 56.8 + - - +
63E GLY 3.2 3.1 - - - -
64E ILE* 2.8 24.7 + - + -
65E LEU 2.9 8.8 + - - -
149G THR* 1.5 46.4 - - - +
165G ILE 3.1 2.2 - - - -
166G TYR* 0.8 330.9 - - + +
286G ASP* 3.8 4.0 + - - -
289G ILE* 2.9 29.6 - - + +
293G LEU* 5.4 0.4 - - - -
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Residues in contact with ARG 62 (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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34E ILE* 4.8 4.2 - - - +
58E ALA 3.3 13.5 + - - +
59E GLN* 2.8 52.7 + - - +
61E LYS* 1.4 72.7 - - - +
63E GLY* 1.3 63.7 + - - +
65E LEU* 2.9 26.3 - - - +
67E LEU* 3.9 30.2 - - + +
69E TYR* 3.9 15.1 + - - -
70E PRO* 4.9 14.1 - - - +
77E THR* 5.7 1.2 + - - -
78E ASN* 4.4 25.7 - - - +
81E ASP* 5.4 0.2 - - - -
203E THR* 4.2 13.0 - - + -
166G TYR* 4.5 0.4 - - - -
286G ASP* 3.5 0.4 + - - +
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Residues in contact with GLY 63 (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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61E LYS 3.2 0.6 - - - -
62E ARG* 1.3 84.7 - - - +
64E ILE* 1.3 60.1 + - - +
65E LEU 3.6 0.7 + - - +
203E THR* 4.9 0.2 - - - +
286G ASP* 3.2 13.8 + - - -
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Residues in contact with ILE 64 (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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38E PRO 4.1 9.4 - - - +
61E LYS* 2.8 26.4 + - + +
63E GLY* 1.3 74.0 - - - +
65E LEU* 1.4 59.8 + - + +
166G TYR* 3.0 26.9 - - + +
169G TYR* 4.4 2.0 - - - +
171G LEU* 1.5 92.4 - - + -
172G PRO* 5.9 1.1 - - + -
173G HIS* 3.5 27.4 - - + +
286G ASP* 4.8 4.4 + - + +
289G ILE* 4.1 0.7 - - + -
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Residues in contact with LEU 65 (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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36E GLY* 3.9 15.9 - - - +
37E ARG 4.2 3.1 - - - +
38E PRO* 3.6 38.4 - - + -
39E ARG* 6.1 0.2 - - - -
53E TYR* 3.8 12.1 - - + -
58E ALA* 4.4 2.5 - - + +
61E LYS 2.9 5.6 + - - +
62E ARG* 2.9 18.9 + - - +
63E GLY 3.4 0.9 - - - +
64E ILE* 1.4 84.7 - - + +
66E THR* 1.3 65.1 + - - +
67E LEU* 3.8 5.3 + - + +
166G TYR* 2.3 66.6 - - + +
169G TYR* 3.8 5.4 - - + -
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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