Contacts of the helix formed by residues 56 - 65 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G VAL 3.4 2.3 + - - +
55G GLY* 1.3 68.4 - - - -
57G GLU* 1.3 64.0 + - - +
58G ALA 2.9 4.9 - - - -
59G GLN* 2.9 27.1 + - + +
60G SER* 3.1 19.8 + - - +
292I ASP* 5.5 0.2 - - - +
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Residues in contact with GLU 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G LYS* 3.6 1.7 + - - -
54G VAL 3.3 21.2 + - - +
56G ASP* 1.3 81.2 + - - +
58G ALA* 1.3 46.5 - - - +
60G SER* 4.4 3.1 - - - +
61G LYS* 4.4 1.1 + - - +
149I THR* 5.2 8.0 + - + +
166I TYR* 2.1 37.3 + - - -
167I GLU* 2.7 24.2 - - - +
292I ASP* 4.7 17.3 - - - +
127P GLU* 5.2 2.7 - - - +
128P GLU* 2.7 34.5 - - - +
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Residues in contact with ALA 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G ILE* 4.9 2.2 - - + +
36G GLY 4.5 1.1 - - - +
53G TYR* 3.6 32.3 - - + +
54G VAL 4.0 1.8 - - - +
55G GLY 3.5 12.5 + - - +
56G ASP 2.9 0.6 - - - -
57G GLU* 1.3 68.4 - - - +
59G GLN* 1.3 65.4 + - - +
62G ARG* 3.3 16.6 + - - +
65G LEU* 4.5 1.1 - - + -
67G LEU* 3.7 22.6 - - + +
166I TYR* 1.5 43.3 + - + +
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Residues in contact with GLN 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33G SER 5.1 6.6 - - - +
34G ILE* 4.4 12.5 - - + +
55G GLY 3.5 4.6 + - - +
56G ASP* 2.9 23.2 + - + +
58G ALA* 1.3 79.2 - - - +
60G SER* 1.3 56.9 + - - +
61G LYS 3.1 0.2 - - - -
62G ARG* 2.8 70.2 + - - +
67G LEU* 5.4 0.2 - - - +
70G PRO* 5.8 3.1 - - - +
203G THR* 3.4 9.4 - - - +
207G GLU* 4.9 13.8 - - + +
288I ASP* 3.8 21.8 - - + +
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Residues in contact with SER 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G ASP 3.1 14.9 + - - -
57G GLU 5.1 0.2 - - - -
58G ALA 3.3 0.6 - - - +
59G GLN* 1.3 73.7 - - - +
61G LYS* 1.3 46.4 - - - +
204G ALA* 3.6 1.7 - - - +
286I ASP* 3.8 5.6 - - - -
288I ASP* 1.6 62.8 + - - +
289I ILE* 1.2 99.5 - - - +
291I LYS* 4.8 0.2 - - - +
292I ASP* 4.6 2.9 - - - -
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Residues in contact with LYS 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57G GLU* 5.8 0.2 - - - +
59G GLN 3.1 0.6 - - - -
60G SER* 1.3 72.6 - - - +
62G ARG* 1.4 55.3 + - - +
63G GLY 3.2 3.1 - - - -
64G ILE* 2.8 25.1 + - + -
65G LEU 2.9 8.7 + - - -
149I THR* 1.5 46.4 - - - +
165I ILE 3.1 2.5 - - - -
166I TYR* 0.8 328.7 - - + +
286I ASP* 3.8 3.8 + - - -
289I ILE* 2.9 29.7 - - + +
293I LEU* 5.2 0.9 - - - +
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Residues in contact with ARG 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G ILE* 4.8 4.2 - - - +
58G ALA 3.3 13.9 + - - +
59G GLN* 2.8 53.4 + - - +
61G LYS* 1.4 73.6 - - - +
63G GLY* 1.3 65.1 + - - +
65G LEU* 2.9 26.8 - - - +
67G LEU* 3.9 28.9 - - + +
69G TYR* 3.9 14.7 + - - -
70G PRO* 4.9 13.3 - - - +
77G THR* 5.7 1.4 + - - -
78G ASN* 4.4 25.7 - - - +
203G THR* 4.2 13.5 - - + -
166I TYR* 4.5 0.4 - - - -
286I ASP* 3.5 0.8 + - - +
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Residues in contact with GLY 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G LYS 3.2 0.8 - - - -
62G ARG* 1.3 84.4 - - - +
64G ILE* 1.3 60.8 + - - +
65G LEU 3.6 0.9 + - - +
286I ASP* 3.2 13.7 + - - -
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Residues in contact with ILE 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G PRO* 4.1 9.0 - - - +
61G LYS* 2.8 26.9 + - + +
63G GLY* 1.3 73.4 - - - +
65G LEU* 1.4 61.1 + - + +
166I TYR* 3.0 30.1 - - + +
169I TYR* 5.6 1.9 - - - +
171I LEU* 1.5 92.8 - - + +
172I PRO* 5.9 0.9 - - + -
173I HIS* 3.5 27.1 - - + -
286I ASP* 4.8 4.7 + - + +
289I ILE* 4.1 0.4 - - + -
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Residues in contact with LEU 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36G GLY* 3.9 15.5 - - - +
37G ARG 4.2 3.1 - - - +
38G PRO* 3.6 38.6 - - + -
53G TYR* 3.8 12.8 - - + -
58G ALA* 4.4 2.2 - - + +
61G LYS 2.9 5.9 + - - +
62G ARG* 2.9 18.3 + - - +
63G GLY 3.4 1.3 - - - +
64G ILE* 1.4 84.7 - - + +
66G THR* 1.3 66.0 + - - +
67G LEU* 3.8 5.1 + - + +
166I TYR* 2.3 64.6 - - + +
169I TYR* 3.8 6.1 - - + -
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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