Contacts of the helix formed by residues 114 - 125 (chain T) in PDB entry 2BTO
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 SER 114 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60T ILE* 4.8 1.3 - - - -
113T LEU* 1.3 82.0 - - - +
115T LYS* 1.3 64.9 + - - +
116T GLY* 3.0 7.7 + - - -
117T GLN* 3.0 33.1 + - - +
118T LEU* 3.2 18.5 + - - +
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Residues in contact with LYS 115 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60T ILE* 3.6 41.7 - - + +
63T GLU* 4.9 21.3 + - - +
64T ILE* 4.8 7.4 - - + +
113T LEU 3.9 0.4 + - - -
114T SER* 1.3 75.7 - - - +
116T GLY* 1.3 59.5 + - - +
118T LEU* 4.0 4.9 - - - +
119T LYS* 3.1 30.8 + - + +
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Residues in contact with GLY 116 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114T SER* 3.0 5.1 - - - -
115T LYS* 1.3 83.0 - - - +
117T GLN* 1.3 63.0 + - - +
118T LEU 3.2 1.3 - - - -
119T LYS* 3.2 9.9 + - - +
120T GLU* 3.2 22.3 + - - +
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Residues in contact with GLN 117 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109T LYS* 4.1 22.5 + - - +
113T LEU* 4.0 9.6 - - + +
114T SER* 3.0 22.6 + - - +
116T GLY* 1.3 71.5 - - - +
118T LEU* 1.3 64.3 + - - +
120T GLU* 3.5 14.1 + - + +
121T PHE* 3.1 23.5 + - + +
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Residues in contact with LEU 118 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43T LEU* 4.5 6.5 - - + -
57T ILE* 6.3 0.7 - - + -
60T ILE* 4.1 15.9 - - + -
61T LEU* 4.8 13.7 - - + -
64T ILE* 3.9 24.2 - - + -
97T LEU* 3.7 28.3 - - + -
109T LYS* 5.5 0.2 - - + -
113T LEU* 3.6 23.0 - - + +
114T SER 3.2 17.3 + - - +
115T LYS 4.0 5.6 - - - +
116T GLY 3.2 0.4 - - - -
117T GLN* 1.3 77.2 - - - +
119T LYS* 1.3 55.6 + - - +
121T PHE* 3.3 21.2 - - + +
122T LEU* 3.0 44.7 + - + +
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Residues in contact with LYS 119 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64T ILE* 5.0 9.2 - - + -
67T GLU* 2.9 29.7 + - - +
68T TYR* 3.3 35.4 - - + +
115T LYS* 3.1 19.5 + - + +
116T GLY* 3.2 11.5 + - - +
118T LEU* 1.3 76.0 - - - +
120T GLU* 1.3 55.5 + - - +
122T LEU* 2.9 5.3 + - - +
123T ASP* 2.6 43.1 + - - +
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Residues in contact with GLU 120 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B SER* 4.0 15.3 - - - +
248B GLY* 3.4 38.0 + - - -
249B PHE 4.4 1.4 + - - -
116T GLY 3.2 12.4 + - - +
117T GLN* 4.0 14.1 + - + +
118T LEU 3.5 0.2 - - - -
119T LYS* 1.3 77.9 - - - +
121T PHE* 1.3 61.0 + - - +
123T ASP* 3.8 8.9 - - + +
124T ALA* 3.4 24.9 + - - +
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Residues in contact with PHE 121 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ALA* 5.9 0.4 - - + -
43T LEU* 4.4 21.3 - - + -
97T LEU 5.1 0.7 - - - -
99T LEU* 4.7 8.2 - - + +
107T ALA* 3.4 37.0 - - + -
108T THR 4.0 26.5 - - - -
109T LYS* 4.3 25.4 - - + +
113T LEU* 5.5 0.2 - - + -
117T GLN 3.1 14.9 + - - +
118T LEU* 3.3 26.9 - - + +
120T GLU* 1.3 78.6 - - - +
122T LEU* 1.3 71.4 + - + +
123T ASP 3.7 0.2 + - - -
124T ALA* 3.9 1.2 + - - +
125T ASN* 3.2 36.7 + - - +
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Residues in contact with LEU 122 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43T LEU* 4.5 10.3 - - + -
64T ILE* 4.0 29.4 - - + -
68T TYR* 4.3 24.0 - - + +
72T LEU* 3.8 23.6 - - + -
99T LEU* 4.2 23.3 - - + -
118T LEU* 3.0 35.7 + - + +
119T LYS* 2.9 7.9 + - - +
121T PHE* 1.3 84.5 - - + +
123T ASP* 1.3 66.6 + - - +
124T ALA 3.5 0.2 + - - -
125T ASN* 3.5 17.0 + - - +
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Residues in contact with ASP 123 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68T TYR* 3.2 21.2 + - - -
119T LYS* 2.6 25.9 + - - +
120T GLU* 3.8 11.0 - - + +
121T PHE 3.4 0.2 - - - -
122T LEU* 1.3 74.9 - - - +
124T ALA* 1.3 60.1 + - + +
125T ASN 3.6 3.6 + - - +
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Residues in contact with ALA 124 (chain T).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B GLY 4.3 13.2 - - - +
48B ASN* 4.2 20.0 - - - +
49B TRP* 4.0 17.0 + - + +
50B SER* 5.2 4.7 + - - -
120T GLU 3.4 14.6 + - - +
121T PHE* 4.4 2.0 - - - +
122T LEU 3.3 0.4 - - - -
123T ASP* 1.3 79.2 - - - +
125T ASN* 1.3 73.3 + - - +
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Residues in contact with ASN 125 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ALA* 3.9 15.2 - - - +
45B PRO 5.1 0.7 - - - +
49B TRP* 3.4 23.9 + - + -
99T LEU* 4.0 26.9 - - + -
101T LYS* 4.5 17.8 + - - +
106T ALA* 5.3 4.5 - - + -
107T ALA* 3.4 25.3 - - + +
121T PHE* 3.2 28.6 + - - +
122T LEU 3.5 15.0 + - - +
123T ASP 3.4 3.9 - - - +
124T ALA* 1.3 91.1 - - - +
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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