Contacts of the helix formed by residues 110 - 123 (chain D) in PDB entry 2JG1
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 110 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84D LYS* 2.7 34.3 + - - +
108D GLU* 3.8 5.4 + - + +
109D ILE* 1.3 75.5 - - - +
111D ASN* 1.3 67.6 + - - +
112D GLN* 3.2 8.7 + - - +
113D GLU* 3.0 40.8 + - - +
114D ALA* 3.1 21.7 + - - +
140D GLY 5.7 0.2 - - - -
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Residues in contact with ASN 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D ASP* 1.3 77.0 - - - +
112D GLN* 1.3 62.6 + - - +
114D ALA* 3.5 5.8 + - - +
115D ALA* 3.1 24.8 + - - +
140D GLY 5.2 5.7 - - - +
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Residues in contact with GLN 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D TYR* 4.6 6.8 + - - -
84D LYS* 3.8 23.5 + - - +
110D ASP* 3.2 11.1 + - - +
111D ASN* 1.3 77.8 - - - +
113D GLU* 1.3 59.4 + - - +
115D ALA* 3.4 5.5 + - - +
116D GLY* 2.7 32.6 + - - -
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Residues in contact with GLU 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D PHE* 4.1 1.2 - - - -
81D TYR* 3.6 18.8 - - + -
82D ASN 4.8 1.1 - - - +
83D ILE* 3.4 24.5 - - + +
84D LYS* 2.7 43.1 + - - +
85D GLY 5.5 0.2 + - - -
108D GLU 4.1 3.3 - - - +
109D ILE* 3.6 18.7 - - + -
110D ASP* 3.0 42.2 + - - +
112D GLN* 1.3 82.2 - - - +
114D ALA* 1.3 57.3 + - - +
117D PHE* 2.7 36.0 + - - +
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Residues in contact with ALA 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D PHE* 4.7 0.2 - - - -
109D ILE* 3.9 6.1 - - - +
110D ASP 3.1 17.6 + - - +
111D ASN* 3.6 7.4 - - - +
113D GLU* 1.3 77.2 - - - +
115D ALA* 1.3 60.4 + - - +
118D ILE* 3.3 14.3 + - - +
140D GLY 6.0 0.4 - - - +
141D LEU* 3.7 23.6 - - + -
142D ASN 6.2 0.4 - - - +
145D TYR* 2.6 35.0 + - + -
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Residues in contact with ALA 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ASN 3.1 14.7 + - - +
112D GLN* 3.8 5.4 - - - +
114D ALA* 1.3 75.5 - - - +
116D GLY* 1.3 66.9 + - - +
118D ILE* 3.3 9.4 + - - +
119D LYS* 3.3 27.4 + - - +
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Residues in contact with GLY 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D TYR* 3.5 23.3 - - - -
112D GLN 2.7 20.8 + - - -
113D GLU 3.2 0.6 + - - -
115D ALA* 1.3 73.6 - - - +
117D PHE* 1.3 61.5 + - - +
119D LYS* 3.2 10.6 + - - +
120D HIS* 3.1 21.0 + - - +
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Residues in contact with PHE 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D LEU* 3.5 27.6 - - + -
7D LEU* 4.2 15.3 - - + -
56D SER* 3.6 19.3 - - - -
57D GLY* 4.0 12.3 - - - -
58D PHE* 3.5 17.9 - + + -
81D TYR* 3.5 25.2 - - + -
113D GLU 2.7 18.6 + - - +
115D ALA 3.3 0.2 - - - -
116D GLY* 1.3 73.0 - - - +
118D ILE* 1.3 58.9 + - + +
120D HIS* 3.2 16.5 + + - +
121D PHE* 2.8 47.8 + + + +
145D TYR* 3.3 28.9 - + - +
149D ILE* 4.4 10.5 - - + -
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Residues in contact with ILE 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D ALA 3.3 15.3 + - - +
115D ALA* 3.3 10.3 + - - +
117D PHE* 1.3 77.0 - - + +
119D LYS* 1.3 67.0 + - + +
121D PHE* 3.4 7.6 + - + +
122D GLU* 3.0 26.5 + - - +
145D TYR* 3.7 21.5 - - + +
148D GLN* 3.9 35.4 - - + +
149D ILE* 4.2 18.8 - - + +
152D ARG* 3.3 37.9 - - + +
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Residues in contact with LYS 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D ALA* 3.3 15.4 + - - +
116D GLY* 3.2 10.2 + - - +
118D ILE* 1.3 78.9 - - + +
120D HIS* 1.3 62.5 + - - +
122D GLU* 3.3 26.5 + - - +
123D GLN* 3.1 31.3 + - - +
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Residues in contact with HIS 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D ALA* 3.0 36.9 + - + -
80D PHE 4.1 9.7 + - - -
81D TYR* 4.1 21.6 - + + -
116D GLY 3.1 9.6 + - - +
117D PHE* 3.5 27.4 - + - +
119D LYS* 1.3 76.4 - - - +
121D PHE* 1.3 63.9 + - - +
123D GLN* 3.2 26.9 + - - +
124D MSE 3.1 35.2 - - + +
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Residues in contact with PHE 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D LEU* 3.6 27.6 - - + -
5D LEU* 3.9 19.5 - - + -
117D PHE* 2.8 46.1 + + + +
118D ILE* 3.6 8.7 - - + +
120D HIS* 1.3 72.5 - - - +
122D GLU* 1.3 67.2 + - - +
124D MSE 3.0 25.5 + - - +
125D MSE 3.5 30.0 + - + +
131D VAL* 4.3 5.2 - - + -
149D ILE* 3.5 30.7 - - + -
152D ARG* 4.0 17.3 - - + -
153D CYS* 3.5 23.6 - - - -
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Residues in contact with GLU 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D ILE* 3.0 20.2 + - - +
119D LYS* 3.4 31.9 + - - +
121D PHE* 1.3 76.4 - - - +
123D GLN* 1.3 59.8 + - + +
124D MSE 3.0 5.4 + - - -
125D MSE 3.1 24.7 + - + +
126D GLU* 4.7 1.2 + - - +
152D ARG* 2.8 47.1 + - + -
156D LYS* 5.8 0.5 - - - -
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Residues in contact with GLN 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D LYS* 3.1 15.1 + - - +
120D HIS* 3.2 30.5 + - - +
122D GLU* 1.3 75.3 - - + +
124D MSE 1.3 58.2 + - + +
125D MSE 3.5 0.4 - - - -
126D GLU* 4.3 10.5 - - - +
127D LYS* 3.7 22.7 - - - +
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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