Contacts of the helix formed by residues 114 - 126 (chain o) in PDB entry 3J9X
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 ASN 114 (chain o).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76o TYR* 2.9 22.3 + - - +
112o ASN 3.7 1.6 + - - -
113o ALA* 1.3 69.7 - - - +
115o PRO* 1.3 63.5 - - - +
116o GLN* 2.8 23.8 + - - +
117o VAL* 2.7 45.5 + - + +
118o LEU* 3.0 10.9 + - - +
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Residues in contact with PRO 115 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104o LYS* 5.0 2.8 - - - +
108o ILE* 3.9 32.5 - - + -
113o ALA 3.2 9.1 - - - +
114o ASN* 1.3 90.5 - - - +
116o GLN* 1.3 54.9 + - - +
118o LEU* 3.2 15.3 + - + +
119o ASP* 2.9 38.1 + - - +
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Residues in contact with GLN 116 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66o TYR* 2.9 44.5 + - - -
114o ASN* 2.8 18.8 + - - +
115o PRO* 1.3 75.2 - - - +
117o VAL* 1.3 69.5 + - - +
119o ASP* 3.3 10.0 + - - +
120o ALA* 3.1 16.8 + - - +
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Residues in contact with VAL 117 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62o VAL* 5.3 0.9 - - + -
63o LEU* 4.1 12.8 - - + -
66o TYR* 4.1 27.8 - - + -
68o ILE* 4.9 8.1 - - + -
76o TYR* 3.7 37.0 - - + +
114o ASN* 2.7 29.2 + - + +
116o GLN* 1.3 84.9 - - - +
118o LEU* 1.3 66.6 + - - +
120o ALA* 3.0 16.1 + - + +
121o VAL* 3.0 14.3 + - + +
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Residues in contact with LEU 118 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76o TYR* 3.6 24.2 - - + -
79o PHE* 3.3 52.2 - - + -
104o LYS* 4.4 12.1 - - + +
107o TYR* 4.4 7.9 - - + -
108o ILE* 3.3 35.7 - - + -
113o ALA* 3.8 18.2 - - + -
114o ASN 3.0 10.0 + - - +
115o PRO* 3.4 11.7 - - + +
116o GLN 3.2 0.2 - - - -
117o VAL* 1.3 77.7 - - - +
119o ASP* 1.3 63.4 + - - +
121o VAL* 3.1 4.4 + - - +
122o VAL* 3.0 19.2 + - - +
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Residues in contact with ASP 119 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104o LYS* 2.7 36.8 + - - +
115o PRO* 2.9 18.8 + - - +
116o GLN* 3.6 10.3 - - - +
118o LEU* 1.3 74.1 - - - +
120o ALA* 1.3 60.8 + - - +
122o VAL* 3.2 7.7 + - - +
123o ASN* 2.8 29.9 + - - +
129o PRO* 4.3 26.6 - - + +
130o THR* 5.6 0.7 + - - +
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Residues in contact with ALA 120 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62o VAL* 4.0 9.0 - - + +
66o TYR* 3.5 39.9 - - + +
116o GLN* 3.1 10.8 + - - +
117o VAL 3.0 12.0 + - - +
119o ASP* 1.3 78.1 - - - +
121o VAL* 1.3 60.3 + - - +
123o ASN* 3.3 20.3 + - - +
124o ILE* 3.4 14.8 - - - +
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Residues in contact with VAL 121 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59o VAL* 4.0 27.8 - - + -
62o VAL* 5.0 8.1 - - + -
63o LEU* 5.1 1.1 - - + -
76o TYR* 4.4 19.1 - - + +
79o PHE* 3.8 13.0 - - + -
80o GLY* 3.6 30.5 - - - +
117o VAL* 3.0 22.7 + - + +
118o LEU* 3.1 8.5 + - - +
120o ALA* 1.3 76.1 - - - +
122o VAL* 1.3 62.7 + - - +
124o ILE* 3.0 17.2 + - - +
125o ILE* 3.2 20.4 + - + +
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Residues in contact with VAL 122 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79o PHE* 3.6 24.2 - - + -
83o VAL* 4.5 7.4 - - + -
100o ILE* 4.2 20.2 - - + -
104o LYS* 5.0 1.6 - - + -
118o LEU 3.0 15.4 + - - +
119o ASP* 3.6 13.0 - - - +
121o VAL* 1.3 74.8 - - - +
123o ASN* 1.3 54.3 + - - +
124o ILE 2.9 1.6 + - - -
125o ILE* 3.2 5.1 + - - +
126o THR* 2.6 53.5 + - + +
128o SER 3.2 19.7 - - - +
129o PRO* 3.9 10.3 - - + -
130o THR* 4.1 8.3 - - + +
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Residues in contact with ASN 123 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119o ASP 2.8 18.1 + - - +
120o ALA* 3.4 11.8 + - - +
121o VAL 3.2 0.4 - - - -
122o VAL* 1.3 74.5 - - - +
124o ILE* 1.3 68.3 + - - +
127o GLY* 3.1 33.8 + - - +
128o SER* 3.4 16.5 - - - +
129o PRO* 3.5 11.2 - - + +
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Residues in contact with ILE 124 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58o ASN* 3.7 37.7 - - + +
59o VAL* 5.0 3.1 - - + +
62o VAL* 3.6 25.4 - - + -
120o ALA 3.4 15.0 - - - +
121o VAL* 3.0 7.6 + - - +
122o VAL 3.0 0.8 - - - -
123o ASN* 1.3 94.8 - - - +
125o ILE* 1.3 71.6 + - + +
126o THR 3.4 1.0 + - - -
127o GLY* 3.6 6.6 + - - -
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Residues in contact with ILE 125 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55o VAL* 3.9 25.4 - - + -
59o VAL* 4.4 5.4 - - + -
80o GLY* 3.2 42.2 - - - +
83o VAL* 3.7 26.9 - - + -
84o ALA* 4.5 14.1 - - + +
87o LEU* 4.8 16.1 - - + +
121o VAL* 3.2 20.0 + - + +
122o VAL* 4.2 1.3 - - - +
124o ILE* 1.3 81.6 - - + +
126o THR* 1.3 60.6 + - + +
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Residues in contact with THR 126 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83o VAL* 4.3 12.8 - - + -
87o LEU* 6.1 2.9 - - + -
96o LEU* 4.6 12.3 - - + -
100o ILE* 4.1 18.4 - - + -
122o VAL* 2.6 29.9 + - + +
124o ILE 4.2 0.2 - - - -
125o ILE* 1.3 78.3 - - + +
127o GLY* 1.3 57.9 + - - +
128o SER* 2.4 34.3 + - - -
134o SER* 5.1 6.2 - - - +
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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