Contacts of the helix formed by residues 114 - 126 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76N TYR* 2.9 21.4 + - - +
112N ASN 3.7 2.5 + - - +
113N ALA* 1.3 70.9 - - - +
115N PRO* 1.4 62.5 - - - +
116N GLN* 2.8 26.4 + - - +
117N VAL* 2.7 40.0 + - + +
118N LEU* 3.0 10.2 + - - +
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Residues in contact with PRO 115 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104N LYS* 4.5 8.1 - - - +
108N ILE* 3.9 28.9 - - + -
113N ALA 3.3 10.3 - - - +
114N ASN* 1.4 89.1 - - - +
116N GLN* 1.3 55.8 + - - +
118N LEU* 3.3 14.2 + - + +
119N ASP* 2.9 38.1 + - - +
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Residues in contact with GLN 116 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66N TYR* 3.2 36.3 + - + -
114N ASN* 2.8 23.5 + - - +
115N PRO* 1.3 75.9 - - - +
117N VAL* 1.3 61.7 + - + +
119N ASP* 3.4 9.7 + - - +
120N ALA* 3.1 18.2 + - - +
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Residues in contact with VAL 117 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62N VAL* 5.5 0.7 - - + -
63N LEU* 3.6 30.1 - - + -
66N TYR* 3.9 29.6 - - + -
68N ILE* 4.3 15.0 - - + -
76N TYR* 3.7 30.1 - - + +
114N ASN* 2.7 22.2 + - + +
116N GLN* 1.3 71.8 - - + +
118N LEU* 1.3 66.1 + - - +
120N ALA* 3.0 8.8 + - + +
121N VAL* 2.9 22.8 + - + +
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Residues in contact with LEU 118 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76N TYR* 3.7 21.5 - - + -
79N PHE* 3.3 52.4 - - + -
104N LYS* 4.0 17.9 - - + +
107N TYR* 4.4 1.8 - - + -
108N ILE* 3.3 35.2 - - + +
113N ALA* 3.8 19.7 - - + -
114N ASN 3.0 12.5 + - - +
115N PRO* 3.5 14.6 - - + +
117N VAL* 1.3 76.3 - - - +
119N ASP* 1.3 62.4 + - - +
121N VAL* 3.2 3.1 + - - +
122N VAL* 3.1 20.6 + - - +
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Residues in contact with ASP 119 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104N LYS* 2.7 37.1 + - - +
115N PRO* 2.9 22.7 + - - +
116N GLN* 3.6 11.2 - - - +
117N VAL 3.2 0.2 - - - -
118N LEU* 1.3 73.6 - - - +
120N ALA* 1.3 61.9 + - - +
122N VAL* 3.1 8.3 + - - +
123N ASN* 2.8 43.4 + - - +
129N PRO* 5.4 12.9 - - + +
130N THR* 5.2 3.8 + - - +
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Residues in contact with ALA 120 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62N VAL* 3.8 12.1 - - + +
66N TYR* 3.5 40.2 - - + +
116N GLN* 3.1 5.0 + - - +
117N VAL* 3.0 10.4 + - - +
119N ASP* 1.3 78.8 - - - +
121N VAL* 1.3 63.0 + - - +
123N ASN* 3.1 20.7 + - - +
124N ILE* 3.3 18.2 + - - +
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Residues in contact with VAL 121 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59N VAL* 4.1 26.7 - - + -
62N VAL* 5.4 4.3 - - + -
63N LEU* 5.0 2.5 - - + -
76N TYR* 4.2 21.3 - - + +
79N PHE* 3.8 12.8 - - + -
80N GLY* 3.5 32.5 - - - -
117N VAL* 2.9 22.7 + - + +
118N LEU* 3.5 7.4 - - - +
119N ASP 3.2 0.2 - - - -
120N ALA* 1.3 76.2 - - + +
122N VAL* 1.3 63.1 + - - +
124N ILE* 3.0 18.2 + - - +
125N ILE* 3.2 18.7 + - + +
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Residues in contact with VAL 122 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79N PHE* 3.7 23.1 - - + -
83N VAL* 4.6 7.4 - - + -
100N ILE* 4.3 20.9 - - + -
104N LYS* 6.0 1.3 - - + -
118N LEU 3.1 14.5 + - - +
119N ASP* 3.1 12.3 + - - +
121N VAL* 1.3 75.6 - - - +
123N ASN* 1.3 55.7 + - - +
124N ILE 3.0 0.3 + - - -
125N ILE* 4.6 5.2 - - - +
126N THR* 2.5 52.8 + - + +
128N SER 3.2 22.2 - - - +
129N PRO* 4.3 6.5 - - + -
130N THR* 4.4 8.5 - - + +
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Residues in contact with ASN 123 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119N ASP* 2.8 30.3 + - - +
120N ALA* 3.1 12.3 + - - +
122N VAL* 1.3 74.2 - - - +
124N ILE* 1.3 63.5 + - + +
127N GLY* 3.2 26.5 - - - +
128N SER* 3.1 1.4 - - - -
129N PRO* 3.0 44.9 - - - +
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Residues in contact with ILE 124 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55N VAL* 5.6 1.3 - - - +
58N ASN* 3.6 40.4 - - + +
59N VAL* 4.7 6.7 - - + +
62N VAL* 3.7 29.4 - - + -
120N ALA 3.3 15.5 - - - +
121N VAL* 3.0 8.5 + - - +
122N VAL 3.0 0.6 - - - -
123N ASN* 1.3 86.3 - - + +
125N ILE* 1.3 72.6 + - + +
126N THR 3.6 0.5 + - - -
127N GLY* 3.9 4.7 + - - -
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Residues in contact with ILE 125 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55N VAL* 4.0 26.2 - - + -
59N VAL* 4.6 2.0 - - + -
80N GLY* 3.1 42.6 - - - +
83N VAL* 3.8 26.2 - - + -
84N ALA* 4.4 14.4 - - + +
87N LEU* 4.5 19.3 - - + +
121N VAL* 3.2 19.6 + - + +
122N VAL 4.2 1.3 - - - +
124N ILE* 1.3 84.0 - - + +
126N THR* 1.3 61.8 + - + +
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Residues in contact with THR 126 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83N VAL* 4.5 4.0 - - + -
87N LEU* 6.0 2.7 - - + -
96N LEU* 4.8 11.0 - - + -
100N ILE* 4.1 20.2 - - + -
122N VAL* 2.5 35.5 + - + +
124N ILE 4.4 0.4 - - - -
125N ILE* 1.3 85.5 - - + +
127N GLY* 1.3 57.7 + - - +
128N SER* 2.5 32.7 + - - +
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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