Contacts of the helix formed by residues 114 - 126 (chain p) 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 p).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76p TYR* 2.9 20.8 + - + +
112p ASN 3.7 2.5 + - - +
113p ALA* 1.3 70.4 - - - +
115p PRO* 1.4 62.4 - - - +
116p GLN* 2.8 26.4 + - - +
117p VAL* 2.7 38.9 + - + +
118p LEU* 3.0 10.4 + - - +
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Residues in contact with PRO 115 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104p LYS* 4.5 8.3 - - - +
108p ILE* 3.9 28.9 - - + -
113p ALA 3.3 10.0 - - - +
114p ASN* 1.4 91.6 - - - +
116p GLN* 1.3 56.5 + - - +
118p LEU* 3.5 13.9 - - + +
119p ASP* 2.9 38.5 + - - +
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Residues in contact with GLN 116 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66p TYR* 3.2 35.5 + - + -
114p ASN* 2.8 22.5 + - - +
115p PRO* 1.3 76.0 - - - +
117p VAL* 1.3 62.8 + - + +
119p ASP* 3.4 8.9 + - - +
120p ALA* 3.1 17.5 + - - +
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Residues in contact with VAL 117 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62p VAL* 5.5 0.4 - - + -
63p LEU* 3.6 31.2 - - + -
66p TYR* 3.9 28.9 - - + -
68p ILE* 4.3 14.4 - - + -
76p TYR* 3.7 28.7 - - + +
114p ASN* 2.7 23.0 + - + +
116p GLN* 1.3 72.2 - - + +
118p LEU* 1.3 66.4 + - - +
120p ALA* 3.0 9.9 + - + +
121p VAL* 2.9 22.1 + - + +
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Residues in contact with LEU 118 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76p TYR* 3.7 21.1 - - + -
79p PHE* 3.3 52.9 - - + -
104p LYS* 4.0 18.6 - - + +
107p TYR* 4.4 2.9 - - + -
108p ILE* 3.3 35.2 - - + +
113p ALA* 3.8 18.6 - - + -
114p ASN 3.0 11.1 + - - +
115p PRO* 3.5 14.1 - - + +
117p VAL* 1.3 77.3 - - - +
119p ASP* 1.3 61.9 + - - +
121p VAL* 3.2 2.1 + - - -
122p VAL* 3.1 20.1 + - - +
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Residues in contact with ASP 119 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104p LYS* 2.7 37.6 + - - +
115p PRO* 2.9 21.8 + - - +
116p GLN* 3.6 11.9 - - - +
118p LEU* 1.3 73.6 - - - +
120p ALA* 1.3 60.1 + - - +
122p VAL* 3.1 8.3 + - - +
123p ASN* 2.8 42.5 + - - +
129p PRO* 5.4 13.4 - - + +
130p THR* 5.2 3.8 - - - +
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Residues in contact with ALA 120 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62p VAL* 3.8 12.3 - - + +
66p TYR* 3.5 40.4 - - + +
116p GLN* 3.1 5.9 + - - +
117p VAL 3.0 10.4 + - - +
119p ASP* 1.3 78.5 - - - +
121p VAL* 1.3 63.5 + - - +
123p ASN* 3.1 21.2 + - - +
124p ILE* 3.3 18.0 + - - +
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Residues in contact with VAL 121 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59p VAL* 4.1 26.2 - - + +
62p VAL* 5.4 4.5 - - + -
63p LEU* 5.0 2.5 - - + -
76p TYR* 4.2 21.5 - - + +
79p PHE* 3.8 13.2 - - + -
80p GLY* 3.5 33.0 - - - +
117p VAL* 2.9 23.0 + - + +
118p LEU* 3.5 7.6 - - - +
120p ALA* 1.3 76.4 - - + +
122p VAL* 1.3 62.6 + - - +
124p ILE* 3.0 18.4 + - - +
125p ILE* 3.2 18.9 + - + +
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Residues in contact with VAL 122 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79p PHE* 3.7 23.8 - - + -
83p VAL* 4.6 7.0 - - + -
100p ILE* 4.3 20.6 - - + -
104p LYS* 6.0 1.6 - - + -
118p LEU 3.1 14.6 + - - +
119p ASP* 3.5 11.9 - - - +
121p VAL* 1.3 77.5 - - - +
123p ASN* 1.3 55.6 + - - +
124p ILE 3.0 0.7 + - - -
125p ILE* 4.6 4.9 - - - +
126p THR* 2.5 52.7 + - + +
128p SER 3.2 22.7 - - - +
129p PRO* 4.3 7.0 - - + -
130p THR* 4.4 8.1 - - + +
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Residues in contact with ASN 123 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123K ASN* 3.8 20.1 + - - +
124K ILE* 3.9 0.7 - - - +
127K GLY 5.3 5.2 - - - +
119p ASP* 2.8 29.8 + - - +
120p ALA* 3.1 12.1 + - - +
122p VAL* 1.3 74.2 - - - +
124p ILE* 1.3 59.9 + - + +
127p GLY* 3.2 27.0 - - - +
128p SER* 3.1 1.8 - - - -
129p PRO* 3.0 43.8 - - - +
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Residues in contact with ILE 124 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58K ASN* 4.7 6.6 + - - +
124K ILE* 4.1 27.8 - - + +
126K THR 5.0 0.7 - - - +
127K GLY* 3.4 33.9 - - - +
55p VAL* 6.1 1.6 - - - -
58p ASN* 3.6 38.4 - - + +
59p VAL* 4.7 5.6 - - + +
62p VAL* 3.7 24.9 - - + -
120p ALA 3.3 15.5 - - - +
121p VAL* 3.0 9.2 + - - +
122p VAL 3.0 0.4 - - - -
123p ASN* 1.3 83.1 - - + +
125p ILE* 1.3 71.4 + - + +
126p THR 3.4 0.4 - - - -
127p GLY 3.9 3.3 + - - -
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Residues in contact with ILE 125 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58K ASN* 4.8 10.6 - - - +
55p VAL* 4.0 26.0 - - + -
59p VAL* 4.7 2.0 - - + -
80p GLY* 3.1 43.1 - - - +
83p VAL* 3.8 25.6 - - + -
84p ALA* 4.4 15.5 - - + +
87p LEU* 4.5 19.2 - - + +
121p VAL* 3.2 19.8 + - + +
122p VAL 4.2 1.8 - - - +
124p ILE* 1.3 83.4 - - + +
126p THR* 1.3 62.7 + - + +
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Residues in contact with THR 126 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61K ALA* 5.7 3.5 - - - +
62K VAL* 5.4 4.3 - - - +
65K GLN* 3.9 22.8 + - - +
124K ILE* 4.8 1.5 - - - +
83p VAL* 4.5 4.3 - - + -
87p LEU* 6.0 3.1 - - + -
96p LEU* 4.8 11.4 - - + -
100p ILE* 4.1 20.2 - - + -
122p VAL* 2.5 36.0 + - + +
124p ILE 4.4 0.2 - - - -
125p ILE* 1.3 85.7 - - + +
127p GLY* 1.3 59.0 + - - +
128p SER* 2.5 29.6 + - - -
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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