Contacts of the helix formed by residues 119 - 130 (chain C) in PDB entry 4DAJ
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 ILE 119 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115C ILE* 3.2 13.8 + - + +
118C VAL* 1.3 97.8 - - + +
120C SER* 1.3 73.7 + - - +
121C MET 3.4 1.6 - - - -
122C ASN* 2.9 13.0 + - - +
123C LEU* 3.1 44.4 - - + +
143C TRP* 4.2 5.4 - - + -
146C ILE* 4.0 35.2 - - + -
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Residues in contact with SER 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C ILE 4.1 0.6 + - - -
116C ILE* 3.3 24.5 + - - +
119C ILE* 1.3 75.6 - - - +
121C MET* 1.3 64.5 + - - +
124C PHE* 2.9 27.4 + - - +
143C TRP* 3.3 15.2 + - - +
146C ILE* 4.6 6.1 - - - +
147C ASP* 3.2 50.0 + - - +
533C TYR* 3.6 6.3 - - - -
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Residues in contact with MET 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C THR 4.6 0.2 - - - +
77C LEU* 4.1 13.9 - - + -
78C ALA* 3.4 46.7 - - + +
81C THR* 4.2 13.2 - - - +
116C ILE* 3.2 17.2 + - + +
117C GLY* 3.4 26.5 - - - +
119C ILE 3.4 0.2 - - - -
120C SER* 1.3 75.1 - - - +
122C ASN* 1.3 56.3 + - - +
124C PHE* 3.8 0.7 - - - +
125C THR* 2.7 37.0 + - - -
530C TRP* 3.6 26.3 - - + -
533C TYR* 3.9 27.1 - - + +
537C THR* 4.5 3.6 - - - +
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Residues in contact with ASN 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C GLY* 5.8 2.6 - - - -
78C ALA* 4.7 11.5 - - - +
117C GLY 4.4 4.8 + - - -
118C VAL* 2.7 28.6 + - - +
119C ILE 2.9 8.8 + - - +
121C MET* 1.3 74.6 - - - +
123C LEU* 1.3 72.5 + - + +
124C PHE 2.9 1.6 + - - -
125C THR* 3.0 6.7 + - - -
126C THR* 2.9 27.0 + - - +
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Residues in contact with LEU 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C ILE* 3.1 34.0 + - + +
122C ASN* 1.3 84.2 - - + +
124C PHE* 1.3 57.0 + - - +
126C THR* 3.3 8.7 - - - -
127C TYR* 2.9 28.2 + - - +
133C TRP* 4.1 18.1 - - + -
135C LEU* 4.6 13.7 - - + -
139C ALA* 4.6 4.0 - - + +
143C TRP* 3.1 49.1 - - + +
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Residues in contact with PHE 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C SER 2.9 21.1 + - - +
121C MET* 3.8 2.7 - - - +
123C LEU* 1.3 74.4 - - - +
125C THR* 1.3 65.7 + - - +
126C THR 3.1 1.5 + - - -
127C TYR* 3.1 16.0 + + - +
128C ILE* 2.9 28.9 + - + +
143C TRP* 3.3 32.9 - + + -
526C ASN* 3.5 28.0 - - + -
529C TYR* 4.2 34.5 - + + -
530C TRP* 3.4 45.3 - + - -
533C TYR* 4.2 11.4 - + - +
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Residues in contact with THR 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C ALA* 4.0 34.9 - - + +
74C THR* 3.6 10.0 - - - -
75C GLY 5.4 0.9 - - - +
121C MET* 2.7 26.1 + - - +
122C ASN* 3.0 5.1 + - - -
124C PHE* 1.3 72.9 - - - +
126C THR* 1.3 58.1 + - - +
128C ILE* 3.3 9.8 + - + +
129C ILE* 2.9 26.4 + - + +
530C TRP* 3.1 25.1 - - + -
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Residues in contact with THR 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C ASN* 2.9 16.3 + - - +
123C LEU* 3.3 12.8 - - - +
125C THR* 1.3 74.1 - - - +
127C TYR* 1.3 59.6 + - - +
128C ILE 3.0 1.1 - - - -
129C ILE* 2.7 26.2 + - + +
130C MET* 2.9 37.7 + - + +
133C TRP* 6.2 2.0 - - + -
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Residues in contact with TYR 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C LEU 2.9 17.2 + - - +
124C PHE* 3.1 19.0 + + - +
126C THR* 1.3 76.9 - - - +
128C ILE* 1.3 66.0 + - + +
130C MET 4.3 0.2 - - - -
131C ASN* 3.4 23.9 + - - -
132C ARG 3.8 11.5 + - - -
133C TRP* 3.4 45.5 - + + -
143C TRP* 5.3 6.5 - + + -
218C GLY 4.4 2.9 + - - -
219C GLU* 3.4 27.6 - - - +
220C CYS* 3.4 32.4 + - + -
221C PHE* 5.9 0.2 - - - -
526C ASN* 5.7 5.2 - - - -
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Residues in contact with ILE 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C VAL* 5.3 5.6 - - - +
124C PHE* 2.9 23.2 + - + +
125C THR* 3.4 13.7 - - + +
127C TYR* 1.3 81.9 - - + +
129C ILE* 1.3 62.3 + - - +
131C ASN* 3.6 17.5 + - - +
526C ASN* 5.8 4.3 - - - +
530C TRP* 5.9 2.9 - - - +
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Residues in contact with ILE 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C VAL* 5.3 10.5 - - + +
71C ALA* 5.5 10.5 - - + -
125C THR* 2.9 14.0 + - + +
126C THR* 2.7 17.8 + - - +
128C ILE* 1.3 69.5 - - - +
130C MET* 1.3 62.8 + - + +
131C ASN* 3.0 18.4 + - - +
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Residues in contact with MET 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C THR* 2.9 37.7 + - + +
129C ILE* 1.3 73.6 - - + +
131C ASN* 1.3 62.2 + - - +
132C ARG* 2.7 38.8 + - + +
134C ALA* 3.4 34.8 - - + -
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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