Contacts of the helix formed by residues 112 - 123 (chain C) in PDB entry 4DQ0
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 THR 112 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87C LEU 3.5 24.5 - - - +
88C ASN* 3.1 35.4 + - - +
108C LEU* 4.2 13.5 - - + -
109C GLU* 2.8 22.0 + - - -
111C LYS* 1.3 80.3 + - - +
113C ILE* 1.3 58.6 + - - +
114C PRO 3.5 0.2 - - - -
115C GLY* 3.3 4.0 + - - -
116C LEU* 2.9 38.0 + - + +
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Residues in contact with ILE 113 (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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105C LEU* 3.8 33.0 - - + +
108C LEU* 4.0 24.5 - - + -
109C GLU 4.1 3.6 - - - +
110C ALA 3.7 10.8 - - - +
111C LYS 3.2 0.4 - - - -
112C THR* 1.3 76.1 - - - +
114C PRO* 1.3 70.3 - - + +
116C LEU* 3.2 2.7 + - + +
117C ILE* 2.9 46.3 + - + +
149C PHE* 3.7 45.8 - - + -
151C PHE* 4.7 1.6 - - + -
159C TYR* 3.8 11.9 - - + +
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Residues in contact with PRO 114 (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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110C ALA 3.9 3.8 - - - +
111C LYS* 3.5 19.1 - - - +
113C ILE* 1.3 95.2 - - + +
115C GLY* 1.3 55.6 + - - +
117C ILE* 3.9 1.7 - - - +
118C ALA* 3.0 30.4 + - - +
159C TYR* 3.5 31.5 - - + +
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Residues in contact with GLY 115 (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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111C LYS 4.8 1.6 + - - -
112C THR 3.3 6.1 + - - -
113C ILE 3.3 0.2 - - - -
114C PRO* 1.3 79.0 - - - +
116C LEU* 1.3 64.6 + - - +
118C ALA* 3.9 4.8 - - - +
119C ASN* 3.1 24.1 + - - +
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Residues in contact with LEU 116 (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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37C LEU* 4.4 12.1 - - + -
87C LEU* 4.2 23.8 - - + +
90C LEU* 4.4 23.6 - - + +
92C PHE* 4.3 21.8 - - + -
105C LEU* 4.0 14.1 - - + -
108C LEU* 3.4 31.9 - - + -
112C THR* 2.9 23.3 + - + +
113C ILE* 3.2 6.3 + - + +
115C GLY* 1.3 75.7 - - - +
117C ILE* 1.3 60.3 + - + +
119C ASN* 3.3 4.1 + - + +
120C MET* 2.9 34.3 + - - +
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Residues in contact with ILE 117 (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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105C LEU* 5.0 6.1 - - + -
113C ILE* 2.9 29.2 + - + +
114C PRO 3.9 2.5 - - - +
116C LEU* 1.3 76.5 - - + +
118C ALA* 1.3 67.8 + - - +
120C MET* 3.2 18.0 + - - +
121C GLN* 3.0 44.3 + - + +
132C ILE* 4.9 8.1 - - + -
151C PHE* 4.3 12.8 - - + -
156C LEU* 4.9 5.2 - - + -
159C TYR* 3.5 56.8 - - + -
160C TYR* 4.3 6.1 - - + +
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Residues in contact with ALA 118 (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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114C PRO 3.0 18.1 + - - +
115C GLY* 3.9 5.6 - - - +
117C ILE* 1.3 76.7 - - - +
119C ASN* 1.3 58.2 + - - +
121C GLN* 3.1 15.9 + - - +
122C ARG* 2.8 31.6 + - - +
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Residues in contact with ASN 119 (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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90C LEU 4.4 1.9 - - - +
91C THR* 3.6 13.7 - - + +
92C PHE* 3.0 61.4 + - + -
115C GLY 3.1 18.4 + - - +
116C LEU* 3.5 7.9 - - + +
117C ILE 3.2 0.2 - - - -
118C ALA* 1.3 76.2 - - - +
120C MET* 1.3 61.8 + - - +
122C ARG* 3.2 22.7 - - - +
123C CYS* 3.1 27.0 + - - -
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Residues in contact with MET 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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37C LEU* 3.7 30.5 - - + -
92C PHE* 4.2 9.6 - - + -
99C ILE* 3.3 30.1 - - + +
101C SER* 4.6 10.8 - - - -
105C LEU* 5.1 5.8 - - - -
116C LEU* 2.9 22.4 + - - +
117C ILE* 3.3 18.4 - - - +
119C ASN* 1.3 75.1 - - - +
121C GLN* 1.3 56.8 + - - +
123C CYS 3.2 6.8 + - - -
124C THR* 2.7 25.5 + - - -
130C ASN* 3.7 23.3 - - + +
132C ILE* 3.7 35.9 - - + -
160C TYR* 3.8 0.9 - - - +
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Residues in contact with GLN 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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117C ILE* 3.0 24.1 + - - +
118C ALA* 3.5 16.8 - - - +
120C MET* 1.3 73.7 - - - +
122C ARG* 1.3 66.0 + - - +
124C THR* 2.9 16.7 + - - -
159C TYR* 2.9 28.7 + - - +
160C TYR* 3.3 44.9 - - + +
163C TRP* 3.6 23.6 - - + +
196C LYS* 2.9 16.6 + - - +
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Residues in contact with ARG 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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91C THR* 4.2 11.9 - - - +
92C PHE 2.7 26.6 + - - -
93C ASP* 3.3 21.4 + - - +
95C GLU* 4.1 10.1 - - - +
118C ALA 2.8 17.1 + - - +
119C ASN* 3.2 24.2 + - - +
121C GLN* 1.3 77.4 - - - +
123C CYS* 1.3 64.9 + - - +
124C THR 3.4 4.0 + - - +
196C LYS* 3.9 10.6 + - - +
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Residues in contact with CYS 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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92C PHE* 3.7 27.8 - - + -
93C ASP 3.8 1.6 - - - -
94C GLY 3.3 32.8 - - - +
95C GLU* 3.5 4.0 - - - -
96C TYR* 2.7 38.6 + - + +
99C ILE* 4.4 1.1 - - + -
119C ASN* 3.1 35.6 + - - +
120C MET 3.2 2.9 + - - +
121C GLN 3.1 0.4 - - - -
122C ARG* 1.3 88.6 - - - +
124C THR* 1.3 55.7 + - - +
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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