Contacts of the helix formed by residues 112 - 128 (chain C) in PDB entry 3LUE
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 PRO 112 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197B GLY* 6.5 1.8 - - - -
73C HIS* 3.9 12.3 - - + -
75C ILE* 3.8 17.3 - - + -
110C LEU 3.6 1.3 - - - +
111C ASN* 1.3 95.9 - - - +
113C LYS* 1.3 64.0 + - - +
114C ALA* 3.4 2.0 - - + +
115C ASN* 3.0 32.8 + - - +
116C ARG* 3.3 5.4 + - - +
177C ARG* 2.8 13.2 - - - +
179C ASP* 5.0 4.9 - - - +
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Residues in contact with LYS 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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195B GLU 3.5 9.3 + - - +
196B ARG* 3.1 51.5 - - - +
197B GLY* 5.2 1.5 - - - +
111C ASN 3.5 2.4 + - - -
112C PRO* 1.3 69.9 - - - +
114C ALA* 1.3 63.7 + - + +
116C ARG* 3.2 19.7 + - - +
117C GLU* 3.2 18.2 + - - +
177C ARG* 4.8 0.4 - - - +
371C HIS* 3.5 34.3 - - + +
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Residues in contact with ALA 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C PRO* 3.4 1.9 - - + +
113C LYS* 1.3 76.9 - - + +
115C ASN* 1.3 64.1 + - - +
117C GLU* 3.7 12.6 - - - +
118C LYS* 2.8 28.7 + - - +
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Residues in contact with ASN 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ILE* 3.3 28.3 - - - +
76C VAL* 3.5 19.0 + - + +
79C TRP* 4.1 21.4 - - + +
111C ASN* 3.2 24.1 + - - +
112C PRO* 3.0 22.8 + - - +
114C ALA* 1.3 77.9 + - - +
116C ARG* 1.3 65.5 + - - +
118C LYS* 3.0 2.9 + - - +
119C MET* 2.9 29.3 + - + +
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Residues in contact with ARG 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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107C GLU* 3.0 52.4 + - - +
111C ASN* 3.5 23.6 - - - +
112C PRO 3.8 4.0 - - - +
113C LYS* 3.2 11.6 + - - +
115C ASN* 1.3 74.9 - - - +
117C GLU* 1.3 61.7 + - - +
119C MET* 3.4 13.5 + - + +
120C THR* 2.9 27.9 + - - -
134C VAL* 4.4 8.2 + - + +
370C VAL* 3.2 34.8 + - + +
371C HIS* 3.8 21.6 + - + +
374C CYS* 3.0 37.0 + - - +
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Residues in contact with GLU 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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113C LYS* 3.2 16.5 + - - +
114C ALA* 3.8 10.8 - - - +
115C ASN 3.2 0.2 - - - -
116C ARG* 1.3 73.6 - - - +
118C LYS* 1.3 66.3 + - - +
120C THR* 2.9 3.5 + - - -
121C GLN* 2.9 25.7 + - - +
367C PRO* 3.9 29.5 - - + +
368C SER* 4.2 13.7 + - - -
370C VAL* 4.0 8.1 - - - -
371C HIS* 2.8 30.7 + - + -
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Residues in contact with LYS 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C TRP* 3.4 53.1 - - + +
80C ASP* 5.7 0.6 + - - -
83C GLU* 4.5 5.9 + - - -
114C ALA 2.8 22.2 + - - +
115C ASN* 3.0 3.8 + - - +
117C GLU* 1.3 71.4 - - - +
119C MET* 1.3 57.4 - - - +
121C GLN* 3.1 16.1 - - + +
122C ILE* 3.0 50.3 + - + +
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Residues in contact with MET 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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12C ASN* 5.7 0.9 - - - -
76C VAL* 6.4 1.6 - - + -
79C TRP* 4.2 14.3 - - + -
86C TRP* 4.2 22.2 - - + -
105C LEU* 3.5 28.5 - - + -
106C THR 4.7 4.9 - - - +
107C GLU* 4.4 8.1 - - + -
111C ASN* 3.5 28.9 - - - +
115C ASN* 2.9 18.0 + - + +
116C ARG* 3.5 11.2 - - - +
118C LYS* 1.3 76.9 - - - +
120C THR* 1.4 59.2 + - - +
122C ILE* 4.6 4.0 - - - +
123C MET* 3.2 32.4 + - - +
132C MET* 3.9 1.0 - - + +
134C VAL* 3.9 25.1 - - + -
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Residues in contact with THR 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ARG 2.9 15.2 + - - -
117C GLU 2.9 8.2 + - - -
119C MET* 1.4 74.2 - - - +
121C GLN* 1.3 59.1 + - - +
123C MET* 3.6 0.9 + - - +
124C PHE* 2.9 51.0 + - + -
132C MET* 4.1 15.0 - - - -
357C ILE* 5.3 2.2 - - + -
362C TYR* 3.7 26.7 - - + -
367C PRO* 4.2 11.9 - - - +
369C ILE* 4.9 6.3 - - + -
370C VAL* 3.0 27.4 - - + +
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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 GLU* 2.9 12.1 + - - +
118C LYS* 3.1 25.7 - - + +
120C THR* 1.3 75.5 - - - +
122C ILE* 1.4 58.6 + - + +
124C PHE* 3.7 0.3 - - - +
125C GLU* 2.9 70.6 + - - +
362C TYR* 3.3 17.0 + - - -
367C PRO* 3.9 21.0 - - + +
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Residues in contact with ILE 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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79C TRP* 3.5 35.7 - - + -
83C GLU* 3.9 30.7 - - + +
86C TRP* 4.1 16.4 - - + -
118C LYS* 3.0 34.0 + - + +
119C MET* 4.4 3.4 - - - +
121C GLN* 1.4 74.6 - - + +
123C MET* 1.3 70.6 + - - +
126C THR* 2.8 38.5 + - - +
127C PHE* 2.9 32.0 + - + -
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Residues in contact with MET 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C TRP* 3.5 41.7 - - + -
90C PHE* 4.0 16.8 - - + -
103C VAL* 3.8 23.3 - - - -
105C LEU* 3.8 14.4 - - + -
119C MET 3.2 20.2 + - - +
120C THR 3.9 2.2 - - - +
122C ILE* 1.3 81.4 - - + +
124C PHE* 1.3 57.6 + - - +
127C PHE* 3.1 38.3 + - + +
128C ASN 3.2 3.8 + - - -
129C THR* 2.7 26.1 + - - +
132C MET* 3.8 26.7 - - + -
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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 THR* 2.9 35.1 + - + +
123C MET* 1.3 76.5 - - - +
125C GLU* 1.3 58.4 + - - +
128C ASN* 3.0 26.5 - - - +
129C THR* 3.0 33.7 - - - +
131C ALA* 4.0 6.3 - - - -
132C MET* 3.6 24.9 - - + -
357C ILE* 3.6 28.5 - - + -
358C SER 4.0 6.7 - - - -
359C LYS* 3.7 36.6 + - + +
362C TYR* 3.3 44.6 - + + -
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Residues in contact with GLU 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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121C GLN* 2.9 41.7 + - - +
124C PHE* 1.3 72.2 - - - +
126C THR* 1.3 67.0 + - - +
128C ASN* 4.4 4.7 + - - +
359C LYS* 4.7 6.5 - - - +
362C TYR* 2.8 32.2 + - + +
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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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83C GLU* 3.9 23.0 + - - +
122C ILE* 2.8 35.6 + - + +
125C GLU* 1.3 76.7 - - - +
127C PHE* 1.3 78.8 + - + -
128C ASN* 3.6 0.8 - - - +
120L LYS* 6.6 0.2 - - - -
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Residues in contact with PHE 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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69C TYR 5.8 0.2 - - - -
83C GLU* 4.0 11.2 - - + -
86C TRP* 3.9 16.8 - - + -
87C HIS* 3.7 40.8 - - + -
90C PHE* 4.2 8.3 - + + -
91C TYR* 4.1 24.1 + + - -
98C PRO* 3.3 31.0 - - + +
99C GLU* 3.8 6.6 - - - +
122C ILE* 2.9 34.2 + - + -
123C MET* 3.4 25.6 - - + +
126C THR* 1.3 90.2 - - + +
128C ASN* 1.3 71.7 + - - +
129C THR* 3.4 5.2 - - - +
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Residues in contact with ASN 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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99C GLU* 3.1 36.6 + - + +
123C MET 3.2 0.6 + - - -
124C PHE 3.0 20.0 + - - +
125C GLU 4.3 4.5 - - - +
126C THR 3.6 1.4 - - - -
127C PHE* 1.3 81.3 - - - +
129C THR* 1.3 61.7 - - - +
130C PRO 3.9 0.2 - - - -
359C LYS* 3.8 21.1 + - - +
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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
------------------------------------------------------------
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