Contacts of the helix formed by residues 111 - 133 (chain C) in PDB entry 4WNP
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 SER 111 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110C LEU* 1.3 77.6 - - - +
112C GLU* 1.3 64.5 + - - +
113C ASP* 3.8 12.3 + - - +
114C THR* 3.0 29.6 + - - -
115C ILE* 3.0 21.9 + - - +
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Residues in contact with GLU 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C LEU 3.8 0.8 + - - -
111C SER* 1.3 73.2 - - - +
113C ASP* 1.3 62.9 + - - +
115C ILE* 3.4 10.2 + - - +
116C ARG* 3.0 32.0 + - - +
215C LEU* 4.3 10.8 - - + +
246C GLU 4.7 1.0 - - - +
247C THR* 3.7 12.6 - - - +
248C SER* 3.0 48.2 + - - -
251C LEU* 3.6 21.8 - - + +
277C PHE* 3.8 15.4 - - + -
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Residues in contact with ASP 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C SER* 3.1 10.9 + - - +
112C GLU* 1.3 78.2 - - - +
114C THR* 1.3 64.3 + - - +
116C ARG* 3.0 32.6 + - - +
117C LEU* 3.0 21.4 + - - +
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Residues in contact with THR 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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103C TYR* 5.0 5.8 - - + +
110C LEU* 4.0 21.1 - - + -
111C SER* 3.0 25.9 + - - -
113C ASP* 1.3 77.5 - - - +
115C ILE* 1.3 57.0 + - - +
117C LEU* 3.2 10.5 + - + +
118C PHE* 2.9 55.3 + - + -
156C PRO* 5.5 10.8 - - + +
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Residues in contact with ILE 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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110C LEU* 3.8 21.1 - - + +
111C SER 3.0 23.8 + - - +
112C GLU* 3.6 7.9 - - - +
114C THR* 1.3 77.2 - - - +
116C ARG* 1.3 56.6 + - - +
118C PHE* 3.3 6.0 + - - +
119C LEU* 2.9 28.6 + - + +
211C VAL* 3.7 32.8 - - + +
214C CYS* 3.9 17.7 - - + -
215C LEU* 3.8 41.5 - - + +
251C LEU* 4.8 3.1 - - + -
277C PHE* 4.1 14.8 - - + -
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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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112C GLU* 3.0 19.4 + - - +
113C ASP* 3.0 38.9 + - - +
115C ILE* 1.3 77.9 - - - +
117C LEU* 1.3 56.8 + - - +
119C LEU* 3.9 1.9 - - - +
120C GLN* 3.0 51.4 + - - +
277C PHE* 3.2 50.8 + - + +
278C LEU* 3.5 15.7 - - - +
279C ASP 5.0 5.8 - - - -
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Residues in contact with LEU 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 ASP 3.0 12.0 + - - +
114C THR* 3.2 11.4 + - + +
116C ARG* 1.3 76.5 - - - +
118C PHE* 1.3 79.0 + - + +
120C GLN* 3.7 14.9 + - - +
121C GLN* 3.3 39.3 + - + +
156C PRO 3.4 26.0 - - - +
157C ASN* 4.0 26.7 - - + +
159C ILE 4.5 2.0 - - - +
160C ARG* 5.5 3.4 - - - +
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Residues in contact with PHE 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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100C LEU* 4.0 21.8 - - + -
103C TYR* 4.0 20.4 - + - -
110C LEU* 3.9 30.1 - - + -
114C THR* 2.9 29.9 + - + +
115C ILE* 3.8 5.4 - - - +
117C LEU* 1.3 98.4 - - + +
119C LEU* 1.3 60.0 + - - +
121C GLN* 3.3 7.6 + - - +
122C ILE* 3.0 38.0 + - + +
144C ILE* 6.2 0.7 - - + -
146C LEU* 4.8 2.9 - - + -
156C PRO 4.7 0.2 - - - -
159C ILE* 4.0 34.5 - - + -
161C VAL* 3.9 23.5 - - + +
214C CYS* 5.6 2.2 - - - -
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Residues in contact with LEU 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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115C ILE 2.9 17.8 + - - +
116C ARG* 4.0 1.6 - - - +
118C PHE* 1.3 75.2 - - - +
120C GLN* 1.3 59.4 + - - +
122C ILE* 3.3 14.9 + - + +
123C ALA* 2.8 28.8 + - - +
207C ILE* 3.5 31.9 - - + -
211C VAL* 3.6 23.6 - - + -
254C LEU* 3.8 26.2 - - + -
258C LEU* 5.7 0.2 - - + -
272C PHE* 3.9 15.3 - - + -
277C PHE* 4.1 10.1 - - + -
278C LEU* 3.7 24.7 - - + -
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Residues in contact with GLN 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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116C ARG* 3.0 38.9 + - - +
117C LEU* 3.8 18.8 - - - +
119C LEU* 1.3 76.6 - - - +
121C GLN* 1.3 58.0 + - + +
123C ALA* 3.3 8.5 + - - +
124C GLY* 3.0 23.2 + - - -
278C LEU* 2.7 43.6 + - + +
279C ASP* 5.0 1.0 - - - +
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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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74C ASN* 3.2 28.4 + - - +
117C LEU* 3.3 38.1 + - + +
118C PHE* 3.3 5.4 + - - +
119C LEU 3.2 0.2 - - - -
120C GLN* 1.3 75.6 - - + +
122C ILE* 1.3 64.8 + - - +
124C GLY* 3.2 10.2 + - - -
125C ALA 3.2 9.2 + - - -
159C ILE 3.2 18.8 + - - -
160C ARG* 3.1 34.9 - - - +
161C VAL* 2.9 44.5 + - + +
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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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74C ASN* 5.6 0.4 - - - -
100C LEU* 5.5 2.2 - - + -
118C PHE* 3.0 23.5 + - + +
119C LEU* 3.3 18.4 + - + +
121C GLN* 1.3 73.9 - - - +
123C ALA* 1.3 64.1 + - - +
125C ALA* 3.2 8.0 + - - +
126C MET* 2.9 25.5 + - + +
139C LEU* 5.9 1.3 - - + -
144C ILE* 4.3 32.3 - - + -
161C VAL* 4.5 9.9 - - + -
163C ILE* 4.3 13.9 - - + -
207C ILE* 4.0 35.2 - - + -
210C ILE* 5.1 14.1 - - + -
272C PHE* 5.5 0.2 - - + -
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Residues in contact with ALA 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 LEU 2.8 18.3 + - - +
120C GLN* 3.5 6.7 - - - +
121C GLN 3.2 0.2 - - - -
122C ILE* 1.3 76.4 - - - +
124C GLY* 1.3 63.3 + - - +
126C MET* 3.3 1.7 + - - -
127C ARG* 3.0 30.9 + - - +
272C PHE* 3.9 27.1 - - + -
273C PHE* 3.5 12.9 - - + -
278C LEU* 4.1 17.7 - - + -
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Residues in contact with GLY 124 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72C HIS* 3.5 21.4 + - - -
74C ASN* 5.0 1.1 - - - -
120C GLN 3.0 14.1 + - - -
121C GLN* 3.2 5.1 + - - -
122C ILE 3.1 0.4 - - - -
123C ALA* 1.3 75.3 - - - +
125C ALA* 1.3 62.6 + - - +
127C ARG* 3.2 24.1 + - - +
128C LEU* 3.5 4.3 + - - +
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Residues in contact with ALA 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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72C HIS* 3.7 13.2 - - - -
74C ASN* 3.7 21.3 - - + +
75C ILE* 3.8 12.9 - - + +
121C GLN 3.2 9.9 + - - +
122C ILE 3.2 4.4 + - - +
124C GLY* 1.3 74.2 - - - +
126C MET* 1.3 61.9 + - - +
128C LEU* 3.2 5.4 + - - +
129C LEU* 3.1 26.6 + - - +
163C ILE* 3.6 26.5 - - + -
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Residues in contact with MET 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 ILE* 2.9 24.4 + - + +
123C ALA* 3.8 6.3 - - - +
125C ALA* 1.3 73.8 - - - +
127C ARG* 1.3 61.0 + - - +
129C LEU* 3.3 22.6 + - + +
130C HIS* 2.8 32.5 + - - +
134C ILE 5.5 1.6 - - - +
139C LEU* 4.1 14.4 - - + -
163C ILE* 4.0 18.2 - - - -
203C ASP* 3.9 28.7 - - + +
207C ILE* 3.8 21.8 - - + -
269C PHE* 4.1 24.7 - - + -
272C PHE* 5.0 2.0 - - + -
273C PHE* 3.9 13.0 - - + -
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Residues in contact with ARG 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 ALA* 3.0 17.8 + - - +
124C GLY* 3.3 14.4 - - - +
126C MET* 1.3 77.3 - - - +
128C LEU* 1.3 61.7 + - - +
130C HIS* 3.4 1.9 + - - +
131C SER* 3.0 25.1 + - - -
273C PHE* 3.4 65.0 + - + +
274C HIS* 3.9 23.0 + - - -
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Residues in contact with LEU 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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70C LEU* 3.9 24.9 - - + -
71C LYS 3.9 16.2 - - - +
72C HIS* 3.8 40.8 - - + -
75C ILE* 4.2 4.3 - - + -
124C GLY 3.5 1.8 + - - -
125C ALA 3.2 8.7 + - - +
127C ARG* 1.3 76.9 - - - +
129C LEU* 1.3 65.6 + - - +
131C SER* 2.8 28.3 + - - +
132C LYS* 3.1 33.3 + - + +
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Residues in contact with LEU 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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70C LEU* 4.1 10.3 - - + -
75C ILE* 3.5 32.1 - - + -
125C ALA* 3.1 12.7 + - + +
126C MET* 3.3 28.7 + - + +
128C LEU* 1.3 75.3 - - - +
130C HIS* 1.3 64.2 + - - +
132C LYS* 3.0 10.0 + - - -
134C ILE* 3.0 56.9 + - + +
136C HIS* 4.0 21.8 - - + +
163C ILE* 5.4 2.5 - - + -
166C PHE* 3.8 27.1 - - + -
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Residues in contact with HIS 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 MET* 2.8 21.2 + - - +
127C ARG 3.7 4.0 - - - +
129C LEU* 1.3 72.6 - - - +
131C SER* 1.3 62.5 + - - +
133C GLY* 3.3 12.4 + - - -
134C ILE 4.3 3.6 + - - +
269C PHE* 3.3 55.8 - + + +
273C PHE* 4.3 16.6 - + + -
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Residues in contact with SER 131 (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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127C ARG* 3.0 14.5 + - - -
128C LEU* 2.8 27.9 + - - +
130C HIS* 1.3 79.3 - - - +
132C LYS* 1.3 64.1 + - - +
133C GLY 3.7 0.2 + - - -
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Residues in contact with LYS 132 (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 GLU* 2.9 33.3 + - - +
70C LEU* 4.2 10.5 - - + +
71C LYS 5.7 0.2 - - - +
128C LEU* 3.2 35.8 - - + +
129C LEU* 3.0 6.7 + - - +
131C SER* 1.3 83.2 + - - +
133C GLY* 1.3 61.1 + - - +
134C ILE* 4.0 16.8 - - + +
171C TYR* 3.6 21.1 - - + -
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Residues in contact with GLY 133 (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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129C LEU 3.1 2.6 + - - -
130C HIS* 3.3 10.7 + - - -
131C SER 3.3 1.2 + - - -
132C LYS* 1.3 80.3 - - - +
134C ILE* 1.3 59.8 + - - +
135C ILE* 5.5 0.7 - - - -
171C TYR* 3.1 5.9 - - - +
172C LEU* 2.8 41.6 + - - +
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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