Contacts of the helix formed by residues 120 - 145 (chain C) in PDB entry 3BVE
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 LEU 120 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C LEU* 4.3 14.6 - - + -
57C LEU* 4.3 2.2 - - + -
101C ILE* 5.3 1.8 - - + +
104C ILE* 3.7 32.1 - - + +
105C VAL* 3.8 30.5 - - + +
108C ALA* 5.3 0.2 - - + -
116C THR* 3.0 32.5 + - + +
117C PHE* 3.3 6.2 + - - +
118C ASN 3.3 0.6 - - - -
119C PHE* 1.3 93.1 - - + +
121C GLN* 1.3 60.5 + - - +
122C TRP 3.4 0.9 - - - -
123C TYR* 3.0 32.7 + - + +
124C VAL* 2.9 27.0 + - + +
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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
----------------------------------------------------------
121A GLN* 5.9 0.4 - - - +
105C VAL* 4.3 9.7 - - - +
117C PHE* 2.9 59.8 + - + +
118C ASN* 3.6 14.1 - - - +
119C PHE 3.2 2.2 - - - -
120C LEU* 1.3 76.6 - - - +
122C TRP* 1.3 65.7 + - - +
124C VAL* 3.4 18.2 + - - +
125C ALA* 3.0 24.4 + - - +
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Residues in contact with TRP 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C HIS* 3.8 25.4 - + - -
56C LYS* 3.6 48.5 - - + +
57C LEU* 4.9 3.4 - - + -
118C ASN 5.0 0.2 + - - -
119C PHE* 2.7 59.9 + + - -
121C GLN* 1.3 76.8 - - - +
123C TYR* 1.3 89.2 + + + +
125C ALA* 3.5 5.0 + - - +
126C GLU* 2.9 67.5 + - - +
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Residues in contact with TYR 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C GLN* 3.0 30.3 + - + +
17C GLU* 2.3 38.5 + - - +
53C HIS* 3.9 23.1 - + + -
57C LEU* 4.1 16.8 - - + -
101C ILE* 3.4 34.7 - - + +
104C ILE* 5.3 1.3 - - + -
120C LEU* 3.0 30.4 + - + +
122C TRP* 1.3 114.4 - + + +
124C VAL* 1.3 59.2 + - - +
126C GLU* 4.8 0.9 - - + -
127C GLN* 2.9 36.2 + - + +
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Residues in contact with VAL 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C ILE* 3.8 23.8 - - + -
102C ASN* 5.4 9.2 - - - +
105C VAL* 3.9 19.1 - - + -
120C LEU 2.9 17.4 + - - +
121C GLN* 3.8 22.2 - - - +
123C TYR* 1.3 75.6 - - - +
125C ALA* 1.3 64.0 + - - +
127C GLN* 4.0 3.4 - - - +
128C HIS* 3.1 25.2 + - + +
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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
----------------------------------------------------------
121C GLN 3.0 18.2 + - - +
122C TRP* 3.8 5.4 - - - +
124C VAL* 1.3 82.3 - - + +
126C GLU* 1.3 63.6 + - + +
128C HIS* 3.4 7.0 + - - +
129C GLU* 3.2 20.6 + - - +
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Residues in contact with GLU 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C GLU* 4.3 6.1 - - - +
53C HIS* 3.5 21.0 + - + +
56C LYS* 4.5 10.8 + - - -
122C TRP* 2.9 54.1 + - + +
123C TYR* 4.2 2.5 - - + +
125C ALA* 1.3 74.1 - - + +
127C GLN* 1.3 58.3 - - - +
129C GLU* 3.3 14.0 + - - +
130C GLU* 3.0 34.4 + - - +
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Residues in contact with GLN 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C GLU* 5.2 1.2 - - - +
50C GLU* 4.5 1.7 - - - +
53C HIS* 5.1 4.4 + - + -
94C GLU* 2.9 54.2 + - - +
97C ILE* 3.7 15.1 - - - +
98C SER* 3.1 22.5 + - - +
101C ILE* 3.6 24.2 - - + +
123C TYR* 2.9 22.2 + - + +
124C VAL* 4.0 3.6 - - - +
126C GLU* 1.3 72.7 - - - +
128C HIS* 1.3 61.4 + - - +
130C GLU* 3.2 15.9 + - - +
131C GLU* 2.8 28.4 + - - +
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Residues in contact with HIS 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C SER* 5.3 0.4 - - - -
124C VAL* 3.1 19.9 + - + +
125C ALA* 3.7 7.4 - - - +
127C GLN* 1.3 75.0 - - - +
129C GLU* 1.3 61.3 + - + +
131C GLU* 3.4 13.9 + - - +
132C VAL* 2.9 53.4 + - + +
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Residues in contact with GLU 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C ALA 3.2 10.3 + - - +
126C GLU* 3.5 16.0 - - - +
128C HIS* 1.3 82.9 - - + +
130C GLU* 1.3 57.3 + - + +
132C VAL* 3.4 6.2 + - + +
133C LEU* 2.9 29.6 + - - +
165C ARG* 4.4 25.7 + - - +
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Residues in contact with GLU 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C HIS* 3.3 21.0 - - + +
49C GLU* 3.9 9.3 - - - +
50C GLU* 2.8 30.3 - - - +
53C HIS* 2.7 31.3 + - - -
94C GLU* 4.1 4.2 - - - +
126C GLU* 3.0 20.8 + - - +
127C GLN* 3.2 20.5 + - - +
129C GLU* 1.3 73.9 - - + +
131C GLU* 1.3 58.8 + - - +
133C LEU* 3.2 9.2 + - + +
134C PHE* 3.0 36.7 + - + -
165C ARG* 4.8 13.0 - - - +
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Residues in contact with GLU 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C TYR* 3.7 19.8 + - + -
94C GLU* 4.3 17.9 - - + -
95C GLN* 3.6 23.1 - - - +
98C SER* 2.6 35.4 + - - +
127C GLN* 2.8 22.8 + - - +
128C HIS* 3.7 13.0 + - - +
130C GLU* 1.3 72.8 - - - +
132C VAL* 1.3 57.5 + - + +
134C PHE* 3.3 2.5 + - - +
135C LYS* 3.0 26.9 + - - +
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Residues in contact with VAL 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C HIS* 2.9 51.0 + - + +
129C GLU* 3.7 6.7 - - + +
131C GLU* 1.3 72.4 - - + +
133C LEU* 1.3 61.8 + - - +
135C LYS* 3.3 23.0 + - - +
136C ASP* 2.9 41.5 + - - +
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Residues in contact with LEU 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C PHE* 3.6 28.7 - - + -
46C HIS* 5.5 2.7 - - - +
129C GLU 2.9 14.7 + - - +
130C GLU* 3.3 13.7 - - + +
132C VAL* 1.3 78.0 - - - +
134C PHE* 1.3 62.7 + - + +
136C ASP* 3.3 9.1 + - + +
137C ILE* 3.0 38.5 + - + +
161C ILE* 3.9 28.3 - - + -
165C ARG* 3.5 39.0 - - - +
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Residues in contact with PHE 134 (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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24C TYR* 3.9 7.6 - + - -
42C PHE* 3.6 23.6 - + - -
43C LEU* 4.1 2.5 - - + -
46C HIS* 3.3 49.1 - + - -
87C PHE* 3.9 29.0 - + - +
90C ALA* 3.6 34.5 - - + -
91C TYR* 4.1 20.7 - - + +
94C GLU* 3.9 12.6 - - + -
130C GLU 3.0 27.7 + - - +
131C GLU 3.3 3.3 + - - +
133C LEU* 1.3 77.8 - - + +
135C LYS* 1.3 60.2 + - - +
137C ILE* 3.4 4.2 + - - +
138C LEU* 3.0 31.4 + - - +
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Residues in contact with LYS 135 (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 TYR* 3.6 40.2 - - + +
131C GLU 3.0 8.7 + - - +
132C VAL* 3.4 24.7 - - - +
134C PHE* 1.3 77.0 - - - +
136C ASP* 1.3 78.9 + - - +
138C LEU* 3.4 3.4 + - - +
139C ASP* 2.9 47.3 + - - +
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Residues in contact with ASP 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C VAL* 2.9 31.4 + - - +
133C LEU* 3.3 8.5 + - + +
135C LYS* 1.3 102.8 + - - +
137C ILE* 1.3 63.4 + - + +
139C ASP* 3.3 7.0 + - - +
140C LYS* 2.9 32.8 + - - +
157C TYR* 5.3 4.4 - - + +
161C ILE* 6.3 1.3 - - + -
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Residues in contact with ILE 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C PHE* 3.2 45.1 - - + -
87C PHE* 3.6 28.3 - - + -
133C LEU* 3.0 30.3 + - + +
134C PHE* 4.0 4.7 - - - +
136C ASP* 1.3 75.5 - - + +
138C LEU* 1.3 57.6 + - - +
140C LYS* 3.2 7.2 + - + +
141C ILE* 2.8 34.1 + - + +
157C TYR* 5.2 1.8 - - + -
158C VAL* 3.8 23.6 - - + -
161C ILE* 3.8 25.6 - - + -
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Residues in contact with LEU 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C THR* 4.1 9.2 - - + +
87C PHE* 4.0 10.5 - - + +
88C GLN* 3.8 52.0 - - + +
91C TYR* 3.8 35.0 - - + -
134C PHE 3.0 18.8 + - - +
135C LYS* 3.7 4.7 - - - +
137C ILE* 1.3 76.5 - - - +
139C ASP* 1.3 58.0 + - - +
141C ILE* 3.3 8.6 + - + +
142C GLU* 2.9 50.9 + - + +
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Residues in contact with ASP 139 (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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135C LYS* 2.9 39.5 + - - +
136C ASP* 3.5 9.1 - - - +
138C LEU* 1.3 76.2 - - - +
140C LYS* 1.3 60.7 + - - +
142C GLU* 3.7 5.6 - - - +
143C LEU* 2.9 30.6 + - - +
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Residues in contact with LYS 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C ASP* 2.9 18.5 + - - +
137C ILE 3.6 4.3 - - - +
139C ASP* 1.3 76.0 - - - +
141C ILE* 1.3 60.3 + - + +
143C LEU* 3.3 25.4 + - + +
144C ILE* 2.9 48.8 + - + +
157C TYR* 3.4 62.8 - - + -
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Residues in contact with ILE 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C LEU* 3.9 26.9 - - + +
84C THR* 3.3 37.7 + - + +
87C PHE* 3.6 42.2 - - + -
137C ILE* 2.8 32.9 + - + +
138C LEU* 3.7 6.5 - - + +
140C LYS* 1.3 72.0 - - + +
142C GLU* 1.3 59.2 + - - +
144C ILE* 4.0 0.9 - - - +
145C GLY* 3.1 27.9 + - - +
146C ASN* 5.8 0.9 - - - +
154C ALA* 4.3 15.7 - - + +
158C VAL* 4.8 5.6 - - + -
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Residues in contact with GLU 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C THR* 3.3 26.7 - - + +
88C GLN* 5.0 7.6 + - - +
138C LEU* 2.9 34.8 + - + +
139C ASP* 3.7 7.4 - - - +
141C ILE* 1.3 76.3 - - - +
143C LEU* 1.3 62.2 + - - +
145C GLY* 3.8 8.6 + - - -
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Residues in contact with LEU 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C ASP 2.9 18.7 + - - +
140C LYS* 3.3 31.6 + - + +
142C GLU* 1.3 75.4 - - - +
144C ILE* 1.3 66.7 + - + +
145C GLY* 4.7 0.2 - - - -
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Residues in contact with ILE 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C LYS* 2.9 40.7 + - + +
141C ILE 4.1 2.5 - - - +
143C LEU* 1.3 83.1 - - + +
145C GLY* 1.3 61.1 + - - +
147C GLU* 5.3 1.9 + - - +
150C GLY* 3.4 35.4 - - - +
153C LEU* 4.0 22.7 - - + +
154C ALA* 3.6 29.4 - - + +
157C TYR* 4.7 5.2 - - + -
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Residues in contact with GLY 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C ILE 3.1 16.1 + - - +
142C GLU* 3.8 7.1 + - - -
143C LEU 3.5 1.2 - - - -
144C ILE* 1.3 82.3 - - - +
146C ASN* 1.3 69.2 + - - +
147C GLU* 3.7 1.3 - - - -
150C GLY* 3.3 22.1 - - - +
154C ALA* 5.5 1.4 - - - +
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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
------------------------------------------------------------
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