Contacts of the helix formed by residues 116 - 139 (chain C) in PDB entry 4B5G
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 ALA 116 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C GLY 3.7 8.1 - - - +
114C SER 3.6 0.8 - - - -
115C SER* 1.3 81.9 - - - +
117C GLU* 1.3 67.5 + - - +
118C GLU* 3.3 7.9 - - + +
119C ARG* 3.3 16.4 + - + +
120C GLN* 3.1 16.3 + - - +
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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
----------------------------------------------------------
116C ALA* 1.3 72.6 - - - +
118C GLU* 1.3 61.1 + - - +
120C GLN* 3.1 16.0 + - - +
121C GLN* 2.5 63.5 + - + +
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Residues in contact with GLU 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ALA* 3.3 5.0 - - + +
117C GLU* 1.3 79.2 - - - +
119C ARG* 1.3 66.1 + - + +
121C GLN* 3.2 11.2 + - - +
122C VAL* 2.8 32.8 + - - +
125C ARG* 3.6 24.0 + - - -
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Residues in contact with ARG 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C TYR* 3.0 20.7 + - - -
92C GLU* 3.6 15.4 + - - -
94C ARG* 3.4 11.3 - - - +
111C PRO* 4.6 1.8 - - - +
112C SER 3.7 15.0 + - - +
113C GLY* 3.7 15.2 - - - -
115C SER* 4.3 4.0 - - - -
116C ALA* 3.3 27.4 - - + +
118C GLU* 1.3 83.4 - - + +
120C GLN* 1.3 60.0 + - - +
122C VAL* 3.2 27.2 - - - +
123C LYS* 2.9 27.2 + - - +
34Y A 4.8 4.2 - - - -
35Y C 2.5 45.7 + - - +
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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
----------------------------------------------------------
113C GLY* 2.8 26.7 - - - +
116C ALA 3.1 5.3 + - - +
117C GLU* 3.1 25.7 + - - +
119C ARG* 1.3 79.3 - - - +
121C GLN* 1.3 56.2 + - - +
123C LYS* 3.2 10.9 + - - +
124C TYR* 2.9 61.8 + - + -
169C SER* 2.7 27.6 + - - -
172C LEU* 3.5 15.4 - - + +
175C GLU* 2.8 27.5 + - - -
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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
----------------------------------------------------------
117C GLU* 2.5 51.2 + - + +
118C GLU* 3.2 13.0 + - - +
120C GLN* 1.3 81.4 - - - +
122C VAL* 1.3 55.9 + - - +
124C TYR* 3.0 20.5 + - - +
125C ARG* 2.9 46.2 + - - +
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Residues in contact with VAL 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C GLU* 3.2 28.9 - - + +
89C PHE* 3.1 29.6 - - + -
92C GLU* 5.1 5.8 - - - +
111C PRO* 4.6 8.3 - - + -
118C GLU* 2.8 21.4 + - - +
119C ARG* 3.2 39.0 - - - +
121C GLN* 1.3 72.3 - - - +
123C LYS* 1.3 64.8 + - - +
125C ARG* 3.7 15.8 - - - +
126C PHE* 2.9 21.7 + - - +
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Residues in contact with LYS 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C LEU* 3.7 19.3 - - + -
111C PRO* 3.2 31.2 + - + +
112C SER* 4.6 0.4 - - - +
113C GLY 3.7 15.0 - - - +
119C ARG 2.9 14.2 + - - +
120C GLN* 3.2 16.6 - - - +
121C GLN 3.2 0.2 - - - -
122C VAL* 1.3 76.3 - - - +
124C TYR* 1.3 58.9 + - + +
126C PHE* 3.0 8.7 + - - +
127C LEU* 2.9 36.8 + - + +
151C ASN* 3.0 31.3 + - - +
152C ILE* 4.2 8.7 - - - -
169C SER* 3.7 12.3 + - - -
170C GLY* 3.9 3.4 - - - +
175C GLU* 3.3 27.6 + - - +
36Y 3DR 5.2 1.2 + - - -
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Residues in contact with TYR 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C GLN* 2.9 54.8 + - + -
121C GLN* 3.0 22.9 + - - +
123C LYS* 1.3 77.4 - - - +
125C ARG* 1.3 56.3 + - + +
127C LEU* 3.3 15.1 + - + +
128C ASP* 2.9 42.3 + - - +
172C LEU* 3.7 20.4 - - + +
174C GLU* 2.8 53.5 + - + +
175C GLU* 4.0 14.6 - - + +
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Residues in contact with ARG 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C GLU* 3.3 31.6 + - - +
89C PHE* 3.4 13.0 - - + -
118C GLU* 3.6 25.3 + - - -
121C GLN* 2.9 28.6 + - - +
122C VAL* 3.7 18.0 - - - +
124C TYR* 1.3 75.3 - - + +
126C PHE* 1.3 57.1 - - - +
128C ASP* 3.5 11.2 - - - +
129C ALA* 2.8 30.1 + - - +
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Residues in contact with PHE 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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84C MET* 3.4 32.1 - - + -
89C PHE* 3.2 31.6 - + + -
94C ARG* 4.4 6.7 - - + -
108C LEU* 4.1 19.5 - - + -
109C TYR 4.6 2.5 - - - -
110C LEU* 3.5 35.7 - - + -
111C PRO* 3.3 33.2 - - + -
122C VAL 2.9 15.2 + - - +
123C LYS 3.0 9.4 + - - +
125C ARG* 1.3 75.1 - - - +
127C LEU* 1.3 63.2 + - + +
129C ALA* 3.2 1.6 + - - +
130C PHE* 2.9 50.4 + + + +
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Residues in contact with LEU 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C LEU* 3.6 40.6 - - + -
123C LYS* 2.9 22.8 + - + +
124C TYR* 3.6 23.8 - - + +
126C PHE* 1.3 76.6 - - + +
128C ASP* 1.3 60.8 + - - +
130C PHE* 4.5 0.9 - - - +
131C TYR* 2.9 35.5 + - - +
152C ILE* 4.2 15.0 - - + -
175C GLU* 4.8 9.4 - - + -
178C TRP* 3.8 55.1 - - + +
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Residues in contact with ASP 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C TYR* 2.9 31.9 + - - +
125C ARG* 3.5 11.3 - - - +
126C PHE 3.2 0.2 - - - -
127C LEU* 1.3 82.1 - - - +
129C ALA* 1.3 55.4 + - - +
131C TYR* 5.1 2.5 - - - -
132C PRO* 4.1 13.2 - - - +
178C TRP* 5.3 3.8 + - - -
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Residues in contact with ALA 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C MET* 5.2 4.2 - - - +
86C ILE* 4.5 15.2 - - + +
89C PHE* 3.7 22.7 - - + -
125C ARG 2.8 16.0 + - - +
126C PHE 3.7 2.5 - - - +
127C LEU 3.1 0.2 - - - -
128C ASP* 1.3 80.8 - - - +
130C PHE* 1.3 60.2 + - - +
131C TYR 3.5 0.7 - - - -
132C PRO* 3.8 9.6 - - - +
133C MET* 3.7 16.4 - - - +
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Residues in contact with PHE 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C MET* 5.7 4.0 - - + -
95C PHE* 3.8 21.3 - + - -
106C ILE* 5.8 0.2 - - + -
108C LEU* 3.5 32.3 - - + -
110C LEU* 5.2 0.7 - - + -
126C PHE* 2.9 37.1 + + + +
127C LEU* 4.1 2.2 - - - +
129C ALA* 1.3 79.1 - - - +
131C TYR* 1.3 64.1 + - - +
132C PRO 3.6 0.4 - - - -
133C MET* 3.3 18.0 - - + +
134C LEU* 3.2 55.7 + - + +
137C MET* 4.1 13.5 - - + -
146C VAL* 4.6 10.8 - - + -
150C TRP* 3.9 16.2 - + - -
178C TRP* 4.2 10.8 - + - -
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Residues in contact with TYR 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 LEU 2.9 17.4 + - - +
128C ASP* 5.1 2.7 - - - -
130C PHE* 1.3 72.8 - - - +
132C PRO* 1.4 68.0 - - + +
133C MET 3.0 2.2 - - - -
134C LEU* 2.8 33.9 + - + +
135C GLU* 3.1 11.8 + - - +
178C TRP* 3.8 21.3 - + - +
181C LYS* 3.6 37.9 + - + +
182C VAL* 4.8 4.0 - - + -
185C LYS* 4.4 8.5 - - - +
186C LEU* 3.2 47.0 - - + +
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Residues in contact with PRO 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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128C ASP 4.1 10.3 - - - +
129C ALA 3.8 14.4 - - - +
130C PHE 3.7 1.8 - - - -
131C TYR* 1.4 95.0 - - + +
133C MET* 1.3 58.8 + - + +
135C GLU* 3.3 13.5 + - + +
136C ALA* 2.9 26.4 + - - +
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Residues in contact with MET 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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81C GLN* 5.2 3.6 - - - +
84C MET* 3.6 47.1 - - + +
95C PHE* 4.3 12.6 - - + -
129C ALA 3.7 20.9 - - - +
130C PHE* 3.3 17.0 - - + +
132C PRO* 1.3 78.7 - - + +
134C LEU* 1.3 59.5 + - - +
136C ALA* 3.2 8.2 + - - +
137C MET* 2.9 57.8 + - + +
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Residues in contact with LEU 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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130C PHE* 3.2 52.4 + - + +
131C TYR* 2.8 20.4 + - + +
133C MET* 1.3 74.8 - - - +
135C GLU* 1.3 60.2 + - - +
137C MET* 3.5 6.2 + - - -
138C LYS* 3.2 17.2 + - - +
146C VAL* 4.7 9.0 - - + -
150C TRP* 4.3 10.8 - - + -
178C TRP* 3.8 22.2 - - + -
182C VAL* 3.9 22.0 - - + -
186C LEU* 5.1 1.1 - - + -
188C TRP* 3.3 44.0 + - + +
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Residues in contact with GLU 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C TYR* 3.1 14.7 + - + +
132C PRO* 3.4 13.7 - - + +
133C MET 3.2 0.2 - - - -
134C LEU* 1.3 77.6 - - - +
136C ALA* 1.3 60.7 + - - +
138C LYS* 3.3 5.7 + - + +
139C ASN* 2.9 46.1 + - - +
186C LEU* 4.2 30.2 - - + +
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Residues in contact with ALA 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C PRO 2.9 14.9 + - - +
133C MET* 3.2 13.0 + - - +
135C GLU* 1.3 76.7 - - - +
137C MET* 1.3 63.5 + - + +
139C ASN* 3.0 18.9 + - - +
140C GLU* 3.2 18.7 + - - +
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Residues in contact with MET 137 (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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95C PHE* 3.9 19.5 - - + -
97C ARG* 5.2 5.8 - - - +
106C ILE* 3.6 34.5 - - + -
130C PHE* 4.1 8.7 - - + -
133C MET* 2.9 44.9 + - + +
134C LEU* 3.9 10.8 - - - +
135C GLU 3.3 0.2 - - - -
136C ALA* 1.3 73.4 - - + +
138C LYS* 1.3 62.0 + - - +
140C GLU* 3.3 28.8 + - - +
141C GLY 4.4 1.0 + - - -
142C ARG 4.9 2.6 - - - +
144C ILE* 3.3 33.5 - - + +
146C VAL* 4.7 12.8 - - - -
188C TRP* 4.1 7.2 - - + -
226C THR* 5.4 0.3 - - - +
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Residues in contact with LYS 138 (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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134C LEU 3.2 11.6 + - - +
135C GLU* 3.5 10.8 - - + +
137C MET* 1.3 79.8 - - - +
139C ASN* 1.3 66.0 + - - +
140C GLU 3.4 2.8 + - - -
141C GLY* 3.8 9.0 + - - -
142C ARG 5.3 0.7 + - - +
186C LEU* 3.7 27.8 - - + +
187C GLY* 4.5 5.4 - - - +
188C TRP* 4.2 17.0 - - + +
226C THR* 4.6 14.9 - - + +
227C PRO* 3.4 39.9 - - + +
228C GLU* 4.1 11.9 + - - -
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Residues in contact with ASN 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C GLU* 2.9 41.2 + - - +
136C ALA* 3.0 11.3 + - - +
138C LYS* 1.3 82.9 - - - +
140C GLU* 1.3 61.6 + - - +
141C GLY* 3.3 1.9 - - - -
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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