Contacts of the helix formed by residues 129 - 150 (chain C) in PDB entry 2R7I
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 129 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127C THR 4.9 4.0 - - - +
128C LEU* 1.3 77.7 - - - +
130C ASP* 1.3 66.1 + - - +
131C TYR* 3.4 10.1 + - - +
132C ASP* 2.8 42.0 + - - +
133C ILE* 3.1 11.6 + - - +
291C HIS* 5.6 2.9 - - - -
292C LEU* 4.0 3.1 - - - -
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Residues in contact with ASP 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C THR* 1.3 73.4 - - - +
131C TYR* 1.3 61.8 + - - +
133C ILE* 3.7 6.3 + - - +
134C ARG* 3.0 62.6 + - - +
291C HIS* 3.3 26.1 - - - +
292C LEU* 3.2 35.4 - - - +
294C SER* 4.4 1.2 + - - -
323C TYR* 4.5 4.7 + - - -
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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
----------------------------------------------------------
129C THR* 2.9 9.8 + - - +
130C ASP* 1.3 78.7 + - - +
132C ASP* 1.3 71.4 + - - +
134C ARG* 3.1 14.4 + - - +
135C PHE* 2.9 29.3 + + + -
169C ARG* 3.5 27.4 - - - -
326C THR* 3.8 31.9 + - + -
327C VAL* 4.1 27.4 + - + +
329C LYS 5.8 0.2 + - - -
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Residues in contact with ASP 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C LEU* 3.7 21.6 - - + +
129C THR* 2.8 38.5 + - - +
131C TYR* 1.3 74.6 - - - +
133C ILE* 1.3 63.2 + - - +
135C PHE* 2.9 7.8 + - - +
136C TYR* 2.8 32.9 + - + -
166C HIS* 3.9 17.4 + - - -
169C ARG* 2.7 36.6 + - - -
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Residues in contact with ILE 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C PHE* 5.4 0.2 - - - -
125C TYR 5.5 2.9 - - - +
128C LEU* 4.0 26.0 - - + +
129C THR 3.1 10.6 + - - +
130C ASP* 3.7 8.3 - - - +
132C ASP* 1.3 76.1 - - - +
134C ARG* 1.3 62.2 + - - +
136C TYR* 3.3 2.0 + - - +
137C MET* 2.9 41.1 + - + +
222C LEU* 4.1 9.4 - - + -
225C MET* 3.8 44.4 - - + +
226C ILE* 4.3 8.5 - - + -
292C LEU* 4.3 22.0 - - + -
323C TYR* 3.3 18.4 - - - +
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Residues in contact with ARG 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ASP* 3.0 44.3 + - - +
131C TYR* 3.1 13.6 + - - +
133C ILE* 1.3 75.9 - - - +
135C PHE* 1.3 58.8 + - - +
138C TYR* 3.0 24.9 + - - +
294C SER* 3.4 27.5 + - - -
296C GLU* 4.1 18.6 + - - +
322C PRO 4.5 2.2 + - - -
323C TYR* 3.1 64.3 + - + +
324C PHE* 3.3 13.2 - - + -
326C THR* 4.5 17.6 + - - -
327C VAL* 4.0 14.3 - - + +
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Residues in contact with PHE 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C TYR* 2.9 23.5 + + + +
132C ASP* 2.9 12.7 + - - +
134C ARG* 1.3 77.5 - - - +
136C TYR* 1.3 91.6 + + - +
138C TYR* 3.4 5.9 + - - +
139C GLU* 3.1 50.0 + - + +
169C ARG* 3.8 50.5 - - + +
327C VAL* 3.8 25.8 - - + -
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Residues in contact with TYR 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C PHE* 3.5 26.0 - + + -
124C LEU* 5.1 0.2 - - + -
128C LEU* 4.2 20.9 - - + -
132C ASP* 2.8 33.2 + - + +
133C ILE 4.2 0.4 - - - +
135C PHE* 1.3 97.9 - + - +
137C MET* 1.3 61.4 + - - +
138C TYR 3.2 0.2 - - - -
139C GLU* 3.1 5.8 + - + +
140C ILE* 2.9 35.5 + - - +
164C ILE* 3.7 22.7 - - + -
166C HIS* 2.7 46.7 + + - -
169C ARG* 3.7 23.5 - - - -
170C LYS 4.4 2.5 - - - -
171C LEU* 3.8 17.9 - - + -
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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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133C ILE* 2.9 31.4 + - + +
134C ARG* 3.7 4.9 - - - +
136C TYR* 1.3 76.0 - - - +
138C TYR* 1.3 57.6 + - - +
140C ILE* 3.3 10.1 + - + +
141C LEU* 2.9 35.2 + - - +
218C LEU* 3.5 46.0 - - + +
221C MET* 5.2 0.4 - - - -
222C LEU* 4.0 22.7 - - + -
225C MET* 3.5 32.3 - - + -
300C PHE* 3.9 23.3 - - + -
304C LEU* 4.9 0.2 - - + -
323C TYR* 4.9 0.4 - - + -
324C PHE* 3.8 11.2 - - + -
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Residues in contact with TYR 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 ARG 3.0 18.7 + - - +
135C PHE 3.5 6.3 - - - +
136C TYR 3.2 0.2 - - - -
137C MET* 1.3 77.7 - - - +
139C GLU* 1.3 66.2 + - - +
141C LEU* 3.4 5.3 + - + +
142C LYS* 2.9 47.0 + - + +
316C ARG* 4.5 4.5 + - - -
319C MET* 3.4 57.6 + - + +
324C PHE* 3.7 32.4 - + + -
327C VAL* 4.2 19.3 - - + -
328C VAL* 4.3 21.0 - - + +
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Residues in contact with GLU 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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93C ASN* 2.7 43.1 + - - +
135C PHE* 3.1 50.8 + - + +
136C TYR* 3.1 13.2 + - + +
138C TYR* 1.3 85.1 - - - +
140C ILE* 1.3 64.8 - - - +
142C LYS* 3.1 19.8 + - - +
143C ALA* 3.1 12.3 + - - +
169C ARG 5.4 2.2 - - - +
171C LEU* 3.9 21.5 - - + +
327C VAL* 5.3 1.0 - - - +
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Residues in contact with ILE 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C PHE* 3.9 24.2 - - + -
136C TYR 2.9 23.2 + - - +
137C MET* 3.7 9.2 - - - +
139C GLU* 1.3 74.6 - - - +
141C LEU* 1.3 52.3 + - - +
143C ALA* 3.0 6.9 + - - +
144C LEU* 2.8 46.3 + - + +
157C VAL* 5.0 8.5 - - + -
162C VAL* 4.2 14.1 - - + -
171C LEU* 3.9 19.1 - - + -
173C LEU* 5.1 8.3 - - + -
218C LEU* 3.8 26.7 - - + -
221C MET* 3.9 19.5 - - + -
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Residues in contact with LEU 141 (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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137C MET* 2.9 18.8 + - + +
138C TYR* 3.7 4.5 - - - +
140C ILE* 1.3 73.8 - - - +
142C LYS* 1.3 61.1 + - - +
144C LEU* 4.1 4.7 - - + +
145C ASP* 2.9 31.7 + - - +
215C MET* 3.5 21.5 - - + -
218C LEU* 3.3 30.1 - - + -
300C PHE* 4.3 3.6 - - + -
315C ALA* 4.1 10.7 - - + +
318C ALA* 3.8 17.3 - - + -
319C MET* 3.6 22.3 - - + +
324C PHE* 3.5 39.3 - - + -
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Residues in contact with LYS 142 (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 PRO* 3.9 30.9 - - + +
93C ASN* 3.8 8.9 + - - +
138C TYR* 2.9 42.9 + - + +
139C GLU* 3.1 30.9 + - - +
141C LEU* 1.3 76.9 - - - +
143C ALA* 1.3 57.6 + - - +
145C ASP* 4.2 1.7 - - - +
146C TYR* 3.2 27.4 + - - +
316C ARG* 5.9 0.4 - - - +
319C MET* 3.8 20.6 - - + -
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Residues in contact with ALA 143 (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 PRO 3.4 20.8 + - - +
93C ASN* 3.7 15.7 - - + +
94C ILE* 4.0 8.8 - - + +
139C GLU 3.1 5.4 + - - +
140C ILE* 3.0 10.9 + - - +
142C LYS* 1.3 76.5 - - - +
144C LEU* 1.3 64.5 + - - +
146C TYR* 3.5 2.4 + - - +
147C CYS* 3.2 25.5 + - - +
173C LEU* 4.0 26.8 - - + +
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Residues in contact with LEU 144 (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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140C ILE* 2.8 39.9 + - + +
141C LEU* 4.1 5.2 - - - +
143C ALA* 1.3 72.9 - - - +
145C ASP* 1.3 64.8 + - - +
147C CYS* 3.5 9.6 + - - -
148C HIS* 2.9 40.3 + - + +
154C HIS* 4.6 1.3 - - + -
157C VAL* 4.2 19.7 - - + -
173C LEU* 3.8 21.1 - - + -
214C ASP* 4.3 24.9 - - + +
215C MET* 4.5 11.4 - - - -
218C LEU* 4.4 22.0 - - + -
315C ALA* 4.4 5.8 - - + -
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Residues in contact with ASP 145 (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 TYR* 2.7 31.6 + - - -
141C LEU 2.9 19.5 + - - +
142C LYS* 4.3 2.2 - - - +
144C LEU* 1.3 76.9 - - - +
146C TYR* 1.3 64.3 + - - +
148C HIS* 4.4 1.8 - - - -
149C SER* 2.9 23.2 + - - -
315C ALA* 3.6 15.1 + - + +
316C ARG* 3.3 46.9 + - - +
319C MET* 4.1 8.3 - - - -
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Residues in contact with TYR 146 (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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87C ASN 4.4 5.5 + - - -
88C LEU* 3.9 21.2 + - + -
89C ARG 4.8 3.1 + - - -
91C GLY* 3.3 24.5 + - - -
92C PRO* 3.7 23.3 - - + -
94C ILE* 3.5 20.9 - - + -
142C LYS 3.2 18.9 + - - +
143C ALA 3.7 4.7 - - - +
144C LEU 3.1 1.0 - - - -
145C ASP* 1.3 78.0 + - - +
147C CYS* 1.3 58.6 + - - +
149C SER* 2.5 26.8 + - - -
150C MET* 2.9 49.5 + - + +
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Residues in contact with CYS 147 (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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88C LEU* 3.9 29.6 - - + -
94C ILE* 5.4 0.4 - - + -
143C ALA 3.2 17.4 + - - +
144C LEU* 3.6 17.7 - - - -
146C TYR* 1.3 81.0 - - + +
148C HIS* 1.3 66.3 + - - +
150C MET* 2.8 23.9 + - - +
151C GLY 3.0 0.5 + - - -
152C ILE* 2.9 34.1 + - + +
154C HIS* 4.5 4.0 - - - -
176C TRP* 3.8 22.4 - - + -
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Residues in contact with HIS 148 (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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11C VAL* 6.4 1.1 - - + -
12C TYR* 3.4 33.2 - + + +
144C LEU* 2.9 32.6 + - + +
145C ASP* 3.9 3.1 - - - +
147C CYS* 1.3 79.3 - - - +
149C SER* 1.3 61.3 + - - +
151C GLY 3.0 10.7 + - - -
152C ILE 3.2 16.3 + - - -
153C MET* 4.6 0.2 - - - -
211C TYR* 3.4 50.3 + + + -
214C ASP* 3.0 35.3 + - + +
215C MET* 4.4 7.5 - - + -
315C ALA* 4.3 17.3 - - + -
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Residues in contact with SER 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C TYR* 3.3 34.3 - - - -
15C VAL* 3.9 17.9 - - - +
19C ARG* 5.8 0.2 + - - -
145C ASP* 2.9 18.4 + - - -
146C TYR* 2.5 25.8 + - - -
148C HIS* 1.3 76.5 - - - +
150C MET* 1.3 70.5 + - - +
151C GLY 3.3 2.4 + - - -
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Residues in contact with MET 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C VAL* 4.4 2.0 - - - -
16C ASN* 4.8 0.2 - - - -
19C ARG* 3.1 34.8 - - - +
23C TYR* 2.8 39.9 + - - +
87C ASN 4.4 8.1 - - - +
88C LEU* 3.6 13.5 - - + -
146C TYR* 2.9 54.7 + - + +
147C CYS 2.8 11.5 + - - +
149C SER* 1.3 89.9 - - - +
151C GLY* 1.3 57.5 - - - -
152C ILE* 3.4 4.6 + - - +
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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
------------------------------------------------------------
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