Contacts of the helix formed by residues 88 - 110 (chain C) in PDB entry 4QI1
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 TRP 88 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C PHE* 4.0 26.0 - + - -
72C GLY* 2.9 36.4 + - - -
73C LEU 3.9 3.5 - - - +
74C THR* 3.5 35.9 - - + +
86C VAL* 3.2 17.0 + - + -
87C TYR* 1.3 68.0 - - - +
89C ALA* 1.3 73.7 + - + +
90C ARG 3.1 2.2 - - - -
91C TYR* 3.0 24.9 + - - +
92C ALA* 3.6 13.2 + - + +
131C LEU* 4.4 17.2 - - + +
135C LEU* 4.8 9.4 - - + -
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Residues in contact with ALA 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C SER* 3.2 13.1 + - - +
66C SER* 4.0 13.0 - - - +
67C MET* 3.7 25.8 - - + -
71C PHE* 5.5 1.6 - - + -
72C GLY* 3.3 19.6 + - - -
87C TYR 3.3 0.8 - - - -
88C TRP* 1.3 88.1 - - + +
90C ARG* 1.3 60.4 + - - +
92C ALA* 3.3 10.3 + - + +
93C ASP 3.1 18.0 + - - -
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Residues in contact with ARG 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C LEU* 4.5 6.5 - - - +
63C SER* 4.4 2.5 - - - -
64C TYR* 3.3 29.9 + - - -
67C MET* 3.9 19.6 - - + +
87C TYR* 3.5 28.7 + - - +
88C TRP 3.1 0.2 - - - -
89C ALA* 1.3 78.2 - - - +
91C TYR* 1.3 67.0 + - + +
93C ASP* 3.4 8.4 - - - +
94C TRP* 2.9 63.0 + - + +
202C GLU* 6.2 0.2 - - - -
212C GLU* 5.3 4.0 + - - -
213C THR* 3.7 40.6 + - - +
216C PHE* 3.6 29.2 - - - +
220C ASP* 3.8 5.1 + - - -
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Residues in contact with TYR 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C TYR 4.4 5.8 - - - -
88C TRP* 3.0 17.0 + - - +
90C ARG* 1.3 88.2 - - + +
92C ALA* 1.3 61.6 + - - +
94C TRP* 4.0 22.9 - + - -
95C LEU* 2.8 31.4 + - - +
127C ILE* 3.8 16.9 - - + +
130C GLY 3.5 20.8 + - - -
131C LEU* 3.5 38.4 - - + -
134C THR* 2.6 39.3 + - + +
197C TRP* 3.6 16.3 - - - -
202C GLU* 4.9 3.1 + - - -
216C PHE* 6.0 0.9 - - - -
301C RET 3.8 14.6 - - + +
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Residues in contact with ALA 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A MPG 5.9 7.4 - - + -
88C TRP* 3.6 9.8 + - + +
89C ALA* 3.3 17.0 + - + +
91C TYR* 1.3 81.5 - - - +
93C ASP* 1.3 64.4 + - - +
95C LEU* 3.2 11.1 + - - +
96C PHE* 3.2 25.3 - - + -
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Residues in contact with ASP 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A MPG 6.0 2.6 - - - +
59C ILE* 4.2 11.4 - - + -
60C ALA* 3.4 31.3 - - - +
63C SER* 3.5 27.2 + - - +
64C TYR* 4.5 9.4 - - - -
67C MET* 5.7 0.3 - - - +
89C ALA 3.1 2.0 + - - -
90C ARG* 3.4 10.3 - - - +
92C ALA* 1.3 77.3 - - - +
94C TRP* 1.3 69.0 + - - +
96C PHE* 3.1 5.5 + - - +
97C THR* 2.9 50.4 + - - +
220C ASP* 5.0 0.3 - - - +
224C LYS* 3.9 7.7 - - - -
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Residues in contact with TRP 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C ARG* 2.9 49.2 + - + +
91C TYR* 3.9 32.1 - + - +
92C ALA 3.3 0.2 - - - -
93C ASP* 1.3 82.3 + - - +
95C LEU* 1.3 64.8 + - - +
97C THR* 3.6 4.5 - - - -
98C THR* 2.6 36.2 + - + -
127C ILE* 3.9 16.2 - - + -
193C TYR* 3.5 24.0 - + - -
216C PHE* 3.8 28.7 - + - -
220C ASP* 3.4 23.1 + - - -
224C LYS* 4.0 0.7 - - - -
301C RET 3.3 61.8 - - + +
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Residues in contact with LEU 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B PHE* 6.4 2.5 - - + -
91C TYR 2.8 18.7 + - - +
92C ALA* 3.4 10.1 - - - +
93C ASP 3.2 0.4 - - - -
94C TRP* 1.3 78.1 - - - +
96C PHE* 1.3 81.1 + - + +
99C PRO* 3.0 21.5 - - - +
123C ASP* 5.0 0.2 - - - +
124C ALA* 4.4 15.9 - - + +
127C ILE* 4.0 23.7 - - + +
128C VAL* 4.0 23.1 - - + -
302C MPG 4.3 3.0 + - - +
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Residues in contact with PHE 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 6.4 0.2 - - + -
128A VAL* 6.2 1.6 - - + -
302A MPG 3.6 36.3 - - - -
304A MPG 3.9 40.8 - - + -
59C ILE* 4.5 6.5 - - + -
92C ALA* 3.2 27.6 - - + -
93C ASP 3.1 4.5 + - - +
95C LEU* 1.3 103.8 - - + +
97C THR* 1.3 63.4 + - - +
98C THR 3.5 0.7 - - - -
99C PRO* 3.5 4.3 - - - +
100C LEU* 3.3 28.5 + - - +
302C MPG 3.3 26.9 + - - -
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Residues in contact with THR 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ILE* 3.7 32.4 - - + +
59C ILE* 3.6 23.3 - - + -
93C ASP* 2.9 39.1 + - - +
94C TRP* 3.6 5.5 - - - -
96C PHE* 1.3 75.3 - - - +
98C THR* 1.3 60.6 + - - +
100C LEU* 3.3 7.6 + - - +
101C LEU* 2.8 34.1 + - - +
224C LYS* 3.2 20.9 + - - +
301C RET 3.9 0.4 - - - +
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Residues in contact with THR 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C TRP* 2.6 26.2 + - + +
97C THR* 1.3 78.6 - - - +
99C PRO* 1.4 62.5 - - - +
101C LEU* 3.3 5.8 + - - +
102C LEU* 3.0 28.9 + - - +
123C ASP* 2.7 33.9 + - - -
127C ILE* 3.7 7.6 - - + +
190C TRP* 3.7 10.0 - - + -
301C RET 3.5 50.7 - - + -
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Residues in contact with PRO 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C TRP 3.5 0.2 - - - +
95C LEU 3.0 28.7 - - - +
96C PHE 3.5 4.9 - - - +
98C THR* 1.4 94.8 - - - +
100C LEU* 1.3 54.5 + - - +
102C LEU* 3.2 8.1 + - + +
103C LEU* 2.8 28.6 + - - +
120C VAL* 3.9 29.3 - - + +
123C ASP* 3.4 10.3 - - + +
124C ALA* 5.6 3.4 - - + +
302C MPG 3.5 35.1 - - - +
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Residues in contact with LEU 100 (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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304A MPG 3.8 48.0 - - + -
52C ILE* 3.5 21.8 - - + +
55C LEU* 3.8 23.6 - - + -
56C ILE* 3.7 24.7 - - + -
59C ILE* 3.9 14.8 - - + -
96C PHE 3.3 16.7 + - - +
97C THR* 3.3 8.1 + - - +
99C PRO* 1.3 78.4 - - - +
101C LEU* 1.3 57.1 + - - +
103C LEU* 3.3 9.7 + - + +
104C ASP* 2.9 24.8 + - - +
302C MPG 4.3 8.7 - - - -
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Residues in contact with LEU 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ILE* 3.8 24.0 - - + -
97C THR 2.8 26.4 + - - +
98C THR 3.6 4.5 - - - +
100C LEU* 1.3 71.7 - - - +
102C LEU* 1.3 59.5 + - - +
104C ASP* 3.3 4.8 + - - +
105C ILE* 3.1 29.0 + - - +
186C ILE* 5.4 1.8 - - + -
190C TRP* 4.1 16.4 - - + +
223C ALA 3.5 26.9 - - - +
224C LYS* 4.3 5.4 - - + +
227C PHE* 3.6 33.9 - - + -
301C RET 3.8 37.0 - - + -
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Residues in contact with LEU 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C THR 3.0 18.8 + - - +
99C PRO* 3.6 8.7 - - + +
101C LEU* 1.3 74.2 - - - +
103C LEU* 1.3 59.2 + - - +
105C ILE* 3.5 7.6 - - + +
106C GLY* 2.8 27.5 + - - -
116C ILE* 4.7 4.1 - - + +
119C LEU* 3.9 37.7 - - + +
120C VAL* 4.5 7.2 - - + -
123C ASP* 3.6 35.9 - - + +
156C LEU* 4.4 12.6 - - + -
160C LEU* 4.8 3.8 - - + -
164C PHE* 3.7 7.6 - - + -
186C ILE* 4.7 13.2 - - + -
190C TRP* 3.9 20.9 - - + -
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Residues in contact with LEU 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A MPG 4.9 11.4 - - + -
48C GLU* 5.1 3.1 - - - +
52C ILE* 3.8 22.0 - - + -
99C PRO 2.8 16.4 + - - +
100C LEU* 3.6 14.1 - - + +
102C LEU* 1.3 75.3 - - - +
104C ASP* 1.3 59.4 + - - +
107C LEU* 2.8 63.9 + - + +
116C ILE* 4.3 15.1 - - + +
302C MPG 4.0 48.0 - - + -
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Residues in contact with ASP 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C PHE* 3.4 31.3 - - - +
52C ILE* 3.5 29.6 - - - +
53C THR* 2.7 31.2 + - - +
56C ILE* 4.0 6.6 - - - +
100C LEU 2.9 11.1 + - - +
101C LEU* 3.3 9.6 + - - +
103C LEU* 1.3 76.8 - - - +
105C ILE* 1.3 63.0 + - - +
107C LEU 3.4 0.2 + - - -
108C LEU* 3.1 18.9 + - - +
227C PHE* 3.9 16.6 - - + -
231C LEU* 3.4 16.3 - - + +
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Residues in contact with ILE 105 (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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101C LEU 3.1 13.6 + - - +
102C LEU* 3.5 13.7 - - - +
104C ASP* 1.3 77.0 - - - +
106C GLY* 1.3 62.9 + - - +
108C LEU* 3.3 5.9 + - + +
109C ALA* 2.9 27.2 + - - +
160C LEU* 4.1 11.0 - - + -
164C PHE* 3.9 15.0 - - + -
179C PHE* 3.7 31.2 - - + -
182C LEU* 3.8 23.3 - - + -
183C ARG* 3.7 29.6 - - - +
186C ILE* 4.1 14.6 - - + -
227C PHE* 4.2 10.1 - - + -
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Residues in contact with GLY 106 (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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102C LEU 2.8 19.5 + - - -
103C LEU 3.8 0.4 - - - -
105C ILE* 1.3 78.3 - - - +
107C LEU* 1.3 57.7 + - - +
109C ALA* 3.3 1.2 + - - -
110C GLY 3.0 22.5 + - - -
111C ALA* 3.0 14.5 + - - +
116C ILE* 4.0 14.4 - - - +
164C PHE* 3.6 22.9 - - - -
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Residues in contact with LEU 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ARG* 3.3 17.8 + - - +
48C GLU* 3.6 30.5 - - + +
49C PHE* 3.8 17.5 - - + -
52C ILE* 3.6 31.0 - - + -
103C LEU* 2.8 35.7 + - + +
104C ASP 3.8 3.4 - - - +
106C GLY* 1.3 76.1 - - - +
108C LEU* 1.3 63.3 + - - +
110C GLY* 3.3 12.0 + - - -
111C ALA 5.7 0.9 - - - +
116C ILE* 4.2 2.4 - - + +
302C MPG 4.3 26.7 - - + -
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Residues in contact with LEU 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ARG* 4.6 6.9 + - - +
49C PHE* 3.6 10.6 - - + -
104C ASP 3.1 13.4 + - - +
105C ILE* 3.5 8.5 - - + +
107C LEU* 1.3 78.7 - - - +
109C ALA* 1.3 60.7 + - - +
110C GLY 3.3 1.2 + - - -
175C THR* 3.4 26.7 - - + +
178C THR* 3.7 5.4 - - + -
179C PHE* 3.6 39.9 - - + +
182C LEU* 3.7 23.1 - - + -
231C LEU* 4.5 4.9 - - + -
236C ALA* 4.1 26.9 - - + +
237C ILE* 4.2 18.6 - - + -
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Residues in contact with ALA 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ILE 2.9 17.2 + - - +
106C GLY* 3.3 5.3 + - - +
108C LEU* 1.3 76.6 - - - +
110C GLY* 1.3 60.9 + - - +
111C ALA 4.3 2.9 - - - +
164C PHE* 3.7 30.1 - - + +
167C ALA* 3.3 25.2 - - + +
168C VAL* 3.3 15.4 + - + -
179C PHE* 3.9 18.2 - - + -
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Residues in contact with GLY 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ARG* 6.0 0.2 - - - -
106C GLY 3.0 4.5 + - - -
107C LEU* 3.3 8.6 + - - -
108C LEU 3.2 5.8 + - - -
109C ALA* 1.3 78.7 - - - +
111C ALA* 1.3 65.3 + - - +
112C SER 3.8 0.5 + - - -
167C ALA* 4.0 7.9 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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