Contacts of the helix formed by residues 90 - 117 (chain C) in PDB entry 4KNF
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 PRO 90 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ASP* 3.6 12.6 - - - +
33C PHE* 4.2 10.5 - - + -
79C MET* 3.4 43.7 - - + +
82C VAL* 3.5 22.4 - - + -
83C TRP* 4.4 3.8 - - + +
88C ASP 3.6 2.0 - - - +
89C THR* 1.4 86.2 - - - +
91C THR* 1.3 64.1 + - - +
92C VAL 3.2 2.5 - - - -
93C PHE* 3.0 6.5 + - + -
94C ARG* 2.9 21.3 + - - +
221C ASN* 3.6 17.7 - - - +
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Residues in contact with THR 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ASP* 3.6 3.2 + - - -
89C THR* 3.1 27.7 + - - +
90C PRO* 1.3 72.8 - - - +
92C VAL* 1.3 64.2 + - + +
94C ARG* 3.2 6.4 + - - -
95C TYR* 3.0 44.8 + - + +
139C PHE* 4.0 16.4 - - + -
142C GLU* 3.6 43.5 + - + +
143C ALA* 5.2 1.1 - - - -
208C TYR* 4.2 1.2 + - - -
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Residues in contact with VAL 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ASP* 3.2 14.5 + - - +
23B LEU* 3.2 49.6 - - + +
25B ILE* 3.8 35.2 - - + +
31B VAL* 5.3 3.6 - - + -
90C PRO 3.1 0.2 + - - -
91C THR* 1.3 78.6 - - + +
93C PHE* 1.3 61.3 + - - +
95C TYR* 3.4 1.4 + - - +
96C ILE* 3.0 29.6 + - + +
139C PHE* 3.8 21.3 - - + -
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Residues in contact with PHE 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLY 3.9 13.9 - - - -
22B ASP* 3.3 19.3 + - - -
23B LEU* 3.4 43.3 - - + -
34B TRP* 3.5 33.4 - + - -
75C HIS* 4.1 15.5 - + + +
78C TYR* 3.6 35.9 - + + -
79C MET* 3.8 18.4 - - + -
82C VAL* 4.0 17.3 - - + -
90C PRO* 3.0 7.2 + - + +
92C VAL* 1.3 78.5 - - - +
94C ARG* 1.3 64.2 + - - +
96C ILE* 3.2 4.2 + - - +
97C ASN* 3.0 25.3 + - - +
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Residues in contact with ARG 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C PHE* 3.6 11.1 - - - -
76C TYR* 2.8 29.9 + - - -
79C MET* 2.7 40.4 - - + +
90C PRO* 2.9 11.2 + - - +
91C THR* 3.4 13.5 - - - +
93C PHE* 1.3 76.9 - - - +
95C TYR* 1.3 61.2 + - + +
97C ASN* 3.5 4.9 + - - +
98C TRP* 3.1 70.9 + - + +
221C ASN* 3.1 27.3 + - - -
224C TYR* 3.4 31.3 - - + +
225C ASN* 2.8 19.2 + - - -
228C ASP* 3.2 9.0 + - - -
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Residues in contact with TYR 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C THR* 3.0 36.9 + - + +
92C VAL 4.2 2.2 - - - +
94C ARG* 1.3 82.1 - - + +
96C ILE* 1.3 62.6 + - + +
98C TRP* 3.6 29.6 - + - +
99C LEU* 2.8 30.7 + - - +
135C LEU* 3.3 23.0 - - + +
138C GLY* 3.3 18.1 - - - -
139C PHE* 3.2 47.6 - + + -
142C GLU* 2.6 39.3 + - + -
224C TYR* 5.2 0.2 - + - -
301C RET 3.8 11.0 - - + +
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Residues in contact with ILE 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 4.2 14.8 - - + -
25B ILE* 6.3 2.2 - - + -
31B VAL* 4.0 22.4 - - + -
34B TRP* 3.4 32.1 - - + +
35B LEU* 3.7 25.4 - - + -
75C HIS* 3.5 11.7 - - + +
92C VAL* 3.0 27.7 + - + +
93C PHE* 3.2 6.9 + - - +
95C TYR* 1.3 76.8 - - + +
97C ASN* 1.3 61.9 + - - +
99C LEU* 3.5 14.4 + - + +
100C LEU* 3.0 24.5 + - + +
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Residues in contact with ASN 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C ILE* 3.5 11.4 - - - +
72C ALA* 3.3 38.7 + - - +
75C HIS* 3.7 26.2 - - + +
76C TYR* 4.3 13.1 - - - -
79C MET* 5.3 3.1 - - - +
93C PHE 3.0 16.1 + - - +
94C ARG* 3.6 6.2 + - - +
96C ILE* 1.3 77.3 - - - +
98C TRP* 1.3 58.0 + - - +
100C LEU* 3.2 2.1 + - - +
101C THR* 2.6 40.3 + - - +
228C ASP* 4.5 1.8 + - - -
232C LYS* 4.1 13.9 - - - +
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Residues in contact with TRP 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C ARG* 3.1 39.7 + - + +
95C TYR* 3.6 41.3 - + - +
96C ILE 3.4 0.2 - - - -
97C ASN* 1.3 78.4 - - - +
99C LEU* 1.3 60.1 + - - +
101C THR* 3.6 3.1 - - - -
102C VAL* 2.7 41.4 + - + +
135C LEU* 3.6 31.0 - - + -
200C TYR* 3.4 26.7 - + - -
224C TYR* 3.7 32.1 - + + -
228C ASP* 3.1 23.8 + - - -
232C LYS* 4.0 4.3 - - - -
301C RET 3.5 36.4 - - + +
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Residues in contact with LEU 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 3.8 34.5 - - + -
95C TYR 2.8 22.1 + - - +
96C ILE* 3.5 13.7 - - + +
98C TRP* 1.3 74.0 - - - +
100C LEU* 1.3 57.5 + - + +
103C PRO* 3.1 25.0 - - + +
132C LEU* 4.2 24.9 - - + -
135C LEU* 4.0 12.4 - - + +
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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
----------------------------------------------------------
34B TRP* 4.8 1.3 - - + -
35B LEU* 3.7 37.2 - - + +
38B ALA* 3.7 18.8 - - + -
39B GLY* 4.8 5.2 - - - +
229B PHE* 5.8 4.9 - - + -
71C ILE* 4.1 17.6 - - + +
75C HIS* 3.4 34.8 - - + +
96C ILE* 3.0 25.5 + - + +
97C ASN 3.8 3.4 - - - +
99C LEU* 1.3 78.3 - - + +
101C THR* 1.3 60.8 + - - +
103C PRO* 3.7 9.1 - - - +
104C LEU* 3.8 18.0 - - - +
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Residues in contact with THR 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C ILE* 3.5 41.1 - - - +
71C ILE* 4.0 15.0 - - + -
97C ASN* 2.6 35.2 + - - +
98C TRP* 3.6 1.0 - - - -
100C LEU* 1.3 78.4 - - - +
102C VAL* 1.3 65.6 + - - +
103C PRO 3.3 2.2 - - - -
104C LEU* 3.1 9.4 + - - +
105C LEU* 3.0 21.1 + - - +
232C LYS* 2.9 28.8 + - + +
301C RET 3.5 3.6 - - - +
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Residues in contact with VAL 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C TRP* 2.7 32.1 + - + +
101C THR* 1.3 70.7 - - - +
103C PRO* 1.4 61.0 - - + +
105C LEU* 3.2 9.6 + - - +
106C VAL* 2.9 27.3 + - + +
131C SER* 3.6 31.9 - - - -
132C LEU* 6.4 0.2 - - + -
134C MET* 4.7 2.9 - - + -
135C LEU* 3.9 17.3 - - + -
197C TRP* 4.3 15.0 - - + -
301C RET 3.7 39.7 - - + -
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Residues in contact with PRO 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C TRP 3.7 0.4 - - - +
99C LEU* 3.1 28.9 - - + +
100C LEU 3.7 5.6 - - - +
101C THR 3.5 3.1 - - - -
102C VAL* 1.4 94.6 - - + +
104C LEU* 1.3 58.2 + - + +
106C VAL* 3.2 6.9 + - + +
107C VAL* 2.9 31.6 + - + +
124C PHE* 4.5 1.7 - - + -
128C LEU* 3.9 28.0 - - + -
131C SER* 5.8 0.2 - - - +
132C LEU* 5.3 9.9 - - + -
135C LEU* 5.6 0.9 - - + -
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Residues in contact with LEU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ALA* 5.9 1.3 - - + -
64C VAL* 3.6 18.9 - - + +
67C LEU* 4.5 19.1 - - + -
68C ILE* 3.7 31.6 - - + +
71C ILE* 4.3 21.8 - - + -
100C LEU 3.8 16.6 - - - +
101C THR* 3.1 8.1 + - - +
103C PRO* 1.3 78.8 - - + +
105C LEU* 1.3 61.8 + - - +
107C VAL* 3.0 16.7 + - + +
108C GLU 2.9 23.4 + - - -
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Residues in contact with LEU 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C ILE* 3.6 28.5 - - + +
101C THR 3.0 11.0 + - - +
102C VAL* 3.6 9.6 - - - +
104C LEU* 1.3 75.1 - - - +
106C VAL* 1.3 58.4 + - - +
108C GLU* 2.9 11.7 + - - +
109C PHE* 2.8 41.9 + - + -
192C ILE* 4.8 2.0 - - + -
197C TRP* 3.4 41.5 - - + +
231C ASN 4.2 16.2 - - - +
232C LYS* 5.4 1.1 - - - +
235C PHE* 3.7 28.9 - - + -
301C RET 3.8 14.1 - - + -
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Residues in contact with VAL 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C VAL* 2.9 28.5 + - + +
103C PRO* 3.3 12.1 - - + +
105C LEU* 1.3 75.6 - - - +
107C VAL* 1.3 56.2 + - - +
109C PHE* 3.3 13.5 - - + +
110C TYR* 2.8 25.6 + - - +
124C PHE* 3.6 28.3 - - + +
127C LEU* 4.0 27.5 - - + +
128C LEU* 4.2 7.2 - - + +
131C SER* 4.5 4.3 - - - +
162C MET* 4.1 25.6 - - + -
197C TRP* 4.9 0.4 - - + -
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Residues in contact with VAL 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C VAL* 4.8 11.9 - - + -
103C PRO* 2.9 19.6 + - + +
104C LEU* 3.0 21.3 + - + +
106C VAL* 1.3 74.4 - - - +
108C GLU* 1.3 60.2 + - - +
110C TYR* 3.3 6.0 + - + +
111C LEU* 2.8 45.2 + - + +
124C PHE* 3.5 27.1 - - + -
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Residues in contact with GLU 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C SER* 3.6 25.7 + - - +
64C VAL* 4.0 19.3 - - + -
65C SER* 2.9 27.1 + - - -
68C ILE* 3.9 7.3 - - - +
104C LEU 2.9 8.3 + - - +
105C LEU* 2.9 21.7 + - - +
107C VAL* 1.3 76.1 - - - +
109C PHE* 1.3 64.6 + - - +
111C LEU* 3.0 11.2 + - + +
112C ILE* 3.0 29.3 + - + +
235C PHE* 3.8 28.8 - - + -
236C GLY* 5.4 0.5 - - - -
239C ILE* 4.1 16.9 - - - +
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Residues in contact with PHE 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C LEU* 2.8 27.9 + - + -
106C VAL* 3.3 17.0 - - + +
108C GLU* 1.3 72.5 - - - +
110C TYR* 1.3 61.9 - - - +
112C ILE* 3.3 4.1 + - - +
113C LEU* 3.0 28.6 + - + +
127C LEU* 4.2 21.1 - - + -
162C MET* 5.0 0.2 - - + -
189C MET* 3.2 39.6 - - + +
192C ILE* 4.0 17.9 - - + -
193C ILE* 3.6 31.2 - - + -
197C TRP* 3.7 29.8 - + - -
235C PHE* 4.0 24.2 - + - -
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Residues in contact with TYR 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C VAL 2.8 10.9 + - - +
107C VAL* 3.6 12.1 - - + +
108C GLU 3.2 0.2 - - - -
109C PHE* 1.3 72.2 - - - +
111C LEU* 1.3 86.0 + - + +
113C LEU* 3.1 12.8 + - - +
114C ALA* 2.9 33.4 + - + +
120C ALA* 3.3 27.4 - - + -
121C ALA* 3.8 28.2 - - + +
124C PHE* 3.4 38.8 - + + +
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Residues in contact with LEU 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B TRP* 6.1 3.4 - - + -
60C THR* 4.4 24.7 - - + -
61C SER* 4.5 21.3 - - - +
64C VAL* 4.8 5.4 - - + -
107C VAL* 2.8 35.3 + - + +
108C GLU* 3.4 13.9 - - + +
110C TYR* 1.3 96.9 - - + +
112C ILE* 1.3 61.9 + - + +
114C ALA* 3.7 10.7 + - + +
115C ALA* 3.8 9.7 + - - +
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Residues in contact with ILE 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C TRP* 6.3 2.0 - - + -
108C GLU* 3.0 21.8 + - + +
109C PHE 3.6 5.8 - - - +
111C LEU* 1.3 74.6 - - + +
113C LEU* 1.3 65.3 + - - +
115C ALA* 3.1 20.6 + - - +
116C CYS* 3.7 7.2 - - - -
182C VAL* 4.5 5.3 - - + +
185C ALA* 4.0 29.6 - - + +
186C TYR* 3.8 23.6 - - + +
189C MET* 3.2 39.9 - - + -
235C PHE* 4.5 8.7 - - + -
239C ILE* 4.3 14.6 - - + -
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Residues in contact with LEU 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C PHE* 3.0 27.5 + - + +
110C TYR* 3.5 10.8 - - - +
112C ILE* 1.3 76.1 - - - +
114C ALA* 1.3 55.4 + - - +
115C ALA 3.1 0.2 - - - -
116C CYS* 3.0 6.8 + - - -
117C THR* 2.8 43.5 + - - +
120C ALA* 3.7 14.6 - - + +
123C LEU* 3.8 34.5 - - + -
124C PHE* 5.3 1.1 - - - +
127C LEU* 4.6 8.3 - - + -
166C LEU* 3.8 28.5 - - + +
186C TYR* 4.3 22.7 - - + -
189C MET* 4.3 8.3 - - + -
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Residues in contact with ALA 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C TYR* 2.9 32.3 + - + +
111C LEU* 3.9 7.9 - - + +
112C ILE 3.3 0.2 - - - -
113C LEU* 1.3 74.6 - - - +
115C ALA* 1.3 59.5 + - - +
116C CYS 3.4 0.4 + - - -
117C THR 4.2 7.3 - - - +
120C ALA* 3.4 17.6 - - + +
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Residues in contact with ALA 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C LEU 3.8 7.4 + - - +
112C ILE* 3.1 13.1 + - - +
113C LEU 3.1 1.0 - - - -
114C ALA* 1.3 78.2 - - - +
116C CYS* 1.3 59.8 + - - +
117C THR 3.9 0.4 - - - -
176C SER* 5.3 1.7 + - - -
182C VAL* 3.9 25.7 - - + +
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Residues in contact with CYS 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ILE* 3.7 15.7 - - - -
113C LEU* 3.0 5.9 + - - -
115C ALA* 1.3 79.8 - - - +
117C THR* 1.3 75.2 + - - +
174C ALA* 3.6 8.0 - - - +
175C VAL* 6.0 0.4 - - - -
176C SER* 3.4 47.9 + - - +
182C VAL* 3.8 19.3 - - + -
183C ASN* 5.8 0.7 - - - +
186C TYR* 3.7 30.7 - - - -
----------------------------------------------------------
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Residues in contact with THR 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C LEU* 2.8 37.0 + - - +
114C ALA* 4.2 7.4 - - - +
115C ALA 3.9 0.6 - - - -
116C CYS* 1.3 87.5 + - - +
118C SER* 1.3 65.9 + - - +
119C VAL* 3.5 29.9 + - + -
120C ALA* 4.0 9.3 + - - +
123C LEU* 5.2 2.7 - - + -
171C GLY 4.6 4.7 - - - +
173C ALA* 4.3 2.5 - - + -
174C ALA* 3.4 35.5 + - + +
186C TYR* 5.0 1.6 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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