Contacts of the helix formed by residues 90 - 115 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D ASP* 3.3 17.7 - - - +
33E PHE* 4.2 10.3 - - + -
79E MET* 3.4 44.2 - - + +
82E VAL* 3.5 22.4 - - + -
83E TRP* 4.7 2.2 - - + -
88E ASP 3.5 6.9 - - - +
89E THR* 1.3 86.4 - - + +
91E THR* 1.3 57.1 + - - +
92E VAL 3.3 0.6 + - - -
93E PHE* 3.4 3.2 + - + -
94E ARG* 3.0 30.7 + - - +
221E ASN* 4.2 11.4 - - - +
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Residues in contact with THR 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D ASP* 3.0 3.2 + - - -
89E THR* 2.9 30.7 + - - +
90E PRO* 1.3 71.1 - - - +
92E VAL* 1.3 58.9 + - - +
94E ARG* 3.4 5.6 + - - +
95E TYR* 3.0 46.8 + - + -
139E PHE* 4.0 15.5 - - + -
142E GLU* 3.6 44.8 + - + +
143E ALA* 4.3 2.5 - - - +
208E TYR* 4.3 2.3 + - - -
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Residues in contact with VAL 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D ASP* 2.8 40.1 + - + +
23D LEU* 2.8 45.8 - - + +
25D ILE* 4.5 20.6 - - + +
31D VAL* 5.2 3.1 - - + -
91E THR* 1.3 76.4 - - - +
93E PHE* 1.3 63.5 + - - -
94E ARG 3.2 0.2 + - - -
95E TYR* 4.9 0.7 - - - -
96E ILE* 2.8 47.7 + - + +
139E PHE* 4.4 16.2 - - + -
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Residues in contact with PHE 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D GLY 3.6 23.6 - - - -
22D ASP* 3.0 24.2 + - - +
23D LEU* 3.6 33.9 - - + -
34D TRP* 3.4 36.3 - + - -
80D ARG* 6.0 0.4 - - - -
75E HIS* 3.8 13.6 - + - +
78E TYR* 3.7 37.2 - + + -
79E MET* 3.6 20.6 - - + +
82E VAL* 3.9 15.9 - - + -
90E PRO* 3.4 3.3 + - + +
92E VAL* 1.3 75.7 - - - +
94E ARG* 1.3 55.6 + - - +
96E ILE* 3.8 2.2 - - - -
97E ASN* 2.9 30.5 + - - +
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Residues in contact with ARG 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E PHE* 3.5 15.0 - - - -
76E TYR* 3.1 14.8 + - - -
79E MET* 3.6 20.9 - - - -
89E THR* 6.1 1.0 - - + +
90E PRO* 3.0 20.5 + - - +
91E THR* 3.5 7.4 - - - +
92E VAL 3.2 0.2 - - - -
93E PHE* 1.3 76.1 - - - +
95E TYR* 1.3 60.2 + - + +
97E ASN* 3.3 5.6 + - - +
98E TRP* 3.0 71.6 + - + +
221E ASN* 3.1 24.9 + - - -
224E TYR* 3.4 30.1 - - + +
225E ASN* 2.9 20.4 + - - -
228E ASP* 3.1 22.4 + - - -
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Residues in contact with TYR 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E THR* 3.0 32.2 + - + +
92E VAL 4.2 1.1 - - - +
94E ARG* 1.3 76.6 - - + +
96E ILE* 1.3 60.4 + - + +
98E TRP* 3.1 33.3 + + - +
99E LEU* 2.7 37.1 + - - +
135E LEU* 3.5 30.6 - - + +
138E GLY* 3.3 17.6 - - - -
139E PHE* 3.5 44.9 - + + -
142E GLU* 2.7 41.6 + - + +
301E RET 3.8 12.7 - - + +
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Residues in contact with ILE 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LEU* 4.3 12.1 - - + -
25D ILE* 5.7 2.7 - - + -
31D VAL* 4.1 22.7 - - + -
34D TRP* 3.4 21.1 - - + +
35D LEU* 4.1 15.9 - - + +
75E HIS* 3.3 28.0 - - + +
92E VAL* 2.8 43.3 + - + +
93E PHE 3.9 0.4 - - - +
95E TYR* 1.3 75.5 - - + +
97E ASN* 1.3 59.4 + - - +
99E LEU* 3.4 12.2 + - + +
100E LEU* 3.1 28.4 + - + +
139E PHE* 6.1 1.6 - - + -
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Residues in contact with ASN 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E ILE* 3.5 7.6 - - - +
72E ALA* 3.4 33.1 - - - +
75E HIS* 3.6 27.0 + - + +
76E TYR* 4.3 13.5 - - - -
79E MET* 4.5 3.2 - - + +
93E PHE 2.9 20.0 + - - +
94E ARG* 3.4 7.7 + - - +
95E TYR 3.2 0.2 - - - -
96E ILE* 1.3 76.7 - - - +
98E TRP* 1.3 57.1 + - - +
100E LEU* 3.3 4.8 + - - +
101E THR* 2.7 41.7 + - - +
228E ASP* 4.5 2.6 + - - -
232E LYS* 4.3 12.7 - - - +
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Residues in contact with TRP 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E ARG* 3.0 35.9 + - + +
95E TYR* 3.1 53.6 + + - +
97E ASN* 1.3 80.8 - - - +
99E LEU* 1.3 60.5 + - - +
101E THR* 3.3 3.8 - - - -
102E VAL* 2.9 38.3 + - + +
135E LEU* 3.6 24.2 - - + +
200E TYR* 3.4 32.8 - + - -
224E TYR* 3.4 32.3 - + + -
228E ASP* 3.2 24.3 + - - -
301E RET 3.6 31.9 - - + -
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Residues in contact with LEU 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D VAL* 6.2 0.7 - - + -
35D LEU* 4.3 27.1 - - + -
95E TYR 2.7 20.4 + - - +
96E ILE* 3.7 14.6 - - + +
98E TRP* 1.3 71.8 - - - +
100E LEU* 1.3 57.6 + - - +
103E PRO* 3.0 26.5 - - + +
132E LEU* 3.7 30.3 - - + -
135E LEU* 3.7 12.6 - - + +
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Residues in contact with LEU 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D TRP* 4.7 1.3 - - - +
35D LEU* 3.9 35.2 - - + +
38D ALA* 3.7 25.8 - - + -
39D GLY* 4.8 6.5 - - - +
229D PHE* 6.0 4.5 - - + -
71E ILE* 4.0 19.2 - - + +
75E HIS* 3.7 22.0 - - + +
96E ILE* 3.1 25.1 + - + +
97E ASN 3.8 4.9 - - - +
98E TRP 3.2 0.2 - - - -
99E LEU* 1.3 79.2 - - + +
101E THR* 1.3 62.4 + - - +
103E PRO* 3.9 6.4 - - - +
104E LEU* 3.6 21.2 + - - +
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Residues in contact with THR 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E ILE* 3.7 34.8 - - + +
71E ILE* 4.0 12.1 - - + -
97E ASN* 2.7 38.3 + - - +
98E TRP* 3.3 8.3 - - - -
100E LEU* 1.3 78.8 - - - +
102E VAL* 1.3 61.7 + - - +
104E LEU* 3.1 10.7 + - - +
105E LEU* 2.9 25.1 + - - +
232E LYS* 3.0 29.0 + - - +
301E RET 3.4 2.4 - - - +
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Residues in contact with VAL 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E TRP* 2.9 23.3 + - + +
101E THR* 1.3 75.1 - - - +
103E PRO* 1.4 59.2 - - + +
105E LEU* 3.0 8.0 + - - +
106E VAL* 2.8 34.8 + - + +
131E SER* 3.7 31.0 - - - +
134E MET* 4.4 4.3 - - + -
135E LEU* 4.1 13.9 - - + -
197E TRP* 4.1 20.6 - - + -
301E RET 3.7 36.6 - - + -
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Residues in contact with PRO 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E TRP 3.7 1.1 - - - +
99E LEU* 3.0 28.9 - - + +
100E LEU* 3.9 4.9 - - - +
101E THR 3.6 2.2 - - - -
102E VAL* 1.4 95.7 - - + +
104E LEU* 1.3 51.3 + - + +
106E VAL* 3.3 3.7 + - + +
107E VAL* 2.8 38.4 + - + +
124E PHE* 4.3 2.3 - - + -
128E LEU* 3.8 28.9 - - + -
131E SER* 5.4 0.9 - - - +
132E LEU* 4.9 11.9 - - + -
135E LEU* 5.5 0.2 - - + -
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Residues in contact with LEU 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D ALA* 5.5 2.0 - - + -
64E VAL* 3.6 25.1 - - + +
67E LEU* 4.3 25.6 - - + -
68E ILE* 3.7 23.1 - - + +
71E ILE* 3.9 24.5 - - + -
100E LEU 3.6 17.5 - - - +
101E THR* 3.1 11.2 + - - +
103E PRO* 1.3 75.5 - - + +
105E LEU* 1.3 60.0 + - - +
106E VAL 3.2 1.1 - - - -
107E VAL* 3.2 14.3 + - + +
108E GLU 2.9 24.6 + - - -
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Residues in contact with LEU 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E ILE* 3.9 22.0 - - + +
101E THR 2.9 15.9 + - - +
102E VAL* 3.0 10.7 + - - +
104E LEU* 1.3 71.7 - - - +
106E VAL* 1.3 57.0 + - - +
108E GLU* 3.2 11.7 - - + +
109E PHE* 2.8 46.2 + - + -
192E ILE* 5.1 1.8 - - + -
197E TRP* 3.5 41.5 - - + +
231E ASN 4.5 13.7 - - - +
232E LYS* 5.9 0.9 - - + -
235E PHE* 3.6 31.6 - - + -
301E RET 4.2 11.9 - - + -
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Residues in contact with VAL 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102E VAL* 2.8 34.4 + - + +
103E PRO* 3.5 10.8 - - + +
105E LEU* 1.3 70.1 - - - +
107E VAL* 1.3 66.1 + - - +
109E PHE* 3.0 17.7 + - + +
110E TYR* 2.9 21.7 + - - +
124E PHE* 3.6 35.9 - - + +
127E LEU* 4.0 26.2 - - + +
128E LEU* 4.1 7.0 - - + +
131E SER* 4.4 11.7 - - - +
162E MET* 5.2 0.9 - - - -
197E TRP* 4.8 6.3 - - + -
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Residues in contact with VAL 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E VAL* 4.6 17.0 - - + -
103E PRO 2.8 20.8 + - - +
104E LEU* 3.2 17.5 + - + +
106E VAL* 1.3 71.7 - - - +
108E GLU* 1.3 64.1 + - - +
110E TYR* 3.2 9.6 + - + +
111E LEU* 3.0 32.0 + - + +
124E PHE* 3.4 29.1 - - + -
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Residues in contact with GLU 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E SER* 2.7 40.9 + - - +
64E VAL* 4.4 9.5 - - + +
65E SER* 3.4 25.6 + - - -
68E ILE* 5.3 0.9 - - - +
104E LEU 2.9 16.1 + - - +
105E LEU* 3.2 17.4 - - + +
107E VAL* 1.3 73.8 - - - +
109E PHE* 1.3 62.8 + - + +
111E LEU* 3.0 14.0 + - - +
112E ILE* 3.0 31.4 + - + +
235E PHE* 4.4 21.8 - - + -
239E ILE* 4.7 14.4 - - - +
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Residues in contact with PHE 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E LEU* 2.8 38.4 + - + -
106E VAL* 3.0 18.4 + - + +
108E GLU* 1.3 73.3 - - - +
110E TYR* 1.3 51.7 + - - +
112E ILE* 3.2 9.2 + - + +
113E LEU* 2.7 45.7 + - + +
127E LEU* 4.8 13.9 - - + -
166E LEU* 5.3 0.7 - - + -
189E MET* 3.3 44.7 - - + +
192E ILE* 3.9 21.8 - - + -
193E ILE* 4.1 20.2 - - + -
197E TRP* 3.8 23.1 - + - -
235E PHE* 4.0 14.8 - + - -
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Residues in contact with TYR 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106E VAL 2.9 14.8 + - - +
107E VAL* 3.2 12.3 + - + +
109E PHE* 1.3 73.4 - - - +
111E LEU* 1.3 79.9 + - + +
113E LEU* 3.6 9.9 - - - +
114E ALA* 2.8 39.3 + - + +
120E ALA* 3.6 26.2 - - + -
121E ALA* 3.9 25.3 - - + +
124E PHE* 3.8 28.9 - + + -
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Residues in contact with LEU 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240D TRP* 6.0 5.4 - - + -
60E THR* 4.5 23.3 - - + -
61E SER* 4.5 20.6 - - - +
64E VAL* 4.8 4.5 - - + -
107E VAL* 3.0 25.9 + - + +
108E GLU* 3.0 17.1 + - - +
110E TYR* 1.3 94.9 - - + +
112E ILE* 1.3 68.1 + - + +
114E ALA* 3.5 12.8 + - + +
115E ALA* 3.9 6.4 + - - +
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Residues in contact with ILE 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E TRP* 6.2 1.3 - - + -
61E SER* 5.8 1.3 - - - +
108E GLU* 3.0 32.6 + - + +
109E PHE* 3.5 12.1 - - + +
111E LEU* 1.3 77.1 - - + +
113E LEU* 1.3 64.6 + - - +
114E ALA 3.3 0.3 + - - -
115E ALA* 3.3 12.7 + - - +
116E CYS* 3.8 10.6 - - - -
182E VAL* 4.6 3.9 - - + +
185E ALA* 3.6 28.0 - - + +
186E TYR* 3.5 36.3 - - + +
189E MET* 3.9 24.9 - - + -
235E PHE* 4.5 2.9 - - + -
239E ILE* 4.3 15.3 - - + -
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Residues in contact with LEU 113 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109E PHE 2.7 29.2 + - - +
110E TYR* 3.3 10.1 + - - +
112E ILE* 1.3 73.6 - - - +
114E ALA* 1.3 57.2 + - - +
116E CYS* 2.9 21.9 + - + +
117E THR* 3.1 24.9 + - + +
120E ALA* 3.9 11.9 - - + +
123E LEU* 3.9 39.3 - - + -
124E PHE* 5.4 0.7 - - - +
127E LEU* 4.2 10.5 - - + -
166E LEU* 4.0 21.3 - - + -
171E GLY* 6.1 1.6 - - - -
186E TYR* 4.4 12.3 - - + -
189E MET* 3.8 24.5 - - + -
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Residues in contact with ALA 114 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110E TYR* 2.8 32.7 + - + +
111E LEU* 3.8 9.9 - - + +
112E ILE 3.3 0.4 + - - -
113E LEU* 1.3 72.2 - - - +
115E ALA* 1.3 58.7 + - - +
116E CYS 3.3 0.7 - - - -
117E THR 3.5 11.7 - - - +
120E ALA* 3.8 15.7 - - + +
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Residues in contact with ALA 115 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111E LEU 3.9 5.8 + - - +
112E ILE* 3.3 10.8 + - - +
113E LEU 3.2 1.2 - - - -
114E ALA* 1.3 76.1 - - - +
116E CYS* 1.3 57.7 - - - +
117E THR 3.9 0.2 - - - -
176E SER* 3.4 17.0 + - - -
178E ALA* 4.9 3.8 - - - +
182E VAL* 4.0 28.9 - - + +
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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