Contacts of the helix formed by residues 90 - 117 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ASP* 3.4 11.0 - - - +
33D PHE* 4.1 14.4 - - + -
79D MET* 3.7 41.7 - - + +
82D VAL* 4.0 17.7 - - + -
83D TRP* 4.8 3.4 - - + -
88D ASP 3.8 5.4 - - - +
89D THR* 1.4 87.7 - - - +
91D THR* 1.3 53.5 + - - +
92D VAL 3.3 2.7 - - - -
93D PHE* 3.1 7.3 + - + -
94D ARG* 2.8 34.3 + - + +
221D ASN* 3.7 13.7 - - - +
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Residues in contact with THR 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ASP* 3.2 3.5 + - - -
89D THR* 3.0 27.8 + - - +
90D PRO* 1.3 71.7 - - - +
92D VAL* 1.3 60.1 + - + +
94D ARG* 3.3 6.8 + - - +
95D TYR* 2.9 42.6 + - + -
139D PHE* 3.7 21.5 - - + -
142D GLU* 3.7 44.5 + - + +
143D ALA* 4.5 2.0 - - - +
208D TYR* 4.5 0.3 + - - -
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Residues in contact with VAL 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ASP* 3.0 17.1 + - + +
23C LEU* 3.1 46.9 - - + +
25C ILE* 4.0 39.9 - - + -
31C VAL* 5.2 1.6 - - + -
91D THR* 1.3 77.1 - - + +
93D PHE* 1.3 58.0 + - - +
95D TYR* 4.2 0.4 - - + +
96D ILE* 2.8 42.5 + - + +
139D PHE* 4.4 14.1 - - + -
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Residues in contact with PHE 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C GLY 3.6 23.6 - - - -
22C ASP* 3.1 22.5 + - - -
23C LEU* 3.7 32.3 - - + -
34C TRP* 3.5 31.6 - + - -
80C ARG* 5.8 0.7 - - - -
75D HIS* 4.1 19.6 - + - +
78D TYR* 3.6 37.0 - + + -
79D MET* 3.5 21.5 - - + -
82D VAL* 3.8 18.4 - - + -
90D PRO* 3.1 5.8 + - + +
92D VAL* 1.3 74.0 - - - +
94D ARG* 1.3 57.9 + - - +
96D ILE* 4.0 1.7 - - - +
97D ASN* 3.0 30.7 + - - +
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Residues in contact with ARG 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D PHE* 3.6 7.9 - - - -
76D TYR* 2.9 32.5 + - - -
79D MET* 3.8 21.0 - - - +
90D PRO* 2.8 19.4 + - + +
91D THR* 3.4 8.5 - - - +
92D VAL 3.2 0.2 - - - -
93D PHE* 1.3 76.5 - - - +
95D TYR* 1.3 59.6 + - + +
97D ASN* 3.4 6.7 - - - +
98D TRP* 3.3 62.9 + - + +
221D ASN* 3.4 24.5 + - - -
224D TYR* 3.4 35.1 - - + +
225D ASN* 2.5 24.2 + - - -
228D ASP* 3.1 9.4 + - - -
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Residues in contact with TYR 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D THR* 2.9 35.0 + - + +
92D VAL* 4.2 2.0 - - - +
94D ARG* 1.3 75.6 - - + +
96D ILE* 1.3 54.9 - - + +
97D ASN 3.2 1.3 - - - -
98D TRP* 3.1 29.4 + + - +
99D LEU* 2.7 36.6 + - - +
135D LEU* 3.5 28.2 - - + +
138D GLY* 3.1 21.0 + - - -
139D PHE* 3.4 45.8 - + + -
142D GLU* 2.5 42.7 + - + -
204D TYR* 4.4 0.3 - - - -
224D TYR* 4.0 1.7 + - - -
301D RET 4.2 8.8 - - + +
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Residues in contact with ILE 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 3.7 19.5 - - + -
25C ILE* 5.2 4.9 - - + -
31C VAL* 3.6 28.0 - - + -
34C TRP* 3.5 34.8 - - + +
35C LEU* 3.8 12.6 - - + -
75D HIS* 3.8 4.0 - - + +
92D VAL* 2.8 32.8 + - + +
93D PHE* 4.0 2.9 - - - +
95D TYR* 1.3 72.2 - - + +
97D ASN* 1.3 62.1 + - - +
99D LEU* 3.4 16.1 + - + +
100D LEU* 3.1 34.3 + - + +
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Residues in contact with ASN 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D ILE* 3.5 3.8 - - - +
72D ALA* 3.4 31.9 + - - +
75D HIS* 3.2 36.7 + - + +
76D TYR* 4.3 15.8 - - - -
79D MET* 4.4 3.9 - - + +
93D PHE 3.0 19.7 + - - +
94D ARG* 3.4 7.4 + - - +
95D TYR 3.2 0.2 - - - -
96D ILE* 1.3 78.1 - - - +
98D TRP* 1.3 63.9 + - - +
100D LEU* 3.2 4.0 + - - +
101D THR* 2.6 36.2 + - - +
228D ASP* 4.4 4.4 + - - -
232D LYS* 4.5 4.2 - - - +
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Residues in contact with TRP 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D ARG* 3.3 39.3 + - + +
95D TYR* 3.1 47.2 + + - +
97D ASN* 1.3 78.1 - - - +
99D LEU* 1.3 61.5 + - - +
100D LEU 3.1 1.6 - - - -
101D THR* 3.2 3.6 - - - -
102D VAL* 2.8 38.3 + - + +
135D LEU* 3.9 24.2 - - + -
200D TYR* 3.4 25.8 - + - -
224D TYR* 3.7 31.6 - + + -
228D ASP* 3.1 24.5 + - - -
232D LYS* 3.8 5.4 - - - -
301D RET 3.5 36.2 - - + +
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Residues in contact with LEU 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C LEU* 4.3 30.5 - - + -
95D TYR 2.7 21.2 + - - +
96D ILE* 3.5 17.9 - - + +
98D TRP* 1.3 73.2 - - - +
100D LEU* 1.3 57.2 + - + +
103D PRO* 3.1 26.3 - - + +
132D LEU* 4.1 26.5 - - + -
135D LEU* 4.0 13.8 - - + +
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Residues in contact with LEU 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C TRP* 4.8 0.9 - - - +
35C LEU* 3.9 35.9 - - + +
38C ALA* 4.0 17.5 - - + -
39C GLY* 4.6 6.3 - - - +
71D ILE* 4.1 18.1 - - + +
75D HIS* 3.6 26.9 - - + +
96D ILE* 3.1 31.2 + - + +
97D ASN 3.7 3.4 - - - +
98D TRP 3.1 0.8 - - - -
99D LEU* 1.3 78.0 - - - +
101D THR* 1.3 59.6 + - - +
103D PRO* 4.0 3.0 - - - +
104D LEU* 3.4 26.0 + - - +
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Residues in contact with THR 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D ILE* 3.7 28.1 - - - +
71D ILE* 4.0 11.9 - - + -
72D ALA 4.4 0.2 - - - +
97D ASN* 2.6 34.2 + - - +
98D TRP* 3.2 6.4 - - - -
100D LEU* 1.3 80.0 - - - +
102D VAL* 1.3 59.5 + - - +
104D LEU* 3.1 9.8 + - - +
105D LEU* 2.8 27.5 + - - +
232D LYS* 3.1 40.8 + - - -
301D RET 3.6 1.9 - - - +
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Residues in contact with VAL 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D TRP* 2.8 30.7 + - + +
101D THR* 1.3 69.4 + - - +
103D PRO* 1.4 53.7 - - + +
105D LEU* 2.8 11.0 + - - +
106D VAL* 2.7 34.3 + - + +
131D SER* 3.7 31.4 - - - +
134D MET* 6.1 1.6 - - + -
135D LEU* 4.3 13.2 - - + -
197D TRP* 4.3 15.3 - - + -
301D RET 3.5 44.6 - - + -
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Residues in contact with PRO 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D TRP 3.7 0.4 - - - +
99D LEU* 3.1 28.3 - - + +
100D LEU 4.0 4.0 - - - +
101D THR 3.7 1.1 - - - -
102D VAL* 1.4 94.8 - - + +
104D LEU* 1.3 53.3 + - + +
106D VAL* 3.1 7.5 + - + +
107D VAL* 2.7 38.9 + - - +
124D PHE* 4.4 3.6 - - + -
128D LEU* 3.8 33.0 - - + -
131D SER* 5.4 0.4 - - - +
132D LEU* 5.2 7.9 - - + -
135D LEU* 5.5 1.6 - - + -
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Residues in contact with LEU 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ALA* 5.7 1.3 - - + -
64D VAL* 3.5 25.6 - - + +
67D LEU* 4.0 33.9 - - + -
68D ILE* 3.7 23.8 - - + +
71D ILE* 4.1 16.2 - - + -
100D LEU 3.4 16.8 - - - +
101D THR* 3.1 13.6 + - - +
103D PRO* 1.3 80.7 - - + +
105D LEU* 1.3 57.8 + - - +
107D VAL* 3.2 20.3 + - + +
108D GLU 3.3 8.7 + - - -
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Residues in contact with LEU 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D ILE* 3.9 17.0 - - + +
101D THR 2.8 11.6 + - - +
102D VAL* 2.8 17.9 + - - +
104D LEU* 1.3 67.9 - - - +
106D VAL* 1.3 63.2 + - - +
108D GLU* 3.1 26.1 + - + +
109D PHE* 3.2 16.5 + - + -
192D ILE* 5.9 0.9 - - + -
197D TRP* 4.0 22.9 - - + +
231D ASN 4.0 17.7 - - - +
232D LYS* 5.7 1.3 - - + -
235D PHE* 3.1 37.9 - - + -
301D RET 3.7 29.6 - - + -
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Residues in contact with VAL 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D VAL* 2.7 24.6 + - + +
103D PRO* 3.4 11.0 - - + +
105D LEU* 1.3 72.0 - - - +
107D VAL* 1.3 62.6 + - - +
109D PHE* 3.0 13.7 + - + +
110D TYR* 2.9 19.5 + - - +
124D PHE* 3.4 30.7 - - + +
127D LEU* 3.9 26.2 - - + +
128D LEU* 4.2 5.2 - - - +
131D SER* 4.4 13.0 - - - +
162D MET* 4.1 26.5 - - + -
197D TRP* 5.0 2.0 - - + -
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Residues in contact with VAL 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D VAL* 4.2 22.2 - - + -
103D PRO 2.7 16.4 + - - +
104D LEU* 3.2 19.5 + - + +
106D VAL* 1.3 72.8 - - - +
108D GLU* 1.3 52.8 + - - +
110D TYR* 3.2 10.3 + - + +
111D LEU* 2.8 45.1 + - + +
124D PHE* 3.4 28.0 - - + -
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Residues in contact with GLU 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D SER* 3.4 43.2 + - - +
64D VAL* 4.0 12.5 - - + +
65D SER* 4.1 11.8 + - - -
68D ILE* 5.8 1.0 - - - +
104D LEU 3.3 8.4 + - - +
105D LEU* 3.1 20.5 + - + +
107D VAL* 1.3 74.6 - - - +
109D PHE* 1.3 61.0 + - - +
111D LEU* 3.3 8.0 + - - +
112D ILE* 3.0 45.1 + - + +
235D PHE* 4.1 21.2 - - + -
239D ILE* 3.8 23.0 - - + +
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Residues in contact with PHE 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D LEU* 3.7 23.3 - - + -
106D VAL* 3.0 18.2 + - + +
108D GLU* 1.3 75.4 - - - +
110D TYR* 1.3 60.6 + - - +
112D ILE* 3.6 3.5 + - + +
113D LEU* 2.8 40.8 + - + +
127D LEU* 4.8 15.3 - - + -
162D MET* 5.3 0.7 - - + -
166D LEU* 5.2 0.9 - - + -
189D MET* 3.3 42.2 - - + -
192D ILE* 4.1 18.2 - - + -
193D ILE* 3.9 29.6 - - + -
197D TRP* 4.3 16.6 - + - -
235D PHE* 3.6 29.4 - + - -
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Residues in contact with TYR 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D VAL 2.9 11.6 + - - +
107D VAL* 3.3 15.0 - - + +
109D PHE* 1.3 76.7 - - - +
111D LEU* 1.3 73.0 + - + +
113D LEU* 3.3 7.3 + - - +
114D ALA* 3.0 35.1 + - + +
120D ALA* 3.4 24.1 - - + +
121D ALA* 3.6 32.0 - - + +
124D PHE* 3.5 33.8 - + + +
127D LEU* 6.1 0.2 - - - +
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Residues in contact with LEU 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C TRP* 5.5 7.6 - - + -
60D THR* 4.1 31.4 - - + +
61D SER* 4.3 17.7 - - - +
64D VAL* 4.7 2.5 - - + -
107D VAL* 2.8 36.1 + - + +
108D GLU* 3.6 22.4 - - - +
110D TYR* 1.3 86.9 - - + +
112D ILE* 1.3 67.1 + - + +
114D ALA* 3.4 14.1 + - - +
115D ALA 4.4 0.7 + - - -
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Residues in contact with ILE 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D TRP* 5.7 5.8 - - + -
61D SER* 5.6 4.3 - - - +
108D GLU* 3.0 33.8 + - + +
109D PHE* 3.8 5.8 - - + +
111D LEU* 1.3 75.9 - - + +
113D LEU* 1.3 57.3 + - - +
114D ALA 2.8 11.8 + - - -
115D ALA* 3.1 20.1 + - - +
116D CYS 4.1 0.7 + - - -
182D VAL* 4.3 14.1 - - + +
185D ALA* 3.9 32.5 - - + +
186D TYR* 4.1 22.4 - - + +
189D MET* 4.3 21.5 - - + -
235D PHE* 5.0 1.1 - - + -
239D ILE* 4.2 16.8 - - + -
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Residues in contact with LEU 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D PHE* 2.8 31.2 + - + +
110D TYR* 3.3 5.8 + - - +
112D ILE* 1.3 71.0 - - - +
114D ALA* 1.3 61.9 + - - +
115D ALA 3.1 1.4 + - - -
116D CYS* 4.0 5.8 - - + +
117D THR* 3.3 32.2 + - + +
120D ALA* 3.4 18.3 - - + +
123D LEU* 3.6 36.1 - - + -
127D LEU* 4.7 2.9 - - + -
166D LEU* 4.2 18.4 - - + -
171D GLY* 5.3 2.7 - - - +
186D TYR* 3.6 31.2 - - + +
189D MET* 3.9 12.1 - - + -
190D MET* 4.8 2.5 - - + -
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Residues in contact with ALA 114 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D TYR* 3.0 22.4 + - + +
111D LEU* 3.5 16.2 - - - +
112D ILE 2.8 4.4 + - - -
113D LEU* 1.3 73.1 - - - +
115D ALA* 1.3 60.7 + - - +
117D THR 3.6 8.3 - - - +
120D ALA* 3.8 11.9 - - + -
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Residues in contact with ALA 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D LEU 4.4 0.8 + - - +
112D ILE 3.1 11.2 + - - +
114D ALA* 1.3 80.9 - - - +
116D CYS* 1.3 64.1 + - - +
117D THR* 3.1 5.2 + - - +
182D VAL* 3.7 28.5 - - + -
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Residues in contact with CYS 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D ILE* 4.9 3.6 - - - -
113D LEU* 3.5 9.7 + - + +
115D ALA* 1.3 78.1 - - - +
117D THR* 1.3 70.1 + - + +
173D ALA* 4.1 1.0 - - - +
174D ALA* 3.2 45.4 + - - +
182D VAL* 3.6 27.4 - - - -
183D ASN* 5.5 1.1 - - - -
186D TYR* 3.6 33.7 - - + -
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Residues in contact with THR 117 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D LEU* 3.3 26.9 + - + +
114D ALA 3.6 13.9 - - - +
115D ALA 3.1 3.4 + - - +
116D CYS* 1.3 88.5 - - + +
118D SER* 1.3 58.3 + - - +
119D VAL* 2.9 25.9 + - - +
120D ALA* 3.2 16.5 + - - +
123D LEU* 4.5 7.5 - - + +
170D GLU 5.3 0.7 - - - +
171D GLY* 5.1 4.3 - - - +
173D ALA* 3.3 35.0 - - + +
186D TYR* 5.7 0.2 - - + -
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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