Contacts of the helix formed by residues 95 - 124 (chain D) in PDB entry 5JKL
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 SER 95 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D TYR* 3.7 4.8 + - - -
41D PHE* 3.6 8.1 - - - -
46D VAL* 6.4 0.2 - - - -
93D TRP 2.9 7.3 + - - +
94D GLU* 1.3 77.7 - - - +
96D GLY* 1.3 60.1 + - - +
97D LEU 3.6 0.7 + - - -
98D ARG* 3.0 31.1 + - - +
99D ALA* 2.9 28.8 + - - +
161D PRO* 3.5 22.5 - - - +
167D GLU* 3.5 14.4 - - - -
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Residues in contact with GLY 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D PHE* 3.6 15.4 - - - -
51D PHE* 3.4 27.7 - - - -
95D SER* 1.3 71.2 - - - +
97D LEU* 1.3 60.7 + - - +
99D ALA* 3.4 1.6 + - - +
100D MET* 3.0 28.4 + - - +
155D LEU* 4.2 2.0 - - - -
167D GLU* 2.8 21.6 + - - -
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Residues in contact with LEU 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D SER* 4.1 3.6 - - - +
96D GLY* 1.3 70.9 - - - +
98D ARG* 1.3 59.7 + - + +
100D MET* 3.2 2.5 + - - +
101D GLU* 2.9 55.1 + - - +
152D VAL* 3.9 35.7 - - + +
155D LEU* 3.9 16.4 - - + +
156D ARG* 4.1 13.9 - - + +
160D ALA* 3.6 19.3 - - + +
161D PRO* 3.6 28.7 - - + -
167D GLU* 2.9 19.1 + - - +
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Residues in contact with ARG 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D TRP 3.5 16.2 - - - +
94D GLU* 2.6 43.4 + - + +
95D SER* 3.0 18.9 + - - +
97D LEU* 1.3 76.7 - - + +
99D ALA* 1.3 56.9 + - - +
101D GLU* 3.3 21.7 + - - +
102D LYS* 2.9 39.4 + - + +
161D PRO* 4.8 19.7 - - + +
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Residues in contact with ALA 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D MET* 3.5 16.9 - - - +
41D PHE* 3.6 28.9 - - + -
55D PHE* 4.0 11.2 - - + -
93D TRP* 3.8 15.6 + - + -
95D SER 2.9 17.9 + - - +
96D GLY 3.8 2.2 - - - +
98D ARG* 1.3 76.6 - - - +
100D MET* 1.3 56.9 + - - +
102D LYS* 3.2 2.0 + - - -
103D ALA* 2.8 29.6 + - - +
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Residues in contact with MET 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D PHE* 3.8 22.7 - - + -
54D TYR* 3.8 26.5 - - + -
55D PHE* 3.8 11.4 - - + -
96D GLY 3.0 20.7 + - - +
97D LEU* 3.7 6.1 - - - +
99D ALA* 1.3 74.2 - - - +
101D GLU* 1.3 57.3 + - - +
103D ALA* 3.3 4.0 + - - +
104D LEU* 2.9 29.1 + - - +
148D LEU* 3.7 27.3 - - + +
151D HIS* 3.9 23.8 - - + -
152D VAL* 3.8 19.8 - - + +
155D LEU* 4.1 13.9 - - + -
170D PHE* 4.5 1.6 - - + -
175D LEU* 4.0 9.9 - - + -
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Residues in contact with GLU 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D LEU* 2.9 31.5 + - + +
98D ARG* 3.6 32.6 + - - +
100D MET* 1.3 75.6 - - - +
102D LYS* 1.4 58.4 + - + +
104D LEU* 3.4 8.5 + - + +
105D LYS* 3.1 40.5 + - - +
152D VAL* 4.0 18.2 - - + -
156D ARG* 2.8 35.9 + - - +
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Residues in contact with LYS 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D MET* 3.8 16.4 - - + -
89D ASP* 6.1 1.6 - - + +
90D LYS* 3.8 25.4 - - - +
93D TRP* 4.0 21.3 - - + +
94D GLU* 5.3 1.6 - - - -
98D ARG* 2.9 28.0 + - + +
99D ALA 3.7 3.8 - - - +
101D GLU* 1.4 74.1 - - + +
103D ALA* 1.3 61.0 + - - +
105D LYS* 3.3 28.8 + - + +
106D LEU* 3.0 27.7 + - - +
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Residues in contact with ALA 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D TYR* 3.8 30.5 - - + +
37D MET* 3.9 6.9 - - + +
55D PHE* 4.2 7.6 - - + -
99D ALA 2.8 16.1 + - - +
100D MET 3.3 4.9 + - - +
102D LYS* 1.3 74.7 - - - +
104D LEU* 1.3 58.9 + - - +
106D LEU* 3.2 6.8 + - - +
107D GLU* 2.8 34.1 + - - +
148D LEU* 3.8 16.6 - - + -
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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
----------------------------------------------------------
100D MET 2.9 13.6 + - - +
101D GLU* 3.5 11.7 - - + +
102D LYS 3.3 0.2 - - - -
103D ALA* 1.3 77.4 - - - +
105D LYS* 1.3 64.9 + - + +
107D GLU* 3.3 2.2 + - - +
108D LYS* 3.0 39.2 + - + +
145D ILE* 3.7 44.0 - - + +
148D LEU* 3.8 16.7 - - + +
149D GLY* 4.3 7.0 - - - +
152D VAL* 4.7 7.9 - - + -
156D ARG* 6.3 0.2 - - - +
7F GLN* 3.7 41.3 - - + +
8F VAL* 4.9 0.7 - - + -
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Residues in contact with LYS 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D GLU* 3.1 24.9 + - - +
102D LYS* 3.6 33.9 - - + +
104D LEU* 1.3 78.4 - - + +
106D LEU* 1.3 56.2 + - - +
108D LYS* 3.3 7.9 + - - +
109D LYS* 2.9 28.6 + - - +
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Residues in contact with LEU 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D TYR* 4.1 27.6 - - + -
30D ALA* 4.0 26.2 - - + -
33D VAL* 3.8 32.8 - - + -
34D TYR* 4.1 24.9 - - + +
102D LYS 3.0 16.5 + - - +
103D ALA* 3.2 5.1 + - - +
105D LYS* 1.3 75.4 - - - +
107D GLU* 1.3 60.5 + - + +
109D LYS* 3.1 17.1 + - + +
110D VAL* 2.9 40.9 + - + +
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Residues in contact with GLU 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D ALA* 6.4 0.2 - - - -
34D TYR* 2.6 31.5 + - - +
58D GLN* 5.0 0.2 - - - +
62D GLU* 3.4 19.1 - - - +
103D ALA 2.8 19.4 + - - +
104D LEU 3.9 2.5 - - - +
106D LEU* 1.3 77.3 - - - +
108D LYS* 1.3 58.0 + - - +
110D VAL* 4.5 5.2 - - - +
111D ASN* 3.0 26.2 + - - +
141D GLN* 2.8 44.7 + - - +
144D ALA* 4.1 14.3 - - + +
145D ILE* 3.9 20.7 - - + +
148D LEU* 3.5 14.8 - - + +
204D MG 4.1 8.8 - - - -
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Residues in contact with LYS 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D LEU* 3.0 30.1 + - + +
105D LYS* 3.8 6.1 - - + +
107D GLU* 1.3 74.4 - - - +
109D LYS* 1.3 61.9 + - - +
112D GLN* 2.9 25.3 + - - +
145D ILE* 4.0 15.9 - - + -
6F SER 4.7 1.0 + - - -
7F GLN 2.9 28.8 + - - +
8F VAL 3.7 9.1 - - - -
9F ARG 2.9 28.8 + - - +
10F GLN* 3.0 37.3 + - - +
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Residues in contact with LYS 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D LEU* 3.9 28.0 - - + +
29D TYR* 4.6 15.0 - - - -
105D LYS 2.9 14.2 + - - +
106D LEU* 3.1 17.7 + - + +
108D LYS* 1.3 78.1 - - - +
110D VAL* 1.3 61.0 + - + +
112D GLN* 3.3 7.9 + - - +
113D SER* 3.1 22.0 + - - -
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Residues in contact with VAL 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D GLN* 3.8 7.2 - - - +
26D LEU* 4.0 25.1 - - + +
27D GLU* 3.5 28.7 - - - +
30D ALA* 4.5 12.8 - - + -
62D GLU* 5.6 0.9 - - - +
106D LEU* 2.9 35.2 + - + +
107D GLU* 4.7 3.6 - - - +
109D LYS* 1.3 73.4 - - + +
111D ASN* 1.3 63.8 - - - +
113D SER* 3.2 4.5 + - - -
114D LEU* 3.0 27.4 + - + +
141D GLN* 3.9 20.4 - - - +
201D FE 4.4 3.1 - - - -
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Residues in contact with ASN 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D GLU 3.0 18.5 + - - +
108D LYS 3.6 0.2 - - - +
109D LYS 3.3 0.2 - - - -
110D VAL* 1.3 73.3 - - - +
112D GLN* 1.3 66.4 + - - +
114D LEU* 3.1 2.7 + - - -
115D LEU* 2.9 44.7 + - - +
138D LEU* 4.2 13.7 - - - +
141D GLN* 3.4 29.4 - - + +
142D VAL* 5.0 8.7 - - - +
145D ILE* 3.9 11.9 - - + +
10F GLN* 3.0 34.9 + - - +
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Residues in contact with GLN 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D LYS 2.9 17.7 + - - +
109D LYS* 3.6 8.1 - - - +
110D VAL 3.3 0.4 - - - -
111D ASN* 1.3 75.2 - - - +
113D SER* 1.3 58.3 + - - +
115D LEU* 3.3 13.4 + - - +
116D GLU* 3.0 57.4 + - - +
10F GLN* 3.5 20.5 + - - +
11F ASN* 5.8 0.9 - - - +
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Residues in contact with SER 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D ARG 5.8 0.3 - - - -
23D GLN* 2.5 26.1 + - - +
26D LEU* 3.5 22.2 - - - +
109D LYS 3.1 9.8 + - - -
110D VAL 3.5 8.1 - - - -
111D ASN 3.2 0.2 - - - -
112D GLN* 1.3 78.2 - - - +
114D LEU* 1.3 56.8 + - - +
116D GLU* 3.3 14.9 + - - +
117D LEU* 2.9 28.8 + - - +
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Residues in contact with LEU 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D GLN* 3.6 28.0 - - + +
69D LEU* 5.7 1.1 - - + -
110D VAL* 3.0 25.8 + - + +
111D ASN* 3.1 6.0 + - - +
113D SER* 1.3 76.5 - - - +
115D LEU* 1.3 58.7 + - - +
117D LEU* 3.3 16.2 + - + +
118D HIS* 2.9 27.2 + - - +
133D ILE* 4.2 9.9 - - + +
137D TYR* 3.9 43.5 - - + +
138D LEU* 3.9 14.8 - - + -
141D GLN* 3.5 32.5 - - + -
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Residues in contact with LEU 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D ASN* 2.9 41.3 + - - +
112D GLN* 3.6 18.4 - - - +
113D SER 3.3 0.2 - - - -
114D LEU* 1.3 75.4 - - - +
116D GLU* 1.3 57.9 + - - +
118D HIS* 3.3 5.2 + - - +
119D LYS* 3.0 27.4 + - - +
138D LEU* 4.0 18.2 - - + -
10F GLN* 4.7 3.1 - - + +
11F ASN* 3.8 38.4 - - + +
127F PRO* 3.7 27.4 - - + +
128F HIS* 5.2 5.6 - - + +
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Residues in contact with GLU 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D GLN* 3.0 47.5 + - - +
113D SER* 3.6 14.7 + - - +
115D LEU* 1.3 73.0 - - + +
117D LEU* 1.3 65.5 + - - +
119D LYS* 3.3 17.2 + - - +
120D LEU* 3.1 23.6 + - - +
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Residues in contact with LEU 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D SER* 4.7 1.6 - - - +
19D ALA* 3.5 38.6 - - + +
20D ILE* 3.8 26.7 - - + +
23D GLN* 4.3 25.1 - - + +
69D LEU* 5.0 2.5 - - + -
113D SER 2.9 17.0 + - - +
114D LEU* 3.4 13.9 - - + +
116D GLU* 1.3 76.3 - - - +
118D HIS* 1.3 55.5 + - - +
120D LEU* 3.3 9.4 + - + +
121D ALA* 2.9 27.2 + - - +
129D LEU* 5.1 6.5 - - + -
133D ILE* 3.7 25.4 - - + -
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Residues in contact with HIS 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D LEU 2.9 16.3 + - - +
115D LEU* 3.3 8.3 + - - +
117D LEU* 1.3 76.8 - - - +
119D LYS* 1.3 58.1 + - - +
121D ALA* 3.2 2.8 + - - +
122D THR* 2.9 50.7 + - - -
130D CYS* 3.6 32.1 - - - +
133D ILE* 4.0 19.7 - - + +
134D GLU* 2.7 35.1 + - + +
138D LEU* 4.4 1.1 - - + -
127F PRO* 3.4 31.1 - - + +
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Residues in contact with LYS 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D LEU 3.0 14.2 + - - +
116D GLU* 3.3 19.5 + - - +
118D HIS* 1.3 76.6 - - - +
120D LEU* 1.3 55.9 + - - +
122D THR* 3.3 8.1 + - - -
123D LYS* 2.9 61.9 + - + +
125F ASN* 5.9 10.3 - - + +
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Residues in contact with LEU 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ASP* 3.6 38.1 - - + +
16D SER* 4.1 11.0 - - - +
19D ALA* 3.8 18.6 - - + -
22D ARG* 5.1 4.0 - - - +
116D GLU 3.1 13.4 + - - +
117D LEU* 3.5 10.8 - - + +
118D HIS 3.2 0.2 - - - -
119D LYS* 1.3 74.7 - - - +
121D ALA* 1.3 64.7 + - - +
123D LYS* 3.2 9.6 + - + +
124D LYS* 3.0 49.1 + - + +
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Residues in contact with ALA 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D SER* 4.8 1.8 - - - -
117D LEU 2.9 16.9 + - - +
118D HIS* 3.7 7.0 - - - +
120D LEU* 1.3 78.9 - - - +
122D THR* 1.3 60.1 + - - +
124D LYS* 3.4 3.7 + - - -
125D ASN 3.1 3.8 + - - -
126D ASP* 3.0 33.3 + - + +
129D LEU* 3.8 35.2 - - + -
130D CYS* 3.7 17.4 - - - +
133D ILE* 4.8 0.4 - - + -
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Residues in contact with THR 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D HIS* 2.9 38.8 + - - -
119D LYS* 3.4 11.8 - - - -
121D ALA* 1.3 75.0 - - - +
123D LYS* 1.3 66.0 + - + +
125D ASN* 3.0 22.9 + - - +
130D CYS* 3.6 8.0 - - - -
125F ASN* 6.1 1.6 - - - +
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Residues in contact with LYS 123 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D LYS* 2.9 52.1 + - + +
120D LEU* 3.2 11.9 + - + +
122D THR* 1.3 79.0 - - + +
124D LYS* 1.3 68.5 - - + +
125D ASN* 3.5 9.2 + - - +
----------------------------------------------------------
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Residues in contact with LYS 124 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ASN* 4.4 8.0 - - - +
13D HIS* 3.7 51.6 + - + -
15D ASP* 3.7 22.2 + - + -
16D SER* 4.3 8.3 - - - +
120D LEU* 3.0 35.6 + - + +
121D ALA* 3.4 3.1 + - - +
122D THR 3.2 0.2 - - - -
123D LYS* 1.3 84.3 - - + +
125D ASN* 1.3 71.3 + - - +
126D ASP* 3.3 7.4 + - + +
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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