Contacts of the helix formed by residues 95 - 124 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TYR* 3.8 4.3 + - - -
41B PHE* 3.5 7.5 - - - -
46B VAL* 6.2 0.9 - - - -
93B TRP 2.9 7.2 + - - +
94B GLU* 1.3 76.0 - - - +
96B GLY* 1.3 63.8 + - - +
97B LEU 3.5 0.9 + - - -
98B ARG* 3.0 30.6 + - - +
99B ALA* 3.0 23.4 + - - +
161B PRO* 3.4 22.5 - - - +
167B GLU* 3.6 16.2 - - - -
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Residues in contact with GLY 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PHE* 3.6 15.0 - - - -
51B PHE* 3.4 27.1 - - - -
95B SER* 1.3 72.6 - - - +
97B LEU* 1.3 62.8 + - - +
99B ALA* 3.5 1.4 + - - +
100B MET* 3.1 28.4 + - - +
155B LEU* 4.2 2.0 - - - -
167B GLU* 2.9 20.2 + - - -
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Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B SER* 4.0 3.6 - - - +
96B GLY* 1.3 76.4 - - - +
98B ARG* 1.3 73.4 + - - +
100B MET* 3.2 2.4 + - - +
101B GLU* 2.9 48.2 + - + +
152B VAL* 3.9 28.9 - - + +
155B LEU* 4.0 15.8 - - + +
156B ARG* 4.0 17.9 - - + -
160B ALA* 3.4 36.6 - - + +
161B PRO* 3.9 6.5 - - + -
167B GLU* 2.9 17.2 + - - +
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Residues in contact with ARG 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B TRP 3.6 14.4 - - - +
94B GLU* 4.2 20.8 + - + +
95B SER* 3.0 21.4 + - - +
97B LEU* 1.3 85.3 - - - +
99B ALA* 1.3 56.2 + - - +
101B GLU* 2.7 46.7 + - - +
102B LYS* 3.0 47.7 + - - +
161B PRO* 3.4 31.9 - - + +
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Residues in contact with ALA 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B MET* 3.4 19.6 - - - +
41B PHE* 3.6 27.6 - - + -
55B PHE* 4.1 12.1 - - + -
93B TRP* 3.8 15.7 + - + -
95B SER 3.0 17.4 + - - +
96B GLY 3.8 2.0 - - - +
98B ARG* 1.3 74.6 - - - +
100B MET* 1.3 53.3 + - - +
102B LYS* 3.2 3.4 + - - +
103B ALA* 2.8 32.1 + - - +
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Residues in contact with MET 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B PHE* 3.8 20.2 - - + -
54B TYR* 3.8 25.6 - - + -
55B PHE* 3.8 11.2 - - + -
96B GLY 3.1 21.8 + - - +
97B LEU 3.2 5.4 + - - +
99B ALA* 1.3 76.4 - - - +
101B GLU* 1.3 56.7 + - - +
103B ALA* 3.3 4.1 + - - +
104B LEU* 2.9 28.4 + - - +
148B LEU* 3.6 28.9 - - + +
151B HIS* 3.9 23.6 - - + -
152B VAL* 3.8 20.1 - - + +
155B LEU* 4.0 16.8 - - + -
170B PHE* 4.4 3.8 - - + -
175B LEU* 3.9 10.8 - - + -
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Residues in contact with GLU 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LEU* 2.9 27.0 + - + +
98B ARG* 2.7 50.5 + - - +
99B ALA 3.3 0.2 - - - -
100B MET* 1.3 75.4 - - - +
102B LYS* 1.3 59.9 + - + +
104B LEU* 3.3 8.4 + - + +
105B LYS* 3.0 26.9 + - - +
152B VAL* 4.0 9.6 - - + -
156B ARG* 2.8 38.8 + - - +
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Residues in contact with LYS 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B MET* 3.9 12.6 - - + -
90B LYS* 3.5 26.4 - - + +
93B TRP* 2.9 63.6 + - + +
94B GLU* 4.1 3.0 + - - -
98B ARG* 3.0 35.6 + - - +
99B ALA 3.7 2.9 - - - +
101B GLU* 1.3 74.4 - - + +
103B ALA* 1.3 60.8 + - - +
105B LYS* 3.3 12.7 + - + +
106B LEU* 2.9 27.7 + - - +
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Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B TYR* 3.8 30.9 + - + +
37B MET* 3.8 7.3 - - + +
55B PHE* 4.1 7.4 - - + -
99B ALA 2.8 16.7 + - - +
100B MET 3.7 4.7 - - - +
102B LYS* 1.3 73.7 - - - +
104B LEU* 1.3 63.4 + - - +
106B LEU* 3.2 7.3 + - - +
107B GLU* 3.0 28.6 + - - +
148B LEU* 3.7 16.2 - - + -
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Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B MET 2.9 14.4 + - - +
101B GLU* 3.4 11.2 - - + +
102B LYS 3.3 0.2 - - - -
103B ALA* 1.3 75.9 - - - +
105B LYS* 1.3 62.3 + - - +
107B GLU* 3.3 1.6 + - - +
108B LYS* 3.0 42.0 + - + +
145B ILE* 3.8 43.3 - - + +
148B LEU* 3.9 14.0 - - + +
149B GLY* 4.4 15.7 - - - +
152B VAL* 4.6 14.8 - - + -
156B ARG* 6.3 0.4 - - - +
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Residues in contact with LYS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B GLU 3.0 14.0 + - - +
102B LYS* 3.5 15.7 - - + +
104B LEU* 1.3 76.2 - - - +
106B LEU* 1.3 57.2 + - - +
108B LYS* 3.4 7.5 + - - +
109B LYS* 3.0 28.9 + - + +
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 5.3 0.4 - - + -
29B TYR* 4.1 26.5 - - + -
30B ALA* 3.9 30.7 - - + -
33B VAL* 3.9 30.5 - - + -
34B TYR* 4.0 24.7 - - + -
102B LYS 2.9 15.0 + - - +
103B ALA* 3.2 9.6 + - - +
105B LYS* 1.3 74.3 - - - +
107B GLU* 1.3 61.3 + - + +
109B LYS* 3.1 16.8 + - + +
110B VAL* 2.9 39.5 + - + +
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Residues in contact with GLU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ALA* 6.4 0.4 - - - -
34B TYR* 2.5 36.2 + - - +
62B GLU* 3.5 15.0 - - - +
103B ALA 3.0 20.3 + - - +
104B LEU 4.0 2.2 - - - +
106B LEU* 1.3 79.3 - - + +
108B LYS* 1.3 58.9 + - - +
110B VAL* 3.5 4.8 + - - +
111B ASN* 2.9 26.2 + - - +
141B GLN* 2.9 37.8 + - - +
144B ALA* 3.9 16.9 - - + +
145B ILE* 3.8 19.9 - - + +
148B LEU* 3.5 13.4 - - + +
202B MG 4.1 8.7 - - - -
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Residues in contact with LYS 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LEU* 3.0 38.8 + - + +
105B LYS* 3.8 6.7 - - - +
107B GLU* 1.3 75.0 - - - +
109B LYS* 1.3 58.1 + - - +
111B ASN* 3.3 6.8 + - - +
112B GLN* 2.8 30.5 + - - +
145B ILE* 4.0 25.6 - - + -
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Residues in contact with LYS 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 4.0 27.4 - - + -
29B TYR* 5.0 10.1 - - + -
105B LYS* 3.0 15.0 + - + +
106B LEU* 3.1 19.9 + - + +
108B LYS* 1.3 74.8 - - - +
110B VAL* 1.3 64.2 + - - +
112B GLN* 3.4 7.8 + - - +
113B SER* 3.1 21.5 + - - -
15H ASP* 5.6 6.9 + - - -
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Residues in contact with VAL 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLN* 3.9 7.2 - - - +
26B LEU* 4.1 23.3 - - + -
27B GLU* 3.6 29.4 - - - +
30B ALA* 4.3 14.4 - - + -
62B GLU* 5.6 0.7 - - - +
106B LEU* 2.9 35.8 + - + +
107B GLU* 3.8 8.7 - - - +
109B LYS* 1.3 73.2 - - - +
111B ASN* 1.3 64.8 + - - +
113B SER* 3.2 4.3 + - - -
114B LEU* 3.0 24.0 + - + +
141B GLN* 3.9 19.3 - - - +
201B FE 4.3 3.1 - - - -
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Residues in contact with ASN 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B GLU 2.9 17.9 + - - +
108B LYS* 3.6 5.4 - - - +
109B LYS 3.3 0.2 - - - -
110B VAL* 1.3 77.1 - - - +
112B GLN* 1.3 63.3 + - - +
114B LEU* 3.1 2.9 + - - +
115B LEU* 2.9 46.9 + - - +
138B LEU* 4.2 12.8 - - - +
141B GLN* 3.4 30.2 - - + +
142B VAL* 5.0 9.7 - - - +
145B ILE* 3.8 19.7 - - + +
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Residues in contact with GLN 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B LYS 2.8 17.3 + - - +
109B LYS* 3.6 8.5 - - - +
110B VAL 3.4 0.2 - - - -
111B ASN* 1.3 77.3 - - - +
113B SER* 1.3 56.0 + - - +
115B LEU* 3.3 18.5 + - - +
116B GLU* 2.9 59.7 + - - +
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Residues in contact with SER 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ARG* 5.8 0.5 - - - +
23B GLN* 2.6 24.3 + - - -
26B LEU* 3.4 26.8 - - - +
109B LYS 3.1 8.1 + - - -
110B VAL 3.4 8.7 - - - -
112B GLN* 1.3 75.9 - - - +
114B LEU* 1.3 57.4 + - - +
116B GLU* 3.2 14.3 + - - +
117B LEU* 2.9 28.2 + - - +
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Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLN* 3.6 31.0 - - + +
69B LEU* 5.7 1.3 - - + -
110B VAL* 3.0 23.4 + - + +
111B ASN* 3.6 6.5 - - - +
113B SER* 1.3 74.8 - - - +
115B LEU* 1.3 58.1 + - - +
117B LEU* 3.3 15.3 + - + +
118B HIS* 2.8 29.1 + - - +
133B ILE* 4.1 8.9 - - + +
137B TYR* 3.9 41.3 - - + +
138B LEU* 3.9 14.8 - - + -
141B GLN* 3.5 35.2 - - + -
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ASN* 2.9 42.6 + - - +
112B GLN* 3.6 19.1 - - - +
113B SER 3.3 0.2 - - - -
114B LEU* 1.3 75.1 - - - +
116B GLU* 1.3 59.2 + - + +
118B HIS* 3.3 6.3 + - + +
119B LYS* 2.9 29.3 + - - +
138B LEU* 4.0 27.6 - - + -
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Residues in contact with GLU 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B GLN* 2.9 47.4 + - - +
113B SER* 3.6 12.0 - - - +
115B LEU* 1.3 72.5 - - - +
117B LEU* 1.3 65.5 + - - +
119B LYS* 3.3 13.1 + - + +
120B LEU* 3.0 23.0 + - - +
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Residues in contact with LEU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B SER 4.7 1.8 - - - +
19B ALA* 3.5 36.6 - - + -
20B ILE* 4.0 26.5 - - + +
23B GLN* 4.3 27.1 - - + +
69B LEU* 5.0 2.7 - - + -
113B SER 2.9 15.7 + - - +
114B LEU* 3.5 12.6 - - + +
116B GLU* 1.3 77.6 - - - +
118B HIS* 1.3 56.9 + - - +
120B LEU* 3.3 10.8 + - + +
121B ALA* 2.9 28.2 + - - +
129B LEU* 4.8 6.5 - - + -
133B ILE* 3.7 24.9 - - + -
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Residues in contact with HIS 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LEU 2.8 17.3 + - - +
115B LEU* 3.6 9.2 - - + +
117B LEU* 1.3 76.8 - - - +
119B LYS* 1.3 58.2 + - - +
121B ALA* 3.3 2.2 + - - +
122B THR* 2.9 52.6 + - - -
130B CYS* 3.5 30.7 - - - +
133B ILE* 3.9 20.7 - - + +
134B GLU* 2.6 38.7 + - + +
138B LEU* 4.3 9.6 - - + -
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Residues in contact with LYS 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LEU 2.9 14.0 + - - +
116B GLU* 3.5 14.4 - - + +
118B HIS* 1.3 77.9 + - - +
120B LEU* 1.3 55.6 + - - +
122B THR* 3.4 7.1 + - - -
123B LYS* 3.0 65.0 + - + +
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ASP* 3.6 43.3 - - + +
16B SER* 3.9 10.1 - - - +
19B ALA* 3.8 19.5 - - + -
22B ARG* 5.2 3.6 - - - +
116B GLU 3.0 12.6 + - - +
117B LEU* 3.5 10.3 - - + +
118B HIS 3.3 0.2 - - - -
119B LYS* 1.3 73.1 - - - +
121B ALA* 1.4 66.9 + - - +
123B LYS* 3.2 11.8 + - + +
124B LYS* 2.9 44.6 + - + +
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Residues in contact with ALA 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B SER* 4.7 4.5 - - - -
117B LEU 2.9 15.9 + - - +
118B HIS* 3.7 7.2 - - - +
120B LEU* 1.4 76.0 - - - +
122B THR* 1.3 61.5 + - - +
124B LYS* 3.4 1.9 + - - +
125B ASN 3.2 4.0 + - - -
126B ASP* 2.9 33.8 + - + +
129B LEU* 3.7 37.2 - - + +
130B CYS* 3.7 17.3 - - - +
133B ILE* 4.6 0.4 - - + -
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Residues in contact with THR 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B HIS* 2.9 44.1 + - - -
119B LYS* 3.5 8.2 - - - +
121B ALA* 1.3 77.4 - - - +
123B LYS* 1.3 59.3 + - + +
125B ASN* 3.1 26.6 + - - +
126B ASP 5.1 0.4 - - - +
130B CYS* 3.6 7.4 - - - -
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Residues in contact with LYS 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LYS* 3.0 52.7 + - + +
120B LEU* 3.2 13.9 + - + +
122B THR* 1.3 77.4 - - + +
124B LYS* 1.3 67.7 + - + +
125B ASN* 3.3 9.8 + - - +
----------------------------------------------------------
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Residues in contact with LYS 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ASN* 4.4 7.3 - - - +
13B HIS* 3.5 52.4 + - + -
15B ASP* 3.7 20.3 + - + -
16B SER* 4.3 8.5 - - - +
120B LEU* 2.9 35.2 + - + +
121B ALA* 3.4 3.3 + - - +
122B THR 3.2 0.2 - - - -
123B LYS* 1.3 82.6 - - - +
125B ASN* 1.3 72.1 + - - +
126B ASP* 3.3 6.4 - - + +
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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