Contacts of the helix formed by residues 95 - 124 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F TYR* 3.7 4.8 + - - -
41F PHE* 3.7 7.6 - - - -
46F VAL* 6.3 0.4 - - - -
93F TRP 2.9 6.3 + - - +
94F GLU* 1.3 77.4 - - - +
96F GLY* 1.3 59.3 + - - +
97F LEU 3.6 1.2 + - - -
98F ARG* 3.1 29.0 + - - +
99F ALA* 2.9 30.1 + - - +
161F PRO* 3.5 22.5 - - - +
167F GLU* 3.7 14.1 - - - -
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Residues in contact with GLY 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F PHE* 3.7 15.8 - - - -
48F LEU* 5.1 0.2 - - - -
51F PHE* 3.5 27.9 - - - -
95F SER* 1.3 72.6 - - - +
97F LEU* 1.3 61.1 + - - +
99F ALA* 3.4 1.7 + - - +
100F MET* 3.0 27.9 + - - +
155F LEU* 4.1 2.5 - - - -
167F GLU* 2.8 21.9 + - - -
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Residues in contact with LEU 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F SER* 3.3 3.6 - - - +
96F GLY* 1.3 71.7 - - - +
98F ARG* 1.3 76.1 + - + +
100F MET* 3.2 1.9 + - - +
101F GLU* 3.0 33.4 + - - +
152F VAL* 3.9 41.7 - - + +
155F LEU* 3.9 15.5 - - + +
156F ARG* 3.9 15.7 - - + -
160F ALA* 3.4 37.0 - - + +
161F PRO* 3.7 10.5 - - + -
167F GLU* 2.8 18.7 + - - +
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Residues in contact with ARG 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93F TRP 3.5 8.5 - - - +
94F GLU* 4.2 24.7 - - + -
95F SER* 3.1 19.6 + - - +
97F LEU* 1.3 90.9 - - - +
99F ALA* 1.3 56.2 + - - +
101F GLU* 2.7 41.3 + - - +
102F LYS* 2.9 55.0 + - - +
161F PRO* 3.8 24.0 - - + +
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Residues in contact with ALA 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F MET* 3.6 14.5 - - - +
41F PHE* 3.6 28.3 - - + -
55F PHE* 4.1 11.0 - - + -
93F TRP* 3.8 13.6 + - + -
95F SER 2.9 16.8 + - - +
96F GLY 3.8 1.8 - - - +
98F ARG* 1.3 72.7 - - - +
100F MET* 1.3 62.1 + - - +
102F LYS* 3.3 6.7 + - - +
103F ALA* 2.9 28.9 + - - +
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Residues in contact with MET 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51F PHE* 3.8 20.6 - - + -
54F TYR* 3.8 18.4 - - + -
55F PHE* 3.8 18.6 - - + -
96F GLY 3.0 22.2 + - - +
97F LEU 3.2 4.5 + - - +
99F ALA* 1.3 74.5 - - - +
101F GLU* 1.3 59.1 + - - +
103F ALA* 3.3 4.4 + - - +
104F LEU* 2.9 28.6 + - - +
148F LEU* 3.7 28.5 - - - +
151F HIS* 3.9 23.6 - - + -
152F VAL* 3.7 18.5 - - + +
155F LEU* 4.0 16.4 - - + -
170F PHE* 4.4 2.2 - - + -
175F LEU* 4.0 10.8 - - + -
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Residues in contact with GLU 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F LEU* 3.0 21.6 + - + +
98F ARG* 2.7 51.3 + - - +
100F MET* 1.3 76.9 - - - +
102F LYS* 1.3 58.5 + - + +
104F LEU* 3.3 8.9 + - + +
105F LYS* 3.0 26.5 + - - +
152F VAL* 4.0 17.0 - - + -
156F ARG* 2.8 38.3 + - - +
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Residues in contact with LYS 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F VAL* 6.1 0.2 - - - +
37F MET* 3.8 12.3 - - + -
90F LYS* 3.6 25.1 - - + +
93F TRP* 2.7 64.9 + - + +
94F GLU* 3.8 6.3 + - - -
98F ARG* 2.9 39.4 + - - +
99F ALA 3.8 3.4 - - - +
101F GLU* 1.3 73.9 - - + +
103F ALA* 1.3 60.4 + - - +
105F LYS* 3.4 25.6 + - - +
106F LEU* 2.9 27.9 + - - +
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Residues in contact with ALA 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F TYR* 3.8 29.6 - - + +
37F MET* 3.8 7.0 - - + +
55F PHE* 4.2 7.9 - - + -
99F ALA 2.9 17.2 + - - +
100F MET 3.6 4.9 - - - +
102F LYS* 1.3 72.3 - - - +
104F LEU* 1.3 65.3 + - - +
106F LEU* 3.3 7.2 + - - +
107F GLU* 2.9 28.1 + - - +
148F LEU* 3.8 16.2 - - + -
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Residues in contact with LEU 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E GLN* 3.7 42.4 - - + +
8E VAL* 4.9 0.7 - - + -
100F MET 2.9 13.3 + - - +
101F GLU* 3.5 12.3 - - + +
103F ALA* 1.3 76.5 - - - +
105F LYS* 1.3 63.0 + - - +
107F GLU* 3.2 3.0 + - - +
108F LYS* 3.0 38.3 + - + +
145F ILE* 3.8 41.5 - - + +
148F LEU* 3.9 17.2 - - + +
149F GLY* 4.3 6.5 - - - +
152F VAL* 4.6 8.1 - - + -
156F ARG* 6.2 0.7 - - - +
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Residues in contact with LYS 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F ASP* 4.6 14.6 + - - +
101F GLU 3.0 14.2 + - - +
102F LYS* 3.6 27.3 + - + +
103F ALA 3.3 0.2 - - - -
104F LEU* 1.3 75.2 - - - +
106F LEU* 1.3 59.2 + - - +
108F LYS* 3.4 8.5 + - - +
109F LYS* 3.0 31.7 + - + +
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Residues in contact with LEU 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F LEU* 5.4 0.2 - - + -
29F TYR* 3.9 31.6 - - + -
30F ALA* 4.1 19.5 - - + -
33F VAL* 3.9 31.2 - - + -
34F TYR* 4.1 26.2 - - + -
102F LYS 2.9 15.1 + - - +
103F ALA* 3.5 8.5 - - - +
105F LYS* 1.3 76.2 - - - +
107F GLU* 1.3 62.5 + - + +
109F LYS* 3.1 15.9 + - + +
110F VAL* 2.9 41.8 + - + +
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Residues in contact with GLU 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F ALA* 6.3 0.9 - - - -
34F TYR* 2.5 37.3 + - + +
58F GLN* 5.3 2.6 - - - +
62F GLU* 3.5 14.5 - - - +
103F ALA 2.9 21.1 + - - +
104F LEU 3.8 3.4 - - - +
106F LEU* 1.3 81.0 - - - +
108F LYS* 1.3 57.6 + - - +
110F VAL* 3.5 4.1 + - - +
111F ASN* 2.9 25.5 + - - +
141F GLN* 2.7 45.8 + - - +
144F ALA* 4.0 17.1 - - + +
145F ILE* 3.8 16.8 - - + +
148F LEU* 3.5 13.0 - - + -
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Residues in contact with LYS 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E SER 4.6 1.6 + - - -
7E GLN* 2.9 30.6 + - - +
8E VAL 3.8 10.3 - - - -
9E ARG 3.0 27.4 + - - -
10E GLN* 3.0 37.0 + - - +
104F LEU* 3.0 30.3 + - + +
105F LYS* 3.9 7.0 - - - +
106F LEU 3.2 0.2 - - - -
107F GLU* 1.3 75.7 - - - +
109F LYS* 1.3 57.6 + - - +
111F ASN* 3.3 0.4 + - - -
112F GLN* 2.9 25.6 + - - +
145F ILE* 3.8 14.4 - - + -
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Residues in contact with LYS 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F LEU* 3.9 28.6 - - + +
29F TYR* 4.8 12.1 - - + -
105F LYS* 3.0 19.2 + - + +
106F LEU* 3.1 18.4 + - + +
108F LYS* 1.3 78.9 - - - +
110F VAL* 1.3 60.7 + - + +
112F GLN* 3.4 7.1 + - - +
113F SER* 3.1 22.2 + - - -
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Residues in contact with VAL 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F GLN* 3.9 6.7 - - - +
26F LEU* 3.9 28.9 - - + +
27F GLU* 3.5 28.3 - - - +
30F ALA* 4.4 13.7 - - + -
62F GLU* 6.1 0.4 - - - -
106F LEU* 2.9 32.0 + - + +
107F GLU* 3.8 7.2 - - - +
109F LYS* 1.3 71.9 - - + +
111F ASN* 1.3 65.8 + - - +
113F SER* 3.1 4.9 + - - -
114F LEU* 3.0 27.5 + - + +
141F GLN* 3.9 16.8 - - - +
201F FE 4.3 2.9 - - - -
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Residues in contact with ASN 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E GLN* 3.0 36.8 + - - +
107F GLU 2.9 18.5 + - - +
108F LYS 3.5 0.7 - - - +
109F LYS 3.3 0.2 - - - -
110F VAL* 1.3 76.3 - - - +
112F GLN* 1.3 56.6 + - - +
114F LEU* 3.1 3.3 + - - +
115F LEU* 2.8 43.3 + - - +
138F LEU* 4.2 16.5 - - - +
141F GLN* 3.3 32.1 - - + +
142F VAL* 5.1 9.5 - - - +
145F ILE* 3.9 10.2 - - + +
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Residues in contact with GLN 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E GLN* 3.4 20.9 + - - +
11E ASN* 5.9 0.5 - - - +
108F LYS 2.9 17.5 + - - +
109F LYS* 3.6 7.6 - - - +
110F VAL 3.3 0.2 - - - -
111F ASN* 1.3 75.6 - - - +
113F SER* 1.3 57.5 + - - +
115F LEU* 3.2 13.1 + - - +
116F GLU* 3.0 59.5 + - - +
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Residues in contact with SER 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F ARG* 5.8 1.4 - - - +
23F GLN* 2.7 22.4 + - - -
26F LEU* 3.4 26.3 - - - +
109F LYS 3.1 8.9 + - - -
110F VAL 3.4 9.0 - - - -
112F GLN* 1.3 77.0 - - - +
114F LEU* 1.3 55.7 + - - +
116F GLU* 3.2 15.7 + - - +
117F LEU* 2.9 28.4 + - - +
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Residues in contact with LEU 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F GLN* 3.6 30.1 - - + +
27F GLU* 4.5 0.4 - - - +
69F LEU* 5.8 1.3 - - + -
110F VAL* 3.0 26.1 + - + +
111F ASN* 3.1 6.3 + - - +
113F SER* 1.3 77.2 - - - +
115F LEU* 1.3 56.8 + - - +
117F LEU* 3.2 16.9 + - + +
118F HIS* 2.9 28.9 + - - +
133F ILE* 4.1 9.7 - - + +
137F TYR* 3.9 40.8 - - + +
138F LEU* 4.0 14.1 - - + -
141F GLN* 3.5 33.7 - - + +
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Residues in contact with LEU 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E GLN* 4.4 7.4 - - + +
11E ASN* 3.8 33.2 - - + +
127E PRO* 3.7 33.4 - - + +
128E HIS* 5.2 4.0 - - + +
111F ASN* 2.8 42.3 + - - +
112F GLN* 3.6 14.6 - - - +
113F SER 3.2 0.2 - - - -
114F LEU* 1.3 74.3 - - - +
116F GLU* 1.3 59.6 + - + +
118F HIS* 3.4 4.3 + - - +
119F LYS* 2.9 28.1 + - - +
138F LEU* 4.1 18.4 - - + -
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Residues in contact with GLU 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112F GLN* 3.0 47.2 + - - +
113F SER* 3.2 15.5 + - - +
115F LEU* 1.3 75.6 - - + +
117F LEU* 1.3 58.1 + - - +
119F LYS* 3.3 10.9 + - + +
120F LEU* 3.0 28.1 + - - +
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Residues in contact with LEU 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F SER 4.6 1.6 - - - +
19F ALA* 3.5 39.3 - - + +
20F ILE* 3.8 28.3 - - + -
23F GLN* 4.4 24.5 - - + +
69F LEU* 5.0 2.9 - - + -
113F SER 2.9 13.2 + - - +
114F LEU* 3.4 16.6 - - + +
116F GLU* 1.3 75.6 - - - +
118F HIS* 1.3 56.5 + - - +
120F LEU* 3.2 9.4 + - + +
121F ALA* 2.9 27.5 + - - +
129F LEU* 4.9 7.0 - - + -
133F ILE* 3.6 24.2 - - + -
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Residues in contact with HIS 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127E PRO* 3.4 36.9 - - + +
114F LEU 2.9 16.1 + - - +
115F LEU* 3.6 8.3 - - - +
116F GLU 3.3 0.2 - - - -
117F LEU* 1.3 76.7 - - - +
119F LYS* 1.3 58.7 + - - +
121F ALA* 3.4 3.0 + - - +
122F THR* 2.9 50.7 + - - -
130F CYS* 3.6 31.9 - - - +
133F ILE* 3.9 20.4 - - + +
134F GLU* 2.8 29.7 + - + -
138F LEU* 4.5 1.1 - - + -
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Residues in contact with LYS 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E ASN* 5.5 16.4 - - + +
115F LEU 2.9 17.3 + - - +
116F GLU* 3.3 9.6 + - + +
118F HIS* 1.3 75.8 + - - +
120F LEU* 1.3 62.8 - - - +
122F THR* 3.3 7.1 + - - -
123F LYS* 3.0 59.4 + - + +
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Residues in contact with LEU 120 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F ASP* 3.6 48.9 - - + +
16F SER* 3.9 10.3 - - - +
19F ALA* 3.8 19.5 - - + -
22F ARG* 5.3 2.9 - - - +
116F GLU 3.0 13.9 + - - +
117F LEU* 3.2 9.8 + - + +
119F LYS* 1.3 78.3 - - - +
121F ALA* 1.3 56.7 + - - +
123F LYS* 3.2 13.4 + - + +
124F LYS* 2.9 45.3 + - + +
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Residues in contact with ALA 121 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F SER* 4.7 4.0 + - - -
117F LEU 2.9 19.3 + - - +
118F HIS* 3.7 6.7 - - - +
120F LEU* 1.3 74.1 - - - +
122F THR* 1.3 60.9 + - - +
124F LYS* 3.5 1.7 + - - -
125F ASN 3.2 3.3 + - - -
126F ASP* 2.9 33.2 + - + +
129F LEU* 3.7 36.1 - - + +
130F CYS* 3.8 18.1 - - - +
133F ILE* 4.7 0.7 - - + -
----------------------------------------------------------
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Residues in contact with THR 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E ASN* 5.9 2.7 - - - +
118F HIS* 2.9 43.6 + - - -
119F LYS* 3.6 8.2 - - - -
121F ALA* 1.3 68.9 - - - +
123F LYS* 1.3 67.1 + - + +
125F ASN* 3.0 21.9 + - - +
126F ASP 5.1 0.2 - - - +
130F CYS* 3.6 8.2 - - - -
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Residues in contact with LYS 123 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119F LYS* 3.0 63.4 + - + +
120F LEU* 3.5 13.0 - - + +
122F THR* 1.3 78.5 - - + +
124F LYS* 1.4 69.1 + - + +
125F ASN* 3.5 10.6 + - - -
----------------------------------------------------------
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Residues in contact with LYS 124 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F ASN* 4.3 8.3 - - - +
13F HIS* 3.6 50.6 + - + -
15F ASP* 3.6 21.9 + - + -
16F SER* 4.1 10.5 - - - +
120F LEU* 2.9 31.3 + - + +
121F ALA* 3.5 3.3 + - - +
122F THR 3.2 0.2 - - - -
123F LYS* 1.4 84.0 - - + +
125F ASN* 1.3 71.8 + - - +
126F ASP* 3.3 6.8 + - + +
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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