Contacts of the helix formed by residues 95 - 124 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C TYR* 3.7 4.6 + - - -
41C PHE* 3.5 12.3 - - - -
46C VAL* 6.3 0.7 - - - -
93C TRP 2.9 7.6 + - - +
94C GLU* 1.3 77.3 - - - +
96C GLY* 1.3 64.2 + - - +
97C LEU 3.5 0.3 + - - -
98C ARG* 3.0 30.9 + - - +
99C ALA 3.0 18.9 + - - -
161C PRO* 3.5 22.7 - - - +
167C GLU* 3.6 13.7 - - - -
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Residues in contact with GLY 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C PHE* 3.6 16.1 - - - -
51C PHE* 3.5 27.3 - - - -
95C SER* 1.3 72.1 - - - +
97C LEU* 1.3 61.5 + - - +
99C ALA* 3.4 1.0 + - - +
100C MET* 3.0 27.9 + - - +
155C LEU* 4.2 1.6 - - - -
167C GLU* 2.8 22.8 + - - -
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Residues in contact with LEU 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C SER* 3.9 4.3 - - - +
96C GLY* 1.3 71.9 - - - +
98C ARG* 1.3 66.2 + - + +
100C MET* 3.2 1.7 + - - -
101C GLU* 2.9 42.0 + - - +
152C VAL* 4.0 33.9 - - + +
155C LEU* 3.9 17.6 - - + +
156C ARG* 4.1 14.4 - - + +
160C ALA* 3.6 31.9 - - + +
161C PRO* 3.8 15.5 - - + -
167C GLU* 2.8 19.2 + - - +
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Residues in contact with ARG 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C LYS* 5.4 1.0 - - - +
93C TRP 3.6 15.9 - - - +
94C GLU* 3.5 41.6 + - + -
95C SER* 3.0 21.6 + - - +
97C LEU* 1.3 79.7 - - + +
99C ALA* 1.3 56.4 + - - +
101C GLU* 3.2 22.9 + - - +
102C LYS* 3.0 54.9 + - - +
161C PRO* 5.1 9.8 - - + +
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Residues in contact with ALA 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C MET* 3.6 16.5 - - - +
41C PHE* 3.6 27.4 - - + -
55C PHE* 3.9 12.6 - - + -
93C TRP* 3.8 15.8 + - + -
95C SER 3.0 18.2 + - - +
96C GLY 3.8 1.8 - - - +
98C ARG* 1.3 75.0 - - - +
100C MET* 1.3 58.4 + - - +
102C LYS* 3.2 2.6 + - - -
103C ALA* 2.9 29.3 + - - +
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Residues in contact with MET 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C PHE* 3.8 23.1 - - + -
54C TYR* 3.8 26.2 - - + -
55C PHE* 3.8 12.1 - - + -
96C GLY 3.0 21.1 + - - +
97C LEU 3.7 4.0 - - - +
99C ALA* 1.3 76.4 - - - +
101C GLU* 1.3 56.0 + - - +
103C ALA* 3.7 3.3 - - - +
104C LEU* 2.9 28.9 + - - +
148C LEU* 3.6 28.1 - - + +
151C HIS* 3.9 24.5 - - + -
152C VAL* 3.7 19.2 - - + +
155C LEU* 4.0 15.7 - - + -
170C PHE* 4.5 1.8 - - + -
175C LEU* 4.1 8.5 - - + -
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Residues in contact with GLU 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C LEU* 2.9 34.4 + - + +
98C ARG* 3.2 34.8 - - - +
100C MET* 1.3 75.7 - - - +
102C LYS* 1.3 66.9 + - + +
104C LEU* 3.4 8.4 + - + +
105C LYS* 3.1 22.2 + - - +
152C VAL* 4.1 10.3 - - + -
156C ARG* 2.8 38.8 + - - +
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Residues in contact with LYS 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C MET* 3.8 15.9 - - + -
90C LYS* 4.1 28.0 - - - +
93C TRP* 4.2 19.0 + - + -
94C GLU* 4.6 1.4 + - - -
98C ARG* 3.0 52.4 + - - +
99C ALA 3.7 4.0 - - - +
101C GLU* 1.3 78.6 + - + +
103C ALA* 1.3 59.8 + - - +
105C LYS* 3.3 17.5 + - + +
106C LEU* 2.9 28.1 + - - +
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Residues in contact with ALA 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C TYR* 3.8 30.3 - - + +
37C MET* 3.9 6.9 - - - +
55C PHE* 4.2 8.1 - - + -
99C ALA 2.9 16.4 + - - +
100C MET 3.7 4.3 - - - +
101C GLU 3.3 0.2 - - - -
102C LYS* 1.3 76.2 - - - +
104C LEU* 1.3 59.3 + - - +
106C LEU* 3.3 7.4 + - - +
107C GLU* 2.9 35.0 + - - +
148C LEU* 3.8 15.5 - - + -
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Residues in contact with LEU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLN* 3.7 42.2 - - + +
8A VAL* 5.1 0.4 - - + -
100C MET 2.9 14.6 + - - +
101C GLU* 3.5 11.2 - - + +
102C LYS 3.3 0.2 - - - -
103C ALA* 1.3 75.7 - - - +
105C LYS* 1.3 61.9 + - - +
107C GLU* 3.3 2.1 + - - +
108C LYS* 3.0 40.5 + - + +
145C ILE* 3.8 41.5 - - + +
148C LEU* 3.9 16.9 - - + +
149C GLY* 4.4 7.6 - - - +
152C VAL* 4.6 7.4 - - + -
156C ARG* 6.2 0.2 - - - +
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Residues in contact with LYS 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C GLU 3.1 13.6 + - - +
102C LYS* 3.6 20.9 - - + +
103C ALA 3.3 0.2 - - - -
104C LEU* 1.3 76.5 - - - +
106C LEU* 1.3 58.3 + - - +
108C LYS* 3.3 8.5 + - - +
109C LYS* 3.0 28.8 + - + +
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Residues in contact with LEU 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU* 5.4 0.4 - - + -
29C TYR* 4.1 29.6 - - + -
30C ALA* 4.0 20.6 - - + -
33C VAL* 3.8 32.8 - - + -
34C TYR* 4.1 24.0 - - + -
102C LYS 2.9 15.1 + - - +
103C ALA* 3.3 8.7 + - - +
105C LYS* 1.3 75.3 - - - +
107C GLU* 1.3 59.6 + - + +
109C LYS* 3.0 16.9 + - + +
110C VAL* 2.8 42.9 + - + +
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Residues in contact with GLU 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ALA* 6.5 0.2 - - - -
34C TYR* 2.6 27.3 + - + +
62C GLU* 3.4 16.5 - - - +
65C HIS* 5.7 0.3 - - - -
103C ALA 2.9 20.5 + - - +
104C LEU 3.9 2.7 - - - +
106C LEU* 1.3 78.2 - - + +
108C LYS* 1.3 58.8 + - - +
110C VAL* 3.5 5.5 + - - +
111C ASN* 2.9 25.6 + - - +
141C GLN* 2.8 44.8 + - - +
144C ALA* 3.9 13.4 - - + +
145C ILE* 3.9 17.6 - - + +
148C LEU* 3.6 12.4 - - + +
202C MG 3.4 19.6 - - - -
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Residues in contact with LYS 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A SER 4.7 1.2 + - - -
7A GLN 2.9 30.0 + - - +
8A VAL 3.7 6.4 - - - -
9A ARG 3.0 26.7 + - - -
10A GLN* 2.9 41.5 + - - +
104C LEU* 3.0 26.6 + - + +
105C LYS* 3.7 7.4 - - - +
107C GLU* 1.3 75.9 - - - +
109C LYS* 1.3 60.3 + - - +
111C ASN* 3.4 0.4 + - - -
112C GLN* 2.8 24.9 + - - +
145C ILE* 4.0 15.0 - - + -
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Residues in contact with LYS 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU* 4.4 22.8 - - + +
29C TYR* 4.4 19.3 + - + -
105C LYS* 3.0 15.6 + - + +
106C LEU* 3.3 19.7 - - + +
108C LYS* 1.3 76.4 - - - +
110C VAL* 1.3 63.1 + - + +
112C GLN* 3.3 7.4 + - - +
113C SER* 3.1 22.0 + - - -
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Residues in contact with VAL 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C GLN* 3.9 5.2 - - - +
26C LEU* 4.0 24.5 - - + -
27C GLU* 3.6 27.4 - - - +
30C ALA* 4.4 14.1 - - + -
62C GLU* 5.5 0.7 - - - +
106C LEU* 2.8 35.3 + - + +
107C GLU* 3.8 8.5 - - - +
109C LYS* 1.3 76.8 - - + +
111C ASN* 1.3 62.2 + - - +
113C SER* 3.2 4.9 + - - -
114C LEU* 3.0 24.2 + - + +
141C GLN* 3.8 20.4 - - - +
201C FE 4.3 3.6 - - - -
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Residues in contact with ASN 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLN* 2.9 35.1 + - - +
107C GLU 2.9 18.8 + - - +
108C LYS 3.6 0.4 - - - +
109C LYS 3.3 0.2 - - - -
110C VAL* 1.3 77.8 - - - +
112C GLN* 1.3 55.9 + - - +
114C LEU* 3.1 2.5 + - - +
115C LEU* 2.9 48.6 + - - +
138C LEU* 4.3 13.5 - - - +
141C GLN* 3.4 31.6 - - + +
142C VAL* 5.1 8.9 - - - +
145C ILE* 3.9 10.4 - - + +
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Residues in contact with GLN 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLN* 3.4 20.1 + - - +
11A ASN* 5.7 1.4 - - - +
108C LYS 2.8 20.4 + - - +
109C LYS* 3.3 8.5 + - - +
111C ASN* 1.3 72.1 - - - +
113C SER* 1.3 58.4 + - - +
115C LEU* 3.3 13.4 + - - +
116C GLU* 2.9 62.2 + - - +
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Residues in contact with SER 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ARG* 5.6 1.6 + - - +
23C GLN* 2.4 28.3 + - - -
26C LEU* 3.5 27.3 - - - +
109C LYS 3.1 8.1 + - - -
110C VAL 3.5 3.4 - - - -
112C GLN* 1.3 76.2 - - - +
114C LEU* 1.3 57.6 + - - +
116C GLU* 3.3 15.2 + - - +
117C LEU* 2.9 27.7 + - - +
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Residues in contact with LEU 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C GLN* 3.5 28.7 - - + +
27C GLU* 4.5 0.4 - - - +
69C LEU* 5.7 1.3 - - + -
110C VAL* 3.0 24.3 + - + +
111C ASN* 3.1 6.3 + - - +
113C SER* 1.3 75.9 - - - +
115C LEU* 1.3 57.1 + - - +
117C LEU* 3.3 16.1 + - + +
118C HIS* 2.9 27.9 + - - +
133C ILE* 4.1 9.6 - - + +
137C TYR* 3.9 43.5 - - + +
138C LEU* 4.0 13.2 - - + -
141C GLN* 3.5 32.8 - - + +
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Residues in contact with LEU 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLN* 4.6 3.1 - - + +
11A ASN* 3.7 38.6 - - + +
127A PRO* 3.9 27.8 - - + +
128A HIS* 5.2 5.2 - - + +
111C ASN* 2.9 40.7 + - - +
112C GLN* 3.6 17.7 - - - +
113C SER 3.3 0.2 - - - -
114C LEU* 1.3 73.3 - - - +
116C GLU* 1.3 61.6 + - - +
118C HIS* 3.3 5.8 + - - +
119C LYS* 3.0 27.9 + - - +
138C LEU* 4.1 17.0 - - + -
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Residues in contact with GLU 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C GLN* 2.9 49.2 + - - +
113C SER* 3.6 12.9 - - - +
115C LEU* 1.3 75.4 - - + +
117C LEU* 1.3 63.6 + - - +
119C LYS* 3.4 8.8 + - + +
120C LEU* 3.0 22.7 + - - +
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Residues in contact with LEU 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C SER 4.6 1.3 - - - +
19C ALA* 3.3 41.3 - - + +
20C ILE* 3.9 27.6 - - + +
23C GLN* 4.5 14.4 - - + +
69C LEU* 5.2 2.0 - - + -
113C SER 2.9 16.6 + - - +
114C LEU* 3.5 20.6 - - + +
116C GLU* 1.3 75.3 - - - +
118C HIS* 1.3 58.6 + - - +
120C LEU* 3.3 7.9 + - + +
121C ALA* 2.9 27.9 + - - +
129C LEU* 5.0 6.5 - - + -
133C ILE* 3.8 27.1 - - + -
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Residues in contact with HIS 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A PRO* 3.4 37.9 - - + +
114C LEU 2.9 16.7 + - - +
115C LEU* 3.6 6.3 - - - +
116C GLU 3.3 0.2 - - - -
117C LEU* 1.3 76.2 - - - +
119C LYS* 1.3 60.4 + - - +
121C ALA* 3.3 2.2 + - - +
122C THR* 2.9 50.9 + - - -
130C CYS* 3.6 29.1 - - - +
133C ILE* 4.0 19.9 - - + +
134C GLU* 2.7 34.0 + - + -
138C LEU* 4.4 1.8 - - + -
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Residues in contact with LYS 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ASN* 5.0 24.3 + - + +
115C LEU 3.0 16.6 + - - +
116C GLU* 3.6 9.4 - - + +
118C HIS* 1.3 77.7 + - - +
120C LEU* 1.3 64.6 + - - +
122C THR* 3.4 7.4 + - - -
123C LYS* 3.0 60.0 + - + +
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Residues in contact with LEU 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ASP* 3.6 40.4 - - + +
16C SER* 3.9 10.3 - - - +
19C ALA* 3.7 19.3 - - + -
22C ARG* 5.2 3.4 - - - +
116C GLU 3.0 14.2 + - - +
117C LEU* 3.6 8.7 - - + +
118C HIS 3.2 0.2 - - - -
119C LYS* 1.3 78.3 - - - +
121C ALA* 1.3 62.9 + - - +
123C LYS* 3.1 13.0 + - + +
124C LYS* 2.9 53.1 + - + +
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Residues in contact with ALA 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C SER* 4.7 4.7 + - - -
117C LEU 2.9 16.7 + - - +
118C HIS* 3.7 7.2 - - - +
120C LEU* 1.3 76.4 - - - +
122C THR* 1.3 60.2 + - - +
124C LYS* 3.5 1.9 + - - -
125C ASN 3.2 3.5 + - - -
126C ASP* 2.9 34.2 + - + +
129C LEU* 3.7 36.6 - - + -
130C CYS* 3.7 17.3 - - - +
133C ILE* 4.5 1.1 - - + -
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Residues in contact with THR 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ASN* 5.8 3.4 - - - +
118C HIS* 2.9 41.6 + - - -
119C LYS* 3.5 9.4 - - + +
121C ALA* 1.3 74.1 - - - +
123C LYS* 1.3 66.8 + - + +
125C ASN* 3.0 22.2 + - - +
130C CYS* 3.6 7.8 - - - -
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Residues in contact with LYS 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C LYS* 3.0 58.0 + - - +
120C LEU* 3.1 17.4 + - + +
122C THR* 1.3 78.2 - - + +
124C LYS* 1.3 67.9 + - + +
125C ASN* 3.3 13.2 + - - +
----------------------------------------------------------
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Residues in contact with LYS 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ASN* 4.3 7.8 - - - +
13C HIS* 3.6 50.9 + - + +
15C ASP* 3.6 24.1 + - - -
16C SER* 4.5 7.6 - - - +
120C LEU* 2.9 34.9 + - + +
121C ALA* 3.6 2.9 - - - +
122C THR 3.2 0.2 - - - -
123C LYS* 1.3 84.3 - - + +
125C ASN* 1.3 71.3 + - - +
126C ASP* 3.3 7.5 + - + +
----------------------------------------------------------
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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