Contacts of the helix formed by residues 95 - 124 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E TYR* 3.7 4.8 + - - -
41E PHE* 3.6 6.8 - - - -
46E VAL* 6.2 0.4 - - - -
93E TRP 2.9 8.0 + - - +
94E GLU* 1.3 77.0 - - - +
96E GLY* 1.3 59.5 + - - +
97E LEU 3.6 0.5 + - - -
98E ARG* 3.0 31.1 + - - +
99E ALA* 2.9 29.5 + - - +
161E PRO* 3.5 22.6 - - - +
167E GLU* 3.5 16.4 - - - -
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Residues in contact with GLY 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E PHE* 3.6 15.7 - - - -
48E LEU* 5.0 0.4 - - - +
51E PHE* 3.4 28.1 - - - -
95E SER* 1.3 71.4 - - - +
97E LEU* 1.3 60.1 + - - +
99E ALA* 3.4 1.4 + - - +
100E MET* 3.0 28.2 + - - +
155E LEU* 4.2 2.7 - - - -
167E GLU* 2.9 21.2 + - - -
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Residues in contact with LEU 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E SER* 4.0 3.4 - - - +
96E GLY* 1.3 74.1 - - - +
98E ARG* 1.3 59.7 + - + +
100E MET* 3.2 2.1 + - - +
101E GLU* 2.9 58.7 + - + +
152E VAL* 3.9 29.8 - - + +
155E LEU* 4.0 16.6 - - + +
156E ARG* 3.9 16.6 - - + +
160E ALA* 3.5 37.0 - - + +
161E PRO* 3.9 11.0 - - + -
167E GLU* 2.8 19.7 + - - +
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Residues in contact with ARG 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90E LYS* 5.8 0.4 - - - +
93E TRP 3.6 14.8 - - - +
94E GLU* 2.4 48.4 + - + -
95E SER* 3.0 16.9 + - - +
97E LEU* 1.3 78.0 - - + +
99E ALA* 1.3 58.3 + - - +
101E GLU* 3.3 18.4 + - - +
102E LYS* 2.9 47.4 + - - +
161E PRO* 5.0 12.8 - - + +
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Residues in contact with ALA 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E MET* 3.4 19.5 - - - +
41E PHE* 3.7 27.1 - - + -
55E PHE* 4.1 11.2 - - + -
93E TRP* 3.8 16.7 + - + -
95E SER 2.9 17.8 + - - +
96E GLY 3.9 1.3 - - - +
97E LEU 3.2 0.2 - - - -
98E ARG* 1.3 77.9 - - - +
100E MET* 1.4 56.3 + - - +
102E LYS* 3.3 2.5 + - - -
103E ALA* 2.9 26.7 + - - +
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Residues in contact with MET 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E PHE* 3.9 20.0 - - + -
54E TYR* 3.6 28.9 - - + -
55E PHE* 3.9 10.5 - - + -
96E GLY 3.0 21.2 + - - +
97E LEU 3.2 4.7 + - - +
99E ALA* 1.4 71.9 - - - +
101E GLU* 1.3 61.5 + - - +
103E ALA* 3.3 3.9 + - - +
104E LEU* 2.9 29.6 + - - +
148E LEU* 3.6 27.1 - - + +
151E HIS* 3.9 23.1 - - + -
152E VAL* 3.8 18.5 - - + +
155E LEU* 4.0 16.6 - - + -
170E PHE* 4.5 1.6 - - + -
175E LEU* 4.0 10.8 - - + -
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Residues in contact with GLU 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97E LEU* 2.9 32.5 + - + +
98E ARG* 3.7 25.0 + - - +
100E MET* 1.3 77.1 - - - +
102E LYS* 1.3 66.4 + - + +
104E LEU* 3.4 8.5 + - + +
105E LYS* 3.1 21.7 + - - +
152E VAL* 4.0 17.9 - - + -
156E ARG* 2.9 35.5 + - - +
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Residues in contact with LYS 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E MET* 3.8 15.7 - - + -
90E LYS* 3.0 39.4 - - - +
93E TRP* 4.1 19.3 - - + +
94E GLU* 4.8 0.2 + - - -
98E ARG* 2.9 32.1 + - - +
99E ALA 3.8 3.1 - - - +
101E GLU* 1.3 77.2 + - + +
103E ALA* 1.3 62.0 + - - +
105E LYS* 3.3 21.0 + - + +
106E LEU* 2.9 27.4 + - - +
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Residues in contact with ALA 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E TYR* 3.8 29.6 - - + +
37E MET* 3.9 6.4 - - + +
55E PHE* 4.3 7.0 - - + -
99E ALA 2.9 17.0 + - - +
100E MET 3.6 5.2 - - - +
102E LYS* 1.3 75.6 - - - +
104E LEU* 1.3 59.4 + - - +
106E LEU* 3.2 7.8 + - - +
107E GLU* 2.9 34.7 + - - +
148E LEU* 3.8 16.6 - - + -
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Residues in contact with LEU 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D GLN* 3.7 41.3 - - + +
8D VAL* 5.1 0.4 - - + -
100E MET 2.9 16.5 + - - +
101E GLU* 3.5 8.3 - - + +
102E LYS 3.3 0.2 - - - -
103E ALA* 1.3 76.7 - - - +
105E LYS* 1.3 62.8 + - - +
107E GLU* 3.3 1.9 + - - +
108E LYS* 3.0 40.2 + - + +
145E ILE* 3.8 41.5 - - + +
148E LEU* 3.8 17.8 - - + +
149E GLY* 4.3 7.0 - - - +
152E VAL* 4.5 9.2 - - + -
156E ARG* 6.3 0.2 - - - +
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Residues in contact with LYS 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E GLU 3.1 13.4 + - - +
102E LYS* 3.5 23.3 - - + +
103E ALA 3.3 0.2 - - - -
104E LEU* 1.3 76.5 - - - +
106E LEU* 1.4 56.0 + - - +
108E LYS* 3.3 7.5 + - - +
109E LYS* 3.0 67.1 + - - +
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Residues in contact with LEU 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E LEU* 5.4 2.5 - - + -
29E TYR* 4.2 25.6 - - + -
30E ALA* 4.0 23.3 - - + -
33E VAL* 3.8 33.0 - - + -
34E TYR* 4.2 21.5 - - + +
102E LYS 2.9 13.8 + - - +
103E ALA* 3.2 9.8 + - - +
105E LYS* 1.4 70.1 - - - +
107E GLU* 1.3 63.3 + - + +
109E LYS* 3.1 11.4 + - + +
110E VAL* 2.9 44.3 + - + +
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Residues in contact with GLU 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E ALA* 6.3 0.7 - - - -
34E TYR* 2.4 37.8 + - - +
58E GLN* 5.3 2.4 - - - +
62E GLU* 3.3 13.5 - - - +
103E ALA 2.9 19.4 + - - +
104E LEU 3.9 2.2 - - - +
106E LEU* 1.3 80.1 - - + +
108E LYS* 1.3 58.8 + - - +
110E VAL* 4.5 5.1 - - - +
111E ASN* 2.9 26.0 + - - +
141E GLN* 2.7 43.8 + - - +
144E ALA* 4.2 16.0 - - + +
145E ILE* 3.8 19.2 - - + +
148E LEU* 3.5 15.5 - - + -
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Residues in contact with LYS 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D SER 4.7 0.8 + - - -
7D GLN* 2.9 29.7 + - - +
8D VAL 3.8 9.6 - - - -
9D ARG 2.9 28.6 + - - -
10D GLN* 2.9 38.4 + - - +
104E LEU* 3.0 30.8 + - + +
105E LYS* 3.8 7.4 - - - +
107E GLU* 1.3 77.9 - - - +
109E LYS* 1.3 57.1 + - - +
111E ASN 3.4 0.3 + - - -
112E GLN* 2.9 23.9 + - - +
145E ILE* 3.9 14.6 - - + -
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Residues in contact with LYS 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E LEU* 4.5 7.5 - - + +
105E LYS* 3.0 56.9 + - - +
106E LEU* 3.1 13.0 + - + +
108E LYS* 1.3 73.8 - - - +
110E VAL* 1.3 65.9 + - + +
112E GLN* 3.3 9.1 + - + +
113E SER* 3.2 20.4 + - - -
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Residues in contact with VAL 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E GLN* 3.8 7.6 - - - +
26E LEU* 4.0 24.9 - - + +
27E GLU* 3.5 27.8 - - - +
30E ALA* 4.5 11.9 - - + -
62E GLU* 5.7 0.7 - - - +
106E LEU* 2.9 37.5 + - + +
107E GLU* 3.8 7.9 - - - +
109E LYS* 1.3 75.2 - - + +
111E ASN* 1.3 58.4 + - - +
113E SER* 3.2 3.8 + - - -
114E LEU* 3.0 32.7 + - + +
141E GLN* 3.9 15.5 - - - +
201E FE 4.4 2.5 - - - -
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Residues in contact with ASN 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D GLN* 2.9 35.1 + - - +
107E GLU 2.9 19.1 + - - +
108E LYS 3.5 1.1 - - - +
110E VAL* 1.3 74.2 - - - +
112E GLN* 1.3 65.3 + - - +
114E LEU* 3.1 2.9 + - - +
115E LEU* 2.9 40.2 + - - +
138E LEU* 4.3 17.5 - - - +
141E GLN* 3.4 29.3 - - + +
142E VAL* 5.0 9.8 - - - +
145E ILE* 3.9 10.7 - - + +
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Residues in contact with GLN 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D GLN* 3.3 21.3 + - - +
11D ASN* 6.1 0.2 - - - +
108E LYS 2.9 17.5 + - - +
109E LYS* 3.6 10.1 - - + +
110E VAL 3.3 0.2 - - - -
111E ASN* 1.3 75.0 - - - +
113E SER* 1.3 57.1 + - - +
115E LEU* 3.3 12.2 + - - +
116E GLU* 3.0 60.3 + - - +
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Residues in contact with SER 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E ARG 5.8 0.3 - - - -
23E GLN* 2.7 22.3 + - - -
26E LEU* 3.4 30.2 - - - +
109E LYS 3.2 8.5 + - - -
110E VAL 3.5 4.0 - - - -
112E GLN* 1.3 76.3 - - - +
114E LEU* 1.3 58.3 + - - +
116E GLU* 3.3 14.5 + - - +
117E LEU* 2.9 28.2 + - - +
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Residues in contact with LEU 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E GLN* 3.6 29.2 - - + +
27E GLU* 4.5 0.2 - - - +
69E LEU* 5.8 1.3 - - + -
110E VAL* 3.0 26.4 + - + +
111E ASN* 3.1 5.4 + - - +
113E SER* 1.3 78.8 - - - +
115E LEU* 1.3 56.1 + - - +
117E LEU* 3.4 12.0 + - + +
118E HIS* 2.9 27.2 + - - +
133E ILE* 4.0 13.6 - - + +
137E TYR* 3.9 40.8 - - + +
138E LEU* 4.0 13.7 - - + -
141E GLN* 3.5 34.1 - - + +
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Residues in contact with LEU 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D GLN* 4.6 7.0 - - + +
11D ASN* 3.8 37.9 - - + +
127D PRO* 3.7 28.8 - - + +
128D HIS* 5.2 5.2 - - + +
111E ASN* 2.9 41.7 + - - +
112E GLN* 3.7 12.1 - - - +
114E LEU* 1.3 72.7 - - - +
116E GLU* 1.3 61.5 + - + +
118E HIS* 3.3 4.8 + - - +
119E LYS* 3.0 30.1 + - - +
138E LEU* 4.0 17.0 - - + -
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Residues in contact with GLU 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112E GLN* 3.0 47.8 + - - +
113E SER* 3.6 12.6 + - - +
115E LEU* 1.3 75.0 - - + +
117E LEU* 1.3 64.2 + - - +
119E LYS* 3.3 13.9 + - - +
120E LEU* 3.0 22.5 + - - +
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Residues in contact with LEU 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E SER* 4.5 2.2 - - - +
19E ALA* 3.5 35.2 - - + +
20E ILE* 3.9 28.9 - - + +
23E GLN* 4.2 29.2 - - + +
69E LEU* 5.3 1.6 - - + -
113E SER 2.9 15.2 + - - +
114E LEU* 3.5 11.0 - - + +
116E GLU* 1.3 78.3 - - - +
118E HIS* 1.3 57.4 + - - +
120E LEU* 3.3 10.1 + - + +
121E ALA* 2.9 27.7 + - - +
129E LEU* 4.8 7.4 - - + -
133E ILE* 3.8 19.1 - - + -
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Residues in contact with HIS 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D PRO* 3.4 34.4 - - + +
114E LEU 2.9 17.5 + - - +
115E LEU* 3.7 6.3 - - - +
117E LEU* 1.3 76.3 - - - +
119E LYS* 1.3 59.4 + - - +
121E ALA* 3.3 2.6 + - - +
122E THR* 2.9 51.4 + - - -
130E CYS* 3.6 31.2 - - - +
133E ILE* 3.9 20.5 - - + +
134E GLU* 2.7 35.4 + - + -
138E LEU* 4.5 0.9 - - + -
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Residues in contact with LYS 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D ASN* 4.6 31.4 - - + +
115E LEU 3.0 18.3 + - - +
116E GLU* 3.6 13.0 - - - +
117E LEU 3.3 0.2 - - - -
118E HIS* 1.3 77.5 + - - +
120E LEU* 1.3 58.2 + - - +
122E THR* 3.3 7.3 + - - -
123E LYS* 2.9 49.2 + - + +
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Residues in contact with LEU 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E ASP* 3.6 39.0 - - + +
16E SER* 3.9 11.4 - - - +
19E ALA* 3.8 18.8 - - + -
116E GLU 3.0 13.7 + - - +
117E LEU* 3.6 10.5 - - + +
119E LYS* 1.3 74.3 - - - +
121E ALA* 1.4 66.3 + - - +
123E LYS* 3.1 13.9 + - + +
124E LYS* 3.0 47.7 + - + +
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Residues in contact with ALA 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E SER* 4.7 4.0 + - - -
117E LEU 2.9 17.1 + - - +
118E HIS* 3.7 4.3 - - - +
120E LEU* 1.4 76.7 - - - +
122E THR* 1.3 59.6 + - - +
124E LYS* 3.5 1.7 + - - -
125E ASN 3.1 3.6 + - - -
126E ASP* 2.9 36.4 + - + +
129E LEU* 3.9 31.8 - - + +
130E CYS* 3.6 22.0 - - - +
133E ILE* 4.6 0.4 - - + -
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Residues in contact with THR 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D ASN* 5.9 2.9 - - - +
118E HIS* 2.9 42.8 + - - -
119E LYS* 3.5 8.2 - - + +
120E LEU 3.2 0.2 - - - -
121E ALA* 1.3 76.1 - - - +
123E LYS* 1.3 59.9 + - + +
125E ASN* 2.9 27.2 + - - +
130E CYS* 3.5 8.9 - - - -
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Residues in contact with LYS 123 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119E LYS* 2.9 35.9 + - + +
120E LEU* 3.1 15.8 + - + +
122E THR* 1.3 76.5 - - + +
124E LYS* 1.3 69.9 + - + +
125E ASN* 3.2 10.8 + - - -
----------------------------------------------------------
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Residues in contact with LYS 124 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E ASN* 4.3 8.1 - - - +
13E HIS* 3.7 59.7 + - + -
15E ASP* 3.9 12.6 + - - -
16E SER* 4.3 7.4 - - - +
120E LEU* 3.0 33.6 + - + +
121E ALA* 4.1 2.7 - - - +
122E THR 3.2 0.2 - - - -
123E LYS* 1.3 84.1 - - + +
125E ASN* 1.3 72.2 + - - +
126E ASP* 3.3 7.2 + - + +
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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