Contacts of the helix formed by residues 90 - 115 (chain D) in PDB entry 4GTU
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 GLU 90 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C HIS* 3.9 16.6 - - + +
78C TYR* 3.4 18.0 - - - +
81C ARG* 2.7 36.9 + - - +
82C LYS* 5.4 7.5 - - - +
89D THR* 1.3 74.6 - - - +
91D GLU* 1.3 67.5 + - - +
93D LYS* 3.0 18.4 + - - +
94D ILE* 2.9 39.2 + - + +
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Residues in contact with GLU 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C HIS* 5.5 3.5 + - - +
89D THR* 3.5 6.1 + - - +
90D GLU* 1.3 77.2 - - - +
92D GLU* 1.3 65.3 + - + +
94D ILE* 3.4 9.6 + - - +
95D ARG* 2.9 59.6 + - + +
144D ARG* 4.2 12.3 + - - -
148D VAL 5.2 5.2 - - - -
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Residues in contact with GLU 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D GLY* 4.1 3.9 - - - -
88D GLU* 2.8 56.0 + - - +
89D THR* 3.1 22.3 + - - +
90D GLU 3.2 0.4 - - - -
91D GLU* 1.3 79.3 - - + +
93D LYS* 1.3 63.9 + - - +
95D ARG 3.1 1.6 + - - -
96D VAL* 2.9 29.6 + - - +
148D VAL* 3.5 32.7 - - + +
151D LYS* 4.6 17.4 - - - +
153D THR* 5.7 0.4 - - + -
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Residues in contact with LYS 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ARG* 3.1 37.8 + - - +
87D GLY* 4.2 22.3 + - - +
88D GLU 3.6 18.8 - - - -
89D THR 3.0 17.0 + - - +
90D GLU* 3.0 24.1 + - - +
92D GLU* 1.3 78.8 - - - +
94D ILE* 1.3 56.8 + - - +
96D VAL* 3.4 4.7 + - - +
97D ASP* 2.8 25.6 + - - +
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Residues in contact with ILE 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C HIS* 3.7 29.4 - - + +
68C LYS 5.7 0.2 - - - +
69C ILE* 3.7 31.4 - - + -
74C ALA 6.0 0.4 - - - +
78C TYR* 4.0 7.4 - - + -
81C ARG* 3.5 12.8 - - - +
90D GLU* 2.9 51.7 + - + +
91D GLU* 3.8 6.1 - - - +
93D LYS* 1.3 71.7 - - - +
95D ARG* 1.3 59.8 + - + +
97D ASP* 3.1 3.5 - - + +
98D ILE* 2.8 38.8 + - + +
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Residues in contact with ARG 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ASP* 4.3 8.7 + - - -
91D GLU* 2.9 49.3 + - + +
92D GLU 3.6 3.1 - - - +
94D ILE* 1.3 73.9 - - + +
96D VAL* 1.3 65.7 + - - +
98D ILE* 4.9 1.1 - - - -
99D LEU* 3.1 27.5 + - - +
139D GLN 5.4 1.0 + - - -
140D PHE* 3.0 67.4 + - + +
144D ARG* 3.2 28.6 - - - +
147D PHE 3.3 23.0 + - - +
148D VAL* 4.2 19.7 - - + -
155D VAL* 5.0 1.2 - - - +
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Residues in contact with VAL 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D CYS 3.5 22.9 - - - +
92D GLU 2.9 21.7 + - - +
93D LYS* 3.8 4.3 - - - +
95D ARG* 1.3 74.5 - - - +
97D ASP* 1.3 70.0 + - - +
100D GLU* 3.0 22.1 + - - +
148D VAL* 3.6 17.9 - - + -
153D THR* 3.7 11.4 - - + +
154D PHE* 3.3 31.4 - - + -
155D VAL* 3.3 29.0 - - + +
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Residues in contact with ASP 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ALA* 3.3 21.5 + - + +
77C CYS* 2.9 39.9 - - - +
81C ARG* 2.6 26.9 + - - +
93D LYS 2.8 12.5 + - - +
94D ILE* 3.1 11.2 - - + +
96D VAL* 1.3 80.7 - - - +
98D ILE* 1.3 60.9 + - - +
100D GLU* 3.2 25.5 - - - +
101D ASN* 3.2 16.1 + - - -
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Residues in contact with ILE 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ASP* 4.6 9.4 - - + +
56C PHE* 4.1 26.0 - - + -
68C LYS 4.3 6.3 - - - +
69C ILE* 3.5 18.4 - - + -
70C THR* 3.4 39.7 - - - +
74C ALA* 3.6 24.0 - - + +
94D ILE* 2.8 23.4 + - + +
95D ARG* 4.5 1.3 - - - +
97D ASP* 1.3 71.3 - - - +
99D LEU* 1.3 68.6 + - - +
101D ASN* 3.3 3.3 + - - +
102D GLN* 3.0 25.5 + - + +
140D PHE* 4.5 11.7 - - + -
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Residues in contact with LEU 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C PHE* 4.2 5.6 - - + -
95D ARG 3.1 21.0 + - - +
96D VAL 4.0 1.3 - - - +
98D ILE* 1.3 79.9 - - - +
100D GLU* 1.3 54.5 + - - +
102D GLN* 3.1 3.2 + - + +
103D ALA* 2.6 49.8 + - + +
137D PHE* 3.6 29.4 - - + -
140D PHE* 3.8 28.5 - - + -
147D PHE* 3.9 13.7 - - + -
155D VAL* 3.7 36.6 - - + +
158D LEU* 5.2 0.2 - - + -
159D ALA* 4.3 11.0 - - + -
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Residues in contact with GLU 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C GLU* 5.2 7.2 - - - +
73D ASN* 3.4 29.1 + - - +
77D CYS* 4.0 10.0 - - - -
96D VAL* 3.0 14.0 + - - +
97D ASP* 3.2 25.2 - - - +
99D LEU* 1.3 76.2 - - - +
101D ASN* 1.3 72.8 + - - +
103D ALA* 3.9 0.8 - - - +
104D MET* 3.2 30.7 + - - +
154D PHE* 3.4 28.8 - - - -
155D VAL* 3.9 6.7 - - + -
158D LEU* 3.8 24.9 - - + +
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Residues in contact with ASN 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C GLN* 3.2 47.2 + - + +
73C ASN* 3.0 37.3 + - - +
74C ALA* 3.1 26.8 - - - +
100C GLU* 5.1 1.4 + - - -
73D ASN* 5.4 1.6 - - - +
97D ASP* 3.2 19.1 + - - +
98D ILE 3.6 6.1 - - - +
99D LEU 3.2 0.4 - - - -
100D GLU* 1.3 89.3 + - - +
102D GLN* 1.3 59.2 + - - +
104D MET* 4.5 3.2 - - - +
105D ASP* 3.6 13.7 + - - +
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Residues in contact with GLN 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C PHE* 3.5 47.0 - - + +
58C ASN* 3.7 26.2 + - - +
70C THR 4.4 3.9 + - - +
71C GLN* 2.9 36.7 + - + +
98D ILE* 3.0 20.7 + - + +
99D LEU* 3.8 5.8 - - + +
101D ASN* 1.3 75.8 - - - +
103D ALA* 1.3 65.8 + - - +
104D MET 3.1 1.6 - - - -
105D ASP* 2.8 23.5 + - - +
106D VAL* 2.9 22.2 + - + +
137D PHE* 5.7 2.0 - - + -
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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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99D LEU* 2.6 32.6 + - + +
100D GLU* 3.9 4.5 - - - +
102D GLN* 1.3 72.2 - - - +
104D MET* 1.3 60.9 + - - +
106D VAL* 3.4 7.0 + - - +
107D SER* 2.9 24.0 + - - -
137D PHE* 4.7 8.0 - - + -
158D LEU* 4.1 24.7 - - + +
159D ALA* 5.0 0.7 - - - +
162D VAL* 3.6 24.0 - - + +
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Residues in contact with MET 104 (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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12D LEU* 4.2 20.2 - - + -
72D SER* 3.7 26.5 - - - +
73D ASN* 3.5 42.0 - - - +
100D GLU 3.2 9.3 + - - +
101D ASN* 4.5 4.0 - - - +
102D GLN 3.1 0.6 - - - -
103D ALA* 1.3 80.5 - - - +
105D ASP* 1.3 56.0 + - - +
107D SER* 2.9 13.8 + - - -
108D ASN* 2.8 39.1 + - - +
158D LEU* 4.2 18.4 - - + -
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Residues in contact with ASP 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ASN* 4.9 3.8 + - - -
71C GLN* 3.1 25.4 + - - -
101D ASN 3.6 8.9 + - - +
102D GLN* 2.8 23.7 + - - +
104D MET* 1.3 79.5 - - - +
106D VAL* 1.3 55.9 + - + +
108D ASN* 3.6 11.1 + - - +
109D GLN* 3.0 47.0 + - - +
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Residues in contact with VAL 106 (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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102D GLN* 2.9 20.8 + - + +
103D ALA* 3.7 5.6 - - - +
105D ASP* 1.3 73.9 - - + +
107D SER* 1.3 66.3 + - - +
109D GLN* 3.1 12.4 + - + +
110D LEU* 3.0 21.7 + - - +
126D TYR* 3.7 9.7 + - - +
133D MET* 4.4 15.9 - - + -
134D MET* 6.1 1.8 - - - -
137D PHE* 4.1 25.1 - - + -
162D VAL* 4.0 9.9 - - + -
166D HIS* 3.4 28.0 - - + -
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Residues in contact with SER 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D LEU* 5.5 8.1 - - - -
103D ALA 2.9 13.5 + - - -
104D MET* 2.9 21.2 + - - -
106D VAL* 1.3 78.9 - - - +
108D ASN* 1.3 62.3 + - - +
110D LEU* 3.0 7.7 + - - +
111D ALA* 2.8 29.7 + - - +
161D ASP* 5.3 2.8 + - - -
162D VAL* 3.8 15.4 - - - +
165D LEU* 5.1 12.6 - - - +
166D HIS* 5.7 0.9 - - - -
208D TYR* 3.9 3.8 + - - -
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Residues in contact with ASN 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ARG* 5.1 6.4 + - - +
12D LEU* 6.0 3.6 - - - +
104D MET* 2.8 28.6 + - - +
105D ASP* 4.0 10.3 - - - +
107D SER* 1.3 76.6 - - - +
109D GLN* 1.3 57.8 + - - +
111D ALA* 4.3 8.5 - - - +
112D ARG* 2.8 56.8 + - - +
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Residues in contact with GLN 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D ASP* 3.0 44.1 + - - +
106D VAL* 3.1 13.1 + - - +
108D ASN* 1.3 77.5 - - + +
110D LEU* 1.3 57.8 + - - +
112D ARG* 4.4 15.6 - - - +
113D VAL* 3.8 17.8 + - - +
126D TYR* 4.0 34.4 + - + -
133D MET* 4.4 10.2 - - - +
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Residues in contact with LEU 110 (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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106D VAL 3.0 10.0 + - - +
107D SER* 3.0 9.4 + - - +
109D GLN* 1.3 78.1 - - - +
111D ALA* 1.3 65.0 + - - +
112D ARG 3.3 0.2 - - - -
113D VAL* 3.3 5.3 + - + +
114D CYS* 3.0 37.2 + - - -
126D TYR* 3.9 18.4 - - + -
165D LEU* 4.1 33.4 - - + +
166D HIS* 4.2 18.6 - - + +
169D PHE* 3.6 33.7 - - + -
208D TYR* 3.5 14.8 - - + +
214D TRP* 4.4 12.1 - - + -
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Residues in contact with ALA 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ARG* 6.2 0.7 - - - +
107D SER 2.8 15.9 + - - +
108D ASN* 4.0 10.5 - - - +
110D LEU* 1.3 75.8 - - - +
112D ARG* 1.3 64.6 + - - +
114D CYS* 3.1 2.9 + - - +
115D TYR* 2.9 39.7 + - + -
208D TYR* 3.2 34.4 + - + -
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Residues in contact with ARG 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C ASN* 5.2 12.9 + - - +
112C ARG* 3.1 58.2 - - - +
108D ASN* 2.8 48.8 + - - +
109D GLN* 4.5 13.6 - - - +
111D ALA* 1.3 71.9 - - - +
113D VAL* 1.3 64.1 + - - +
115D TYR* 3.1 14.7 + - - +
116D SER* 3.0 21.2 + - - +
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Residues in contact with VAL 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D GLN 3.8 11.7 + - - +
110D LEU* 3.3 20.8 + - + +
111D ALA 3.2 0.6 - - - -
112D ARG* 1.3 79.9 - - - +
114D CYS* 1.3 70.6 + - - +
116D SER* 3.1 28.9 + - - +
119D PHE* 4.4 18.3 - - + -
122D LEU* 3.7 43.9 - - + +
123D LYS* 5.2 5.8 - - - +
125D GLU* 5.9 0.2 - - - +
126D TYR* 4.3 15.0 - - + -
169D PHE* 5.0 6.1 - - + -
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Residues in contact with CYS 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D LEU* 3.0 29.8 + - - +
111D ALA 3.1 4.5 + - - +
113D VAL* 1.3 89.5 - - - +
115D TYR* 1.3 63.2 + - + +
116D SER 3.2 1.6 - - - -
119D PHE* 4.4 5.8 - - - -
169D PHE* 5.0 1.1 - - - -
208D TYR* 4.1 11.7 - - + -
212D ALA* 3.9 0.2 - - - +
213D VAL* 3.1 36.8 + - - +
214D TRP* 3.0 55.0 - - + +
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Residues in contact with TYR 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ARG* 6.0 2.5 - - - -
111D ALA* 2.9 25.7 + - + +
112D ARG* 3.1 7.7 + - - +
114D CYS* 1.3 77.9 - - - +
116D SER* 1.3 60.1 + - - +
117D PRO* 4.0 5.5 - - - +
208D TYR* 3.4 32.1 - + + +
209D THR* 3.0 27.6 + - - +
211D VAL* 4.8 10.1 - - + -
212D ALA* 3.2 37.9 - - + +
213D VAL* 5.4 0.2 - - - -
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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