Contacts of the helix formed by residues 94 - 119 (chain D) in PDB entry 3GTU
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 94 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C HIS* 4.9 5.6 - - + -
78C TYR* 3.2 32.5 - - + +
81C ARG* 2.8 39.3 + - - +
82C LYS* 6.1 1.3 - - - -
93D THR* 1.3 71.3 - - - +
95D GLU* 1.3 67.8 + - - +
97D LYS* 3.4 11.7 + - - +
98D ILE* 3.0 46.4 + - + +
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Residues in contact with GLU 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C HIS* 3.5 28.7 + - + +
93D THR* 3.1 16.1 + - - +
94D GLU* 1.3 84.5 + - - +
96D GLU* 1.3 63.1 + - + +
98D ILE* 3.6 8.8 + - - +
99D ARG* 3.3 28.2 + - - +
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Residues in contact with GLU 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D GLY* 3.4 13.5 - - - -
92D GLU 2.9 24.3 + - - -
93D THR* 2.8 28.3 + - - +
95D GLU* 1.3 76.8 - - + +
97D LYS* 1.3 64.1 + - - +
99D ARG* 3.3 5.4 + - - +
100D VAL* 3.0 28.1 + - - +
152D ALA* 3.4 25.5 - - + +
154D GLU 4.8 2.4 + - - -
155D LYS* 3.2 46.5 + - - +
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Residues in contact with LYS 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ARG* 3.2 40.8 - - - +
91D GLY* 3.2 30.3 - - - +
92D GLU* 3.7 16.2 + - - +
93D THR 2.9 14.6 + - - +
94D GLU* 3.7 9.1 + - - +
96D GLU* 1.3 74.7 - - - +
98D ILE* 1.3 65.5 + - - +
100D VAL* 3.1 6.6 + - - +
101D ASP* 3.0 30.3 + - - +
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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
----------------------------------------------------------
67C HIS* 3.8 32.1 - - + +
68C LYS 5.8 0.7 - - - +
69C ILE* 3.6 27.4 - - + -
78C TYR* 4.1 16.8 - - + -
81C ARG* 4.3 8.5 - - - +
94D GLU* 3.0 43.5 + - + +
95D GLU* 3.8 7.2 - - - +
97D LYS* 1.3 76.6 - - - +
99D ARG* 1.3 63.4 + - + +
101D ASP* 3.4 4.3 + - - +
102D ILE* 3.0 41.3 + - + +
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Residues in contact with ARG 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ASP* 5.8 0.4 + - - -
95D GLU* 3.3 15.6 + - - +
96D GLU 3.6 7.9 - - - +
97D LYS 3.3 0.2 - - - -
98D ILE* 1.3 78.6 - - + +
100D VAL* 1.3 57.5 + - - +
102D ILE* 3.3 6.0 + - + +
103D ILE* 2.9 35.6 + - - +
144D PHE* 3.0 63.9 + - + -
145D LEU* 4.6 1.0 - - - +
148D PHE* 3.3 36.4 - - - -
151D PHE* 2.7 41.7 + - - +
152D ALA* 4.1 15.7 - - - -
153D GLY* 4.4 1.1 - - - +
159D VAL* 5.7 0.4 - - - -
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Residues in contact with VAL 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D ARG* 4.6 3.4 - - - +
90D CYS* 5.4 0.9 - - + -
91D GLY 3.8 20.6 - - - +
96D GLU 3.0 19.0 + - - +
97D LYS* 3.4 9.9 - - - +
99D ARG* 1.3 73.5 - - - +
101D ASP* 1.3 66.1 + - - +
103D ILE 3.4 0.3 + - - -
104D GLU* 2.9 28.4 + - - +
152D ALA* 4.1 9.0 - - + -
157D THR* 3.8 21.8 - - - +
158D PHE* 3.6 36.6 - - + -
159D VAL* 3.2 20.9 - - + +
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Residues in contact with ASP 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ALA* 3.8 20.3 - - + +
77C ARG* 3.6 22.5 + - - +
81C ARG* 2.7 33.4 + - - -
81D ARG* 3.0 29.8 + - - +
97D LYS* 3.0 14.4 + - - +
98D ILE* 3.7 7.4 - - - +
100D VAL* 1.3 76.7 - - - +
102D ILE* 1.3 63.3 + - - +
104D GLU* 3.5 1.4 + - - +
105D ASN* 2.8 32.0 + - - +
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Residues in contact with ILE 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ASP* 5.1 9.4 - - + +
56C PHE* 3.8 31.0 - - + -
68C LYS 4.5 5.4 - - - +
69C ILE* 3.9 33.0 - - + -
70C THR* 4.0 18.6 - - - +
71C GLN* 4.1 7.0 - - + +
74C ALA* 4.2 5.8 - - + -
98D ILE* 3.0 35.0 + - + +
99D ARG* 3.7 7.0 - - + +
100D VAL 3.3 0.2 - - - -
101D ASP* 1.3 79.1 - - - +
103D ILE* 1.3 58.4 + - + +
105D ASN* 3.3 1.7 + - - +
106D GLN* 2.8 31.3 + - + +
144D PHE* 5.1 7.0 - - + -
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Residues in contact with ILE 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C PHE* 4.0 19.7 - - + -
99D ARG 2.9 21.8 + - - +
100D VAL 3.9 2.9 - - - +
102D ILE* 1.3 74.4 - - - +
104D GLU* 1.3 63.1 + - - +
106D GLN* 4.1 2.9 - - + -
107D VAL* 2.8 32.9 + - + +
141D PHE* 4.3 6.7 - - + -
144D PHE* 3.4 36.8 - - + -
151D PHE* 3.8 21.1 - - + +
159D VAL* 3.6 23.6 - - + +
163D THR* 3.4 24.9 - - - +
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Residues in contact with GLU 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ARG* 4.6 1.4 + - - -
100C GLU* 4.3 10.7 - - - +
101C ASN* 6.0 0.2 - - - -
77D ASN* 3.4 38.3 + - - +
81D ARG* 2.8 46.8 + - - +
100D VAL 2.9 18.6 + - - +
101D ASP 3.5 3.8 - - - +
103D ILE* 1.3 75.4 - - - +
105D ASN* 1.3 75.3 + - - +
107D VAL* 3.1 23.0 - - - +
108D MET* 3.4 8.3 + - - +
158D PHE* 3.5 15.1 - - + -
159D VAL* 3.9 10.9 - - + +
162D LEU* 4.4 4.9 - - + -
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Residues in contact with ASN 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C GLN* 3.5 28.9 - - + +
73C ASN* 2.9 45.5 + - - +
74C ALA* 3.9 9.5 - - - +
77C ARG* 5.9 0.6 - - - +
77D ASN* 5.5 2.4 + - - +
101D ASP* 2.8 25.8 + - - +
102D ILE 3.3 1.6 + - - -
104D GLU* 1.3 87.6 + - - +
106D GLN* 1.3 65.7 + - - +
108D MET* 3.1 11.6 + - - +
109D ASP* 3.0 24.9 + - - +
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Residues in contact with GLN 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C PHE* 3.6 49.8 - - + +
58C ASN* 5.7 1.6 - - - +
70C THR* 5.1 0.3 + - - -
71C GLN* 3.1 27.1 + - - +
102D ILE* 2.8 20.9 + - + +
103D ILE* 3.7 7.9 - - - +
105D ASN* 1.3 78.0 - - - +
107D VAL* 1.3 57.5 + - - +
109D ASP* 3.1 13.7 + - - +
110D PHE* 3.0 25.7 + - - +
137D GLN* 3.4 28.1 + - - +
140D GLN* 4.6 1.6 - - - +
141D PHE* 4.0 10.3 - - + -
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Residues in contact with VAL 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D ILE* 2.8 26.2 + - + +
104D GLU* 3.1 20.9 - - - +
106D GLN* 1.3 68.8 - - - +
108D MET* 1.3 56.7 + - - +
110D PHE* 3.6 7.9 - - - +
111D ARG* 2.7 47.2 + - - +
141D PHE* 4.1 16.6 - - + -
162D LEU* 4.0 26.0 - - + +
163D THR* 3.9 31.9 - - - +
166D ILE* 4.3 12.2 - - + +
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Residues in contact with MET 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C ASN* 4.5 6.1 - - - +
104C MET* 6.6 0.2 - - + -
16D LEU* 5.9 2.2 - - + -
76D SER* 5.7 4.0 - - - -
77D ASN* 3.3 39.3 - - - +
104D GLU 3.7 7.6 - - - +
105D ASN* 3.1 18.3 + - - +
107D VAL* 1.3 83.2 - - + +
109D ASP* 1.3 63.0 + - - +
111D ARG* 3.3 27.1 + - - +
112D THR* 2.8 36.4 + - - +
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Residues in contact with ASP 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ASN* 4.6 5.5 + - - -
71C GLN* 3.1 28.6 + - - +
105D ASN* 3.0 13.6 + - - +
106D GLN* 3.1 15.4 + - - +
108D MET* 1.3 80.6 - - - +
110D PHE* 1.3 63.5 + - - +
112D THR* 3.4 7.3 + - - -
113D GLN* 3.3 27.9 + - - +
137D GLN* 6.2 0.9 - - - +
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Residues in contact with PHE 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D GLN* 3.0 13.2 + - - +
107D VAL* 3.6 10.3 - - - +
109D ASP* 1.3 77.4 - - - +
111D ARG* 1.3 62.3 + - - +
113D GLN* 3.2 24.7 + - - +
114D LEU* 3.3 9.9 + - - +
130D TYR* 3.2 23.8 - + - -
134D LEU* 3.5 21.5 - - + -
137D GLN* 3.8 33.2 - - + +
138D LEU* 3.9 11.9 - - + -
141D PHE* 3.8 26.7 - + + -
166D ILE* 3.8 19.7 - - + -
167D LEU* 4.8 9.4 - - + -
170D ASN* 3.3 22.7 - - - -
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Residues in contact with ARG 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D LEU* 3.6 34.2 - - - +
19D ALA* 5.4 1.2 - - - +
76D SER* 5.6 2.4 - - - -
77D ASN* 4.8 2.4 + - - -
107D VAL* 2.7 29.0 + - - +
108D MET* 3.7 37.8 - - - +
110D PHE* 1.3 69.7 - - - +
112D THR* 1.3 56.2 + - - +
114D LEU* 3.1 4.4 + - + +
115D ILE* 2.8 52.4 + - + +
162D LEU* 3.4 42.2 + - - +
165D ASP* 3.9 22.0 + - - -
166D ILE* 3.7 23.4 - - + +
169D GLN* 5.1 5.1 + - - +
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Residues in contact with THR 112 (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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108D MET* 2.8 30.4 + - - +
109D ASP* 3.5 8.8 - - - -
111D ARG* 1.3 75.2 - - - +
113D GLN* 1.3 59.9 + - + +
115D ILE* 3.2 10.4 + - - +
116D ARG* 2.8 62.7 + - + +
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Residues in contact with GLN 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D ASP* 3.5 14.4 + - - +
110D PHE* 3.2 27.1 + - - +
112D THR* 1.3 77.9 - - + +
114D LEU* 1.3 58.2 + - - +
116D ARG* 3.5 11.3 - - - +
117D LEU* 2.9 29.6 + - - +
130D TYR* 4.1 18.0 - - + -
133D GLU* 5.4 3.3 - - - +
137D GLN* 4.4 13.3 - - - +
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Residues in contact with LEU 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D PHE 3.3 6.4 + - - +
111D ARG* 3.1 9.3 + - + +
113D GLN* 1.3 76.8 - - - +
115D ILE* 1.3 56.0 + - + +
117D LEU* 3.1 9.7 + - + +
118D CYS* 2.7 57.8 + - - -
130D TYR* 3.5 38.8 - - + +
166D ILE* 3.6 24.5 - - + -
169D GLN* 3.8 33.7 - - + +
170D ASN* 4.2 9.0 - - - +
173D PHE* 5.0 9.0 - - + -
218D TRP* 5.3 3.8 - - + -
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Residues in contact with ILE 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D LEU* 5.1 9.4 - - + -
111D ARG* 2.8 50.6 + - + +
112D THR* 3.7 7.0 - - - +
114D LEU* 1.3 72.0 - - + +
116D ARG* 1.3 55.0 + - - +
118D CYS* 3.2 3.3 + - - -
119D TYR* 2.8 61.9 + - + +
169D GLN* 5.9 4.3 - - - +
212D ASN* 6.0 2.7 - - - +
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Residues in contact with ARG 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C LYS* 5.0 15.2 - - - +
112D THR* 2.8 42.9 + - + +
113D GLN* 3.5 9.7 - - - +
115D ILE* 1.3 76.7 - - - +
117D LEU* 1.3 56.6 + - - +
119D TYR* 5.1 1.8 - - - -
120D SER* 2.9 39.1 + - - +
126D LEU* 6.0 4.5 - - + -
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Residues in contact with LEU 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D GLN 2.9 18.4 + - - +
114D LEU* 3.1 11.0 + - + +
116D ARG* 1.3 78.4 - - - +
118D CYS* 1.3 63.8 + - - +
120D SER* 4.0 3.9 + - - -
123D HIS* 2.7 60.8 + - + +
126D LEU* 3.7 20.6 - - + +
127D LYS* 3.5 30.5 - - - +
130D TYR* 3.9 20.0 - - + -
173D PHE* 3.6 22.7 - - + -
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Residues in contact with CYS 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D LEU* 2.7 43.7 + - - +
115D ILE* 3.9 4.9 - - - +
117D LEU* 1.3 82.1 - - - +
119D TYR* 1.3 60.8 + - + +
123D HIS* 3.9 5.8 - - - -
173D PHE* 5.0 1.1 - - - -
212D ASN* 3.6 19.7 - - - +
216D ALA* 4.9 0.2 - - - -
217D GLN* 2.8 33.0 + - - +
218D TRP* 3.2 39.4 + - + -
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Residues in contact with TYR 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D ILE* 2.8 49.6 + - + +
116D ARG* 4.4 1.3 - - - +
118D CYS* 1.3 73.1 - - + +
120D SER* 1.3 68.3 + - - +
121D SER 3.5 0.9 + - - -
212D ASN* 4.1 13.7 - - + +
213D ASN* 3.2 28.6 + - - +
215D MET* 3.7 37.3 - - + +
216D ALA* 3.8 27.8 - - + -
217D GLN* 4.1 14.2 + - - +
----------------------------------------------------------
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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