Contacts of the helix formed by residues 86 - 111 (chain D) in PDB entry 1GUM
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 LEU 86 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C TYR* 3.9 17.7 - - + -
77C ASP* 4.2 32.1 - - + +
78C LYS* 3.9 33.4 - - + +
85D ASN* 1.3 77.3 - - - +
87D LYS* 1.3 61.8 + - - +
89D ARG* 3.2 15.4 - - + +
90D THR* 2.5 53.5 + - - +
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Residues in contact with LYS 87 (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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61C ASP* 4.8 4.9 + - - +
63C MET* 3.9 28.1 - - + +
74C TYR* 3.2 33.3 + - - -
78C LYS* 5.4 4.6 - - - +
85D ASN* 2.7 16.0 + - - +
86D LEU* 1.3 85.2 - - + +
88D GLU* 1.3 65.2 - - + +
90D THR* 3.4 4.6 + - - +
91D LEU* 3.1 28.0 + - + +
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Residues in contact with GLU 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D GLY* 3.6 9.2 - - - -
84D LYS* 3.0 38.2 + - - +
85D ASN* 3.0 35.2 + - - +
87D LYS* 1.3 76.1 - - + +
89D ARG* 1.3 54.8 + - - +
91D LEU* 2.7 30.7 + - + +
92D ILE* 3.0 15.9 + - - +
149D VAL* 4.0 18.2 - - + +
150D GLY* 4.1 25.4 - - - +
152D GLN* 5.2 1.7 + - - -
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Residues in contact with ARG 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ASP* 4.4 2.8 + - - -
89C ARG* 2.9 41.5 - - - +
73D HIS* 5.1 5.5 + - - +
77D ASP* 3.0 41.2 + - - -
82D PHE* 3.5 55.6 + - + +
85D ASN 2.7 22.8 + - - +
86D LEU* 3.2 21.8 - - + +
88D GLU* 1.3 73.1 - - - +
90D THR* 1.3 65.6 + - - +
92D ILE* 3.3 5.7 + - - +
93D ASP* 2.9 25.7 + - + +
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Residues in contact with THR 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C MET* 3.9 23.6 - - + -
65C LEU* 4.2 17.7 - - + -
70C SER* 5.5 3.3 - - - +
74C TYR* 3.8 20.5 - - + +
86D LEU* 2.5 45.0 + - - +
87D LYS* 3.5 8.0 - - - -
88D GLU 3.0 0.2 + - - -
89D ARG* 1.3 74.8 - - - +
91D LEU* 1.3 61.7 + - + +
93D ASP* 3.3 8.7 - - - +
94D MET* 3.1 26.7 + - + +
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Residues in contact with LEU 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C MET* 5.6 8.7 - - + -
87D LYS* 3.1 20.2 - - + +
88D GLU* 2.7 13.9 + - + +
90D THR* 1.3 68.7 - - + +
92D ILE* 1.3 71.5 + - - +
93D ASP 3.0 1.8 - - - -
94D MET* 3.0 11.2 + - - -
95D TYR* 2.7 53.0 + - + +
149D VAL* 3.8 25.6 - - + -
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Residues in contact with ILE 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D PHE* 4.0 17.5 - - + -
83D GLY* 3.9 22.7 - - - +
88D GLU 3.2 18.6 - - - +
89D ARG* 3.5 7.0 - - - +
91D LEU* 1.3 75.8 - - - +
93D ASP* 1.3 53.9 + - - +
95D TYR* 3.2 3.1 + - - +
96D VAL* 2.7 44.6 + - + +
149D VAL* 4.0 21.3 - - + +
154D SER* 3.2 28.9 - - - +
155D LEU* 4.1 9.2 - - + +
156D ALA* 3.7 29.4 - - + +
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Residues in contact with ASP 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C SER* 3.1 29.8 + - - +
73C HIS* 3.3 29.8 + - - +
73D HIS* 4.3 4.1 + - - -
82D PHE* 4.3 15.7 - - + -
89D ARG* 2.9 18.8 + - + +
90D THR* 3.3 9.5 - - - +
92D ILE* 1.3 79.1 - - - +
94D MET* 1.3 64.0 + - - +
96D VAL* 3.0 7.3 + - - +
97D GLU* 2.8 38.8 + - - +
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Residues in contact with MET 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LEU* 4.4 16.8 - - + -
52C PHE* 3.8 7.0 - - - -
64C LYS 3.6 5.8 - - - +
65C LEU* 2.8 42.2 - - + -
66C VAL* 2.7 51.1 - - + +
67C GLN* 4.2 3.7 - - + +
70C SER* 3.6 16.2 - - - -
90D THR* 3.1 16.5 + - + +
91D LEU* 3.0 15.3 + - - +
93D ASP* 1.3 78.2 - - - +
95D TYR* 1.3 70.7 + - + +
97D GLU* 3.2 1.7 + - - +
98D GLY 2.9 20.1 + - - -
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Residues in contact with TYR 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LEU* 4.3 23.1 - - + -
52C PHE* 4.5 6.1 - + - -
91D LEU* 2.7 48.6 + - + +
92D ILE 3.5 5.2 - - - +
94D MET* 1.3 76.7 - - + +
96D VAL* 1.3 64.0 + - - +
98D GLY* 3.4 0.7 + - - -
99D THR* 2.7 30.8 + - - +
135D VAL* 5.3 0.2 - - + -
136D PHE* 4.0 19.4 - + + -
139D ILE* 3.4 32.1 - - + +
148D LEU* 4.2 15.7 - - + -
149D VAL* 3.5 29.5 - - + +
156D ALA* 3.7 21.5 - - + -
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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
----------------------------------------------------------
72D LEU* 5.4 3.4 - - + -
73D HIS* 5.8 4.0 - - + +
92D ILE* 2.7 28.0 + - + +
93D ASP* 3.4 6.1 - - - +
95D TYR* 1.3 77.7 - - - +
97D GLU* 1.3 70.5 + - - +
99D THR* 3.1 5.6 + - - -
100D LEU* 2.9 39.2 + - + +
155D LEU* 4.1 20.9 - - + +
156D ALA* 3.5 31.2 - - - +
159D ILE* 4.2 17.7 - - + -
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Residues in contact with GLU 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C GLN* 3.3 28.9 - - + +
69C ARG* 4.0 14.6 - - + +
70C SER* 2.8 30.1 - - - +
73C HIS* 4.7 0.2 - - - -
69D ARG* 3.0 39.5 + - - +
73D HIS* 3.8 17.2 + - - -
93D ASP* 2.8 25.6 + - - +
96D VAL* 1.3 77.8 - - - +
98D GLY* 1.3 65.2 + - - +
100D LEU* 3.2 6.9 + - - +
101D ASP* 3.0 26.2 + - - +
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Residues in contact with GLY 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C PHE* 3.7 19.1 - - - -
67C GLN* 3.6 19.6 - - - -
94D MET 2.9 11.1 + - - -
97D GLU* 1.3 77.2 - - - +
99D THR* 1.3 63.5 + - - +
101D ASP* 2.9 18.3 + - - +
102D LEU 3.3 1.0 + - - -
132D TYR* 3.3 20.4 - - - -
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Residues in contact with THR 99 (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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52C PHE* 5.1 0.4 - - - -
95D TYR 2.7 19.7 + - - -
96D VAL* 3.1 4.6 + - - -
98D GLY* 1.3 76.1 - - - +
100D LEU* 1.3 58.3 + - - +
102D LEU* 2.8 13.3 + - + +
103D LEU* 2.7 25.9 + - - +
132D TYR* 4.5 4.0 - - - -
136D PHE* 3.7 18.5 - - + -
156D ALA 5.3 1.4 + - - -
159D ILE* 4.0 19.1 - - + +
160D LEU* 4.1 18.4 + - + +
163D THR* 3.4 31.6 - - + +
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Residues in contact with LEU 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D SER* 4.6 7.6 - - - +
68D THR* 6.1 2.2 - - + -
69D ARG* 3.9 47.1 - - + +
72D LEU* 4.6 12.3 - - + -
96D VAL* 2.9 35.2 + - + +
97D GLU* 3.4 9.6 - - - +
99D THR* 1.3 76.3 - - - +
101D ASP* 1.3 63.9 + - - +
103D LEU* 3.6 28.5 - - + +
104D GLU* 3.1 28.5 + - - +
159D ILE* 4.0 13.2 - - + -
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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
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54C GLN* 4.4 6.2 + - - +
67C GLN* 3.3 28.5 + - - +
69D ARG* 4.8 10.6 + - - -
97D GLU 3.0 15.7 + - - +
98D GLY 2.9 9.5 + - - +
99D THR 2.9 0.6 - - - -
100D LEU* 1.3 80.8 - - - +
102D LEU* 1.3 60.1 + - - +
104D GLU* 3.3 16.5 - - - +
105D LEU* 4.2 7.8 - - - +
132D TYR* 3.7 13.8 + - - +
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Residues in contact with LEU 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D GLY 3.3 2.8 + - - +
99D THR* 2.8 14.8 + - + +
101D ASP* 1.3 73.0 - - - +
103D LEU* 1.3 66.1 + - - +
104D GLU 2.9 5.3 + - - -
105D LEU* 3.0 33.3 + - + +
106D LEU* 3.9 3.0 + - + +
124D MET* 4.2 7.9 - - + +
127D LYS* 4.1 9.6 - - + -
128D ALA* 4.1 21.8 - - + +
132D TYR* 4.0 45.5 + - + -
133D PHE* 4.5 7.0 - - + -
160D LEU* 6.1 1.3 - - + -
163D THR* 4.0 13.7 - - + -
167D LEU* 3.9 26.2 - - + -
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Residues in contact with LEU 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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18D SER* 3.9 6.1 - - - +
99D THR 2.7 13.7 + - - +
100D LEU* 3.3 27.3 + - + +
102D LEU* 1.3 77.1 - - - +
104D GLU* 1.3 64.4 + - - +
106D LEU* 2.8 38.4 + - + +
107D ILE* 3.0 26.0 + - + +
159D ILE* 4.8 0.7 - - + -
162D GLN* 3.7 35.4 - - + +
163D THR* 3.7 30.9 - - + +
166D ALA* 4.8 3.8 - - + -
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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
----------------------------------------------------------
15D ARG* 2.7 43.5 + - - -
69D ARG* 5.7 2.8 + - - -
100D LEU* 3.1 13.9 + - - +
101D ASP* 3.3 19.7 - - - +
103D LEU* 1.3 80.3 - - - +
105D LEU* 1.3 60.1 + - + +
107D ILE* 3.0 8.6 + - - +
108D MET* 2.8 56.8 + - + +
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Residues in contact with LEU 105 (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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101D ASP 4.2 9.4 - - - +
102D LEU* 3.3 26.0 - - + +
104D GLU* 1.3 80.7 - - + +
106D LEU* 1.3 61.8 + - + +
108D MET* 3.9 25.5 - - + +
109D HIS* 3.2 24.3 + - - +
120D GLU* 4.9 8.7 - - - +
123D ASN* 4.5 8.3 - - - +
124D MET* 3.5 46.0 - - + +
127D LYS* 4.4 14.6 - - + -
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Residues in contact with LEU 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 LEU 4.8 2.9 - - - +
103D LEU* 2.8 26.6 + - + +
105D LEU* 1.3 82.4 - - + +
107D ILE* 1.3 64.3 + - + +
109D HIS* 3.2 4.0 - - - +
110D PRO* 3.1 20.1 - - - +
124D MET* 3.7 27.8 - - + -
163D THR* 4.2 5.2 - - + +
166D ALA* 3.5 37.9 - - + +
167D LEU* 3.8 24.2 - - + +
170D LYS* 4.2 21.1 + - + +
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Residues in contact with ILE 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D GLY* 3.6 28.7 - - - +
15D ARG* 4.0 51.4 - - + +
18D SER* 6.0 0.7 - - - +
103D LEU* 3.0 31.4 + - + +
104D GLU* 3.3 15.0 - - - +
106D LEU* 1.3 80.0 - - + +
108D MET* 1.3 60.6 + - + +
110D PRO* 3.5 11.7 - - - +
111D PHE* 4.1 10.4 - - - -
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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
----------------------------------------------------------
15D ARG* 5.9 0.2 - - - +
104D GLU* 2.8 49.3 + - + +
105D LEU* 3.9 28.7 - - + +
107D ILE* 1.3 73.9 - - + +
109D HIS* 1.3 68.8 + - - +
110D PRO* 3.2 2.5 - - - -
111D PHE* 2.9 23.5 + - - +
112D LEU* 3.8 18.8 - - + +
120D GLU* 5.3 8.5 - - - +
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Residues in contact with HIS 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D LEU 3.2 12.1 + - - +
106D LEU 3.2 11.2 - - - +
108D MET* 1.3 78.1 - - - +
110D PRO* 1.3 68.9 - - + +
111D PHE 2.9 1.7 + - - -
112D LEU* 3.0 19.1 + - + +
117D GLN* 2.9 69.2 + - + +
118D GLN* 6.1 0.2 - - - -
120D GLU* 4.2 11.7 - - + -
121D VAL* 3.6 11.0 - - + +
124D MET* 3.7 20.4 - - + -
170D LYS* 2.7 32.8 + - - +
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Residues in contact with PRO 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D LEU 3.1 11.4 - - - +
107D ILE* 3.5 9.2 - - - +
108D MET 3.2 4.7 - - - -
109D HIS* 1.3 102.1 - - + +
111D PHE* 1.3 72.0 + - + +
112D LEU 3.2 5.6 + - - +
117D GLN* 3.7 13.0 + - - +
170D LYS* 5.2 2.5 - - - +
208D PRO* 4.0 29.6 - - + +
212D TYR* 5.8 0.2 - - + -
213D VAL* 4.2 25.5 - - + +
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Residues in contact with PHE 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D ILE 4.1 11.2 - - - -
108D MET* 2.9 16.1 + - - +
110D PRO* 1.3 96.1 - - + +
112D LEU* 1.3 65.6 - - + +
113D LYS* 4.0 6.2 + - - +
212D TYR* 4.2 21.3 - + - -
213D VAL* 3.9 22.7 - - + -
216D VAL* 3.7 31.9 - - + -
217D TYR* 3.5 40.1 + + - +
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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