Contacts of the helix formed by residues 84 - 106 (chain D) in PDB entry 1SHZ
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 PHE 84 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D LYS* 3.6 29.2 - - - -
69D ARG* 6.0 0.2 - - - -
76D PHE* 4.3 19.1 - + - -
80D ALA 4.1 12.8 - - - -
81D ARG 3.2 9.8 + - - +
82D GLU 3.0 1.4 - - - -
83D GLU* 1.3 90.5 - - + +
85D ARG* 1.3 66.5 + - - +
86D PRO* 3.2 3.1 - - - -
87D THR* 2.9 10.6 + - - +
88D ILE* 2.8 38.1 + - + +
191D PRO* 4.4 1.6 - - + -
196D ILE* 3.7 36.3 - - + -
199D ALA* 4.0 19.5 - - + -
201D ARG* 3.8 22.0 - - - -
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Residues in contact with ARG 85 (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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82D GLU* 3.1 51.5 + - - +
84D PHE* 1.3 79.1 - - - +
86D PRO* 1.3 70.6 - - + +
88D ILE* 3.3 4.6 + - - +
89D TYR* 3.1 51.5 + - + +
139D THR* 3.4 27.3 + - - +
188D ASP* 5.0 6.4 - - - +
189D TYR* 2.9 34.0 + - + +
191D PRO* 3.7 17.9 - - + +
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Residues in contact with PRO 86 (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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82D GLU 3.4 10.5 - - - +
83D GLU* 3.5 13.9 - - - +
84D PHE 3.4 1.3 - - - -
85D ARG* 1.3 100.1 - - + +
87D THR* 1.3 60.7 + - + +
89D TYR* 3.8 0.7 + - + +
90D SER* 3.2 16.8 + - - -
131D MET* 6.1 2.2 - - + -
136D MET* 3.5 23.0 - - + -
137D VAL 3.1 44.0 + - - +
138D GLU* 5.5 1.6 - - - -
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Residues in contact with THR 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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83D GLU 3.7 18.2 - - - +
84D PHE* 2.9 15.8 + - + +
86D PRO* 1.3 77.9 - - + +
88D ILE* 1.3 62.0 + - - +
89D TYR 3.2 0.2 - - - -
90D SER* 3.4 2.2 + - - -
91D ASN* 2.8 39.2 + - - -
135D GLY 3.6 17.0 - - - +
136D MET* 5.4 3.4 - - + -
199D ALA* 4.2 11.4 - - - +
200D ARG 4.3 7.0 + - - -
201D ARG* 4.0 31.6 - - - +
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Residues in contact with ILE 88 (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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84D PHE* 2.8 20.9 + - + +
85D ARG* 3.7 4.3 - - - +
87D THR* 1.3 74.2 - - - +
89D TYR* 1.3 66.7 + - + +
91D ASN* 3.1 12.4 - - - +
92D VAL* 3.0 21.9 + - - +
177D PHE* 3.4 39.0 - - + -
184D LEU* 4.2 14.6 - - + -
189D TYR* 3.7 23.1 - - + +
191D PRO* 3.7 28.5 - - + -
195D ASP* 4.1 15.5 - - + +
199D ALA* 4.2 13.0 - - + -
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Residues in contact with TYR 89 (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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85D ARG* 3.1 43.5 + - + +
86D PRO 3.8 4.7 - - - +
88D ILE* 1.3 78.1 - - + +
90D SER* 1.3 63.5 + - - +
92D VAL* 3.0 13.8 + - - +
93D ILE* 3.0 17.6 + - - +
137D VAL* 3.5 26.5 - - + +
139D THR* 3.6 22.8 + - + +
142D PHE* 3.4 55.1 - + + -
184D LEU* 3.0 34.8 + - + -
186D VAL 4.5 2.6 + - - -
189D TYR* 3.4 25.0 - + - +
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Residues in contact with SER 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D PRO 3.2 16.2 + - - -
87D THR 3.6 6.1 - - - -
89D TYR* 1.3 78.5 - - - +
91D ASN* 1.3 63.6 + - - +
93D ILE* 4.7 2.0 - - - +
94D LYS* 3.0 57.4 + - - +
135D GLY* 3.6 23.6 - - - -
136D MET 4.0 2.0 + - - -
137D VAL* 4.0 16.4 - - - +
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Residues in contact with ASN 91 (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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87D THR* 2.8 23.5 + - - -
88D ILE* 3.1 16.9 - - - +
90D SER* 1.3 77.1 + - - +
92D VAL* 1.3 61.4 + - - +
94D LYS* 4.6 1.4 - - - +
95D GLY* 3.2 15.2 + - - -
174D VAL* 3.6 21.3 - - + +
177D PHE* 4.4 13.2 - - + -
199D ALA* 3.7 10.9 - - - +
200D ARG* 3.3 49.9 + - - +
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Residues in contact with VAL 92 (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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88D ILE 3.4 14.4 - - - +
89D TYR* 3.0 6.8 + - - +
91D ASN* 1.3 74.5 - - - +
93D ILE* 1.3 61.6 + - - +
95D GLY* 3.0 3.0 + - - -
96D MET* 2.8 28.1 + - - +
142D PHE* 4.5 8.1 - - + -
149D ILE* 4.2 18.2 - - + -
174D VAL* 5.0 7.0 - - - +
177D PHE* 3.5 33.0 - - + -
178D LEU* 3.5 29.1 - - + +
181D LEU* 4.3 8.7 - - + -
184D LEU* 4.5 11.9 - - + -
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Residues in contact with ILE 93 (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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89D TYR 3.0 12.7 + - - +
90D SER* 4.2 3.4 - - - +
92D VAL* 1.3 71.1 - - - +
94D LYS* 1.3 69.1 + - + +
95D GLY 2.9 0.9 - - - -
96D MET* 3.2 6.5 + - - +
97D ARG* 2.9 32.9 + - + +
122D LEU* 4.4 10.0 - - + +
125D PHE* 3.7 41.3 - - + -
137D VAL* 3.8 26.7 - - + -
141D VAL 5.1 1.6 - - - +
142D PHE* 3.6 31.6 - - + -
145D TYR* 5.0 8.3 - - + -
149D ILE* 4.1 20.6 - - + -
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Residues in contact with LYS 94 (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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90D SER* 3.0 38.5 + - - +
91D ASN* 4.6 1.6 - - - +
93D ILE* 1.3 80.5 - - + +
95D GLY* 1.3 61.8 + - - +
97D ARG* 3.5 11.3 + - - +
98D VAL* 3.1 29.1 + - - +
125D PHE* 4.4 15.0 - - + -
127D THR* 3.5 21.9 + - - +
132D ALA* 2.9 28.5 + - - +
133D ALA 5.8 0.4 - - - -
135D GLY* 4.4 6.3 - - - -
137D VAL* 5.7 1.2 - - - +
26F ALA* 3.8 29.2 - - + -
27F GLU 5.5 1.6 - - - +
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Residues in contact with GLY 95 (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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91D ASN 3.2 14.6 + - - -
92D VAL 3.0 7.1 + - - -
93D ILE 2.9 1.0 - - - -
94D LYS* 1.3 75.4 - - - +
96D MET* 1.3 65.7 + - - +
98D VAL* 3.1 6.5 + - - +
99D LEU* 3.0 23.4 + - - +
170D LEU* 3.7 13.9 - - - +
174D VAL* 4.1 17.5 - - - -
178D LEU* 6.1 0.4 - - - -
26F ALA* 5.9 0.9 - - - -
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Residues in contact with MET 96 (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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92D VAL 2.8 17.7 + - - +
93D ILE* 3.2 4.7 + - - +
95D GLY* 1.3 72.4 - - - +
97D ARG* 1.3 52.0 + - - +
99D LEU* 2.9 18.9 + - + +
100D VAL* 2.8 39.0 + - + +
122D LEU* 3.4 29.8 - - + -
149D ILE* 3.8 28.9 - - + +
152D LEU* 3.8 20.0 - - + -
153D TRP* 3.9 16.6 - - + +
158D ILE* 4.1 8.3 - - - -
178D LEU* 3.6 38.9 - - + +
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Residues in contact with ARG 97 (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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93D ILE* 2.9 29.0 + - + +
94D LYS* 3.6 11.1 - - - +
96D MET* 1.3 74.1 - - - +
98D VAL* 1.3 64.6 - - + +
100D VAL* 3.3 11.4 - - - +
101D ASP* 3.1 24.8 + - - +
122D LEU* 3.1 32.1 - - + +
123D MET* 3.0 43.0 + - - +
125D PHE* 3.6 26.3 + - - -
127D THR* 4.1 24.8 - - - +
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Residues in contact with VAL 98 (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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94D LYS 3.1 16.9 + - - +
95D GLY* 3.5 7.2 - - - +
97D ARG* 1.3 76.9 - - + +
99D LEU* 1.3 58.2 + - - +
101D ASP* 3.9 2.7 - - - +
102D ALA* 3.0 26.3 + - - +
168D PHE* 3.8 29.8 - - + -
169D GLN 3.8 13.5 - - - +
170D LEU* 4.0 10.3 - - + -
23F ILE* 4.5 3.1 - - + +
24F ILE 3.9 14.1 - - - +
25F GLY* 3.4 27.4 - - - -
26F ALA* 3.4 11.2 - - + +
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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
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95D GLY 3.0 14.5 + - - +
96D MET* 2.9 27.8 + - - +
98D VAL* 1.3 76.3 - - - +
100D VAL* 1.3 62.8 + - - +
102D ALA* 3.3 3.2 + - - +
103D ARG* 3.1 21.0 + - - +
153D TRP* 4.2 15.7 - - + -
158D ILE* 3.6 27.4 - - + +
161D ALA* 4.1 6.5 - - + +
162D TYR* 4.1 24.7 - - + +
168D PHE* 4.1 11.9 - - + -
170D LEU* 3.7 30.5 - - + -
174D VAL* 5.2 1.3 - - + -
178D LEU* 4.4 9.0 - - + -
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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
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96D MET* 2.8 28.0 + - + +
97D ARG* 3.3 5.4 - - - +
99D LEU* 1.3 71.8 - - - +
101D ASP* 1.3 68.7 + - - +
103D ARG* 3.1 14.8 + - - +
104D GLU* 3.1 20.5 + - - +
110D TRP* 5.5 5.6 - - + -
119D GLY* 4.1 14.4 - - - +
122D LEU* 4.9 3.1 - - + -
123D MET* 3.1 43.1 - - + +
152D LEU* 3.8 28.7 - - + -
158D ILE* 5.0 7.9 - - + -
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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
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97D ARG 3.1 9.0 + - - +
98D VAL* 3.9 5.4 - - - +
100D VAL* 1.3 83.2 - - - +
102D ALA* 1.3 56.8 + - - +
104D GLU* 3.4 9.3 + - - +
105D LYS* 2.9 64.1 + - - +
123D MET* 3.2 27.9 - - + +
23F ILE* 4.1 13.5 - - + +
24F ILE* 4.3 14.0 + - - +
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Residues in contact with ALA 102 (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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98D VAL 3.0 19.6 + - - +
99D LEU 3.7 4.7 - - - +
100D VAL 3.2 0.2 - - - -
101D ASP* 1.3 76.7 - - - +
103D ARG* 1.3 58.8 + - - +
105D LYS* 4.4 2.7 - - - -
106D LEU* 2.9 40.4 + - + +
161D ALA* 4.7 2.9 - - + -
168D PHE* 3.6 42.2 - - + -
23F ILE* 4.1 12.1 - - + +
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Residues in contact with ARG 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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152C ARG* 5.8 1.0 - - - +
155C GLU* 3.3 26.1 + - - +
99D LEU 3.1 13.4 + - - +
100D VAL* 3.3 15.9 + - - +
102D ALA* 1.3 80.6 - - - +
104D GLU* 1.3 97.1 + - - +
107D HIS* 3.3 1.5 + - - +
108D ILE* 3.0 60.7 + - + +
109D PRO* 5.6 0.2 - - - +
110D TRP* 3.1 64.7 - - - +
116D GLN* 4.4 0.6 + - - -
157D GLY 4.0 24.0 - - - +
158D ILE* 4.4 12.1 - - + +
161D ALA* 4.5 7.1 - - + +
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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
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47C GLN* 5.3 0.3 + - - -
155C GLU* 3.7 28.5 - - - +
158C ARG* 3.2 52.9 + - - +
159C SER* 4.4 8.0 + - - +
162C LEU* 5.8 3.5 - - + +
100D VAL 3.1 6.7 + - - +
101D ASP* 3.8 11.8 - - - +
103D ARG* 1.3 99.9 + - - +
105D LYS* 1.3 70.2 + - + +
107D HIS* 2.9 28.9 + - - -
123D MET* 5.8 2.8 - - - +
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Residues in contact with LYS 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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270A LYS* 4.5 11.1 + - - -
162C LEU* 3.5 33.4 - - + +
101D ASP* 2.9 55.7 + - - +
102D ALA 4.1 1.6 - - - +
104D GLU* 1.3 89.7 + - - +
106D LEU* 1.3 60.2 + - - +
107D HIS* 3.3 12.2 + - - -
22F SER* 3.9 18.8 - - - +
23F ILE* 3.8 26.9 - - + +
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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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266A HIS* 5.5 2.7 - - + -
270A LYS* 4.8 7.5 - - - +
102D ALA* 2.9 34.0 + - + +
105D LYS* 1.3 71.0 - - - +
107D HIS* 1.3 71.3 + - - +
108D ILE* 3.5 28.2 + - + +
161D ALA* 5.0 1.8 - - - -
164D ARG* 4.0 38.6 + - + +
167D GLU* 4.6 14.4 - - + +
168D PHE* 4.1 23.8 - - + -
23F ILE* 4.2 19.1 - - + -
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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
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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