Contacts of the helix formed by residues 92 - 121 (chain F) in PDB entry 4DEM
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 ASP 92 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89F ARG 5.1 2.4 + - - +
90F LYS* 3.1 10.0 + - - +
91F GLN* 1.3 77.9 - - - +
93F ALA* 1.3 66.9 + - - +
94F ASP* 3.2 14.9 + - - +
95F SER* 2.8 41.3 + - - -
96F LEU* 2.9 21.8 + - - +
98F ARG* 4.3 1.7 + - - -
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Residues in contact with ALA 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F ASP* 1.3 74.2 - - - +
94F ASP* 1.3 69.0 + - - +
96F LEU* 3.4 10.0 + - - +
97F GLN* 3.1 24.0 + - - +
100F TRP* 5.3 1.9 - - - -
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Residues in contact with ASP 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F ASP* 3.2 9.9 + - - +
93F ALA* 1.3 85.4 - - - +
95F SER* 1.3 57.2 + - - +
97F GLN* 3.3 18.8 + - - +
98F ARG* 3.0 50.6 + - - +
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Residues in contact with SER 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F PHE* 3.7 26.2 - - - -
90F LYS 3.8 12.5 + - - -
92F ASP* 2.8 33.8 + - - -
94F ASP* 1.3 74.2 - - - +
96F LEU* 1.3 60.1 + - - +
98F ARG* 2.9 29.7 + - - +
99F ALA 3.0 22.0 + - - -
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Residues in contact with LEU 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F VAL* 6.2 2.7 - - + -
82F PHE* 4.0 16.4 - - + -
83F ARG* 3.5 44.6 - - + +
91F GLN* 3.3 35.7 - - + +
92F ASP 2.9 17.7 + - - +
93F ALA* 3.9 6.3 - - - +
95F SER* 1.3 72.4 - - - +
97F GLN* 1.3 61.4 + - - +
99F ALA* 3.1 7.9 + - + +
100F TRP* 2.9 51.3 + - + +
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Residues in contact with GLN 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F GLN* 3.4 26.0 + - + +
93F ALA 3.1 17.7 + - - +
94F ASP* 3.6 19.0 + - - +
95F SER 3.3 0.2 - - - -
96F LEU* 1.3 77.7 - - - +
98F ARG* 1.3 60.6 + - - +
100F TRP* 3.4 22.2 + - + +
101F THR* 2.9 31.0 + - - +
160F TYR* 3.7 30.5 + - + -
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Residues in contact with ARG 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F ASP* 4.3 1.6 + - - -
94F ASP* 3.0 35.4 + - - +
95F SER* 2.9 38.2 + - - +
96F LEU 3.2 0.2 - - - -
97F GLN* 1.3 76.6 - - - +
99F ALA* 1.3 56.2 + - - +
101F THR* 3.1 7.2 + - - -
102F VAL* 2.9 33.8 + - - +
160F TYR* 3.4 35.1 + - + +
161F CYS* 4.2 7.9 - - - -
164F GLN* 3.4 34.4 + - - +
166F TYR* 3.3 21.1 + - - -
230F MET* 3.6 12.6 - - + -
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Residues in contact with ALA 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F VAL* 3.7 10.1 - - + +
79F VAL* 3.9 13.7 - - + +
82F PHE* 3.7 44.2 - - + -
95F SER 3.0 9.0 + - - +
96F LEU* 3.1 10.3 + - + +
98F ARG* 1.3 75.5 - - - +
100F TRP* 1.3 56.5 + - - +
102F VAL 3.3 0.7 + - - -
103F GLY* 3.0 24.4 + - - -
230F MET* 3.6 12.0 - - - +
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Residues in contact with TRP 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F GLU* 5.2 3.2 + - - -
30F ASP* 4.3 25.7 - - + +
31F PHE* 3.6 14.9 - + + +
34F HIS* 3.1 60.4 - + + -
38F ILE* 5.5 0.2 - - - -
79F VAL* 3.5 35.8 - - + +
83F ARG* 4.8 14.2 - - - +
93F ALA 5.3 1.3 - - - -
96F LEU* 2.9 30.7 + - + +
97F GLN* 3.6 34.5 - - + +
99F ALA* 1.3 72.6 - - - +
101F THR* 1.3 57.8 + - - +
103F GLY 3.4 0.5 + - - -
104F TRP* 3.0 34.0 + - - -
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Residues in contact with THR 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F ILE* 4.2 17.8 - - + +
97F GLN* 2.9 22.4 + - - +
98F ARG* 3.1 6.0 + - - -
100F TRP* 1.3 74.9 - - - +
102F VAL* 1.3 62.8 + - + +
104F TRP* 3.2 4.9 + - - +
105F CYS* 2.9 28.0 + - - -
156F LEU* 3.9 21.9 - - + +
157F LEU* 5.8 0.7 - - - -
160F TYR* 3.7 51.0 - - + -
161F CYS* 5.8 0.4 - - - -
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Residues in contact with VAL 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F VAL* 4.1 8.1 - - + -
98F ARG 2.9 20.1 + - - +
99F ALA 4.0 2.2 - - - +
101F THR* 1.3 76.6 - - + +
103F GLY* 1.3 63.5 + - - +
105F CYS* 3.1 8.1 + - - +
106F VAL* 3.1 22.2 + - - +
157F LEU* 4.0 11.9 - - + -
161F CYS* 4.0 8.5 - - - -
170F LEU* 3.9 19.1 - - + -
174F PHE* 4.2 15.9 - - + -
226F ALA* 3.9 28.0 - - + -
230F MET* 3.8 25.1 - - + -
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Residues in contact with GLY 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F PHE* 3.7 9.2 - - - -
75F GLY* 3.2 34.8 - - - -
78F VAL* 3.8 11.1 - - - +
99F ALA 3.0 12.7 + - - -
100F TRP 3.4 4.0 + - - -
101F THR 3.2 0.2 - - - -
102F VAL* 1.3 76.9 - - - +
104F TRP* 1.3 59.0 + - - +
106F VAL* 3.1 2.9 + - - +
107F GLU* 3.1 16.8 + - - +
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Residues in contact with TRP 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F PHE* 2.9 51.7 + + - -
32F VAL* 4.3 6.7 - - - -
34F HIS* 4.7 5.2 - - + -
35F PHE* 3.5 49.4 - + + +
38F ILE* 3.8 32.8 - - + -
67F ALA* 3.5 22.2 - - + -
68F ILE* 3.9 5.2 - - + -
72F TYR* 3.8 23.3 - + - -
100F TRP 3.0 24.8 + - - +
101F THR 3.2 8.3 + - - +
103F GLY* 1.3 71.9 - - - +
105F CYS* 1.3 59.1 + - - +
107F GLU* 3.2 21.5 + - + +
108F LEU* 2.9 37.9 + - + +
156F LEU* 5.0 1.1 - - + -
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Residues in contact with CYS 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F THR* 2.9 18.9 + - - -
102F VAL* 3.1 12.1 + - - +
104F TRP* 1.3 76.8 - - - +
106F VAL* 1.3 61.9 + - - +
108F LEU* 3.2 6.8 + - - -
109F LEU* 3.0 20.6 + - - +
153F ILE* 3.6 39.7 - - + +
156F LEU* 3.7 20.9 - - - -
157F LEU* 4.1 16.4 - - - -
174F PHE* 3.6 19.8 - - + -
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Residues in contact with VAL 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74F ARG* 3.7 29.6 - - + +
75F GLY* 4.5 4.7 - - - -
78F VAL* 3.7 20.9 - - + -
102F VAL* 3.1 15.2 + - + +
103F GLY 3.1 5.6 + - - +
105F CYS* 1.3 75.0 - - - +
107F GLU* 1.3 56.6 + - - +
109F LEU* 3.3 5.1 + - + +
110F GLN* 3.0 25.8 + - - +
174F PHE* 3.7 21.5 - - + -
218F TYR* 4.2 8.7 - - + +
222F LEU* 3.9 26.5 - - + -
223F PRO* 4.6 5.2 - - + -
226F ALA* 5.5 0.4 - - + -
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Residues in contact with GLU 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F PHE* 4.1 14.1 - - + -
67F ALA* 4.7 6.5 - - - +
70F GLY* 5.9 0.7 - - - -
72F TYR* 3.4 35.5 + - + -
74F ARG* 3.5 10.7 + - - +
75F GLY* 2.8 27.7 + - - -
103F GLY 3.1 16.9 + - - +
104F TRP* 3.2 29.4 + - + +
106F VAL* 1.3 77.1 - - - +
108F LEU* 1.3 57.6 + - - +
110F GLN* 3.3 10.7 + - - +
111F ALA* 2.9 27.9 + - - +
127F ARG* 4.4 16.1 + - - -
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Residues in contact with LEU 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F PHE* 5.5 0.7 - - + -
38F ILE* 4.9 4.7 - - + -
42F LEU* 4.4 4.3 - - + -
63F LEU* 3.5 30.3 - - + -
67F ALA* 4.2 15.3 - - + -
104F TRP* 2.9 24.1 + - + +
105F CYS* 3.2 7.2 + - - +
107F GLU* 1.3 73.2 - - - +
109F LEU* 1.3 61.2 + - - +
111F ALA* 3.2 4.1 + - - +
112F PHE* 2.9 29.6 + - - +
149F LEU* 4.0 16.2 - - + +
152F CYS* 3.8 23.1 - - + -
153F ILE* 3.9 11.0 - - + +
156F LEU* 3.6 31.2 - - + -
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Residues in contact with LEU 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105F CYS 3.0 13.3 + - - +
106F VAL* 3.5 9.6 - - - +
108F LEU* 1.3 75.6 - - - +
110F GLN* 1.3 62.4 + - - +
112F PHE* 3.4 14.8 + - + +
113F PHE* 3.0 55.7 + - + -
150F GLU* 5.1 2.0 - - + -
153F ILE* 3.7 22.8 - - + +
154F TYR* 5.5 0.4 - - - +
174F PHE* 4.6 8.1 - - + -
177F SER* 4.9 4.5 - - - -
178F SER* 3.3 26.5 - - - +
218F TYR* 4.2 10.5 - - + -
222F LEU* 3.5 31.0 - - + -
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Residues in contact with GLN 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F ARG* 3.5 36.3 - - - +
106F VAL 3.0 13.1 + - - +
107F GLU* 3.4 14.6 - - - +
109F LEU* 1.3 77.0 - - - +
111F ALA* 1.3 55.7 + - - +
113F PHE* 3.3 3.0 + - - +
114F LEU* 2.9 37.8 + - - +
126F ARG* 5.0 7.9 - - - +
127F ARG* 3.6 27.8 - - - +
218F TYR* 2.6 37.2 + - - -
401F YS4 5.5 2.8 + - - -
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Residues in contact with ALA 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66F ASN 3.4 24.5 - - - +
67F ALA* 4.2 7.6 - - + -
107F GLU 2.9 16.3 + - - +
108F LEU* 3.2 10.1 + - - +
110F GLN* 1.3 73.9 - - - +
112F PHE* 1.3 65.3 + - - +
114F LEU* 3.6 10.9 - - - +
115F VAL* 3.1 30.5 + - - +
127F ARG* 5.3 0.4 - - - +
149F LEU* 3.8 18.2 - - + -
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Residues in contact with PHE 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F LEU 2.9 13.0 + - - +
109F LEU* 3.4 16.4 - - + +
111F ALA* 1.3 75.7 - - - +
113F PHE* 1.3 93.0 + + - +
115F VAL 3.5 0.2 + - - -
116F ALA* 3.3 19.1 + - + +
146F ALA* 3.1 38.7 - - + +
147F ASN* 3.8 23.8 - - - -
149F LEU* 3.9 4.9 - - + +
150F GLU* 3.6 46.7 - - + +
178F SER* 5.2 0.7 - - - -
182F GLU* 3.9 15.5 - - - -
401F YS4 4.0 18.8 - - + -
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Residues in contact with PHE 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109F LEU* 3.0 45.9 + - + -
110F GLN* 3.6 6.7 - - - +
112F PHE* 1.3 109.8 - + - +
114F LEU* 1.3 56.9 + - - +
117F ASP* 2.8 32.6 + - - +
178F SER* 4.2 7.6 - - - -
181F THR* 3.5 33.2 - - + -
182F GLU* 4.4 7.6 - - + -
218F TYR* 3.8 34.3 - + - +
401F YS4 3.3 45.0 - + + -
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Residues in contact with LEU 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66F ASN* 4.0 12.8 - - - +
110F GLN* 2.9 31.5 + - - +
111F ALA* 3.6 12.3 - - - +
113F PHE* 1.3 72.1 - - - +
115F VAL* 1.3 83.6 + - + +
117F ASP* 4.2 5.6 - - - -
118F ASP* 2.9 32.5 + - - +
126F ARG* 3.7 44.9 - - + +
127F ARG* 3.3 44.4 - - - +
401F YS4 5.6 2.0 - - - +
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Residues in contact with VAL 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F VAL* 5.6 0.7 - - + -
66F ASN* 3.4 41.1 - - + +
111F ALA 3.1 21.1 + - - +
112F PHE 4.0 2.9 - - - +
114F LEU* 1.3 84.6 - - + +
116F ALA* 1.3 61.6 + - - +
118F ASP* 3.6 4.1 + - - +
119F ILE* 3.4 21.0 + - - +
132F TRP* 4.2 11.9 - - + -
133F TYR* 5.0 2.1 - - - +
142F ALA* 3.5 39.3 - - + +
145F ASP* 5.1 0.2 - - + -
146F ALA* 3.8 10.5 - - + +
149F LEU* 4.3 7.0 - - + -
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Residues in contact with ALA 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112F PHE* 3.3 15.8 + - + +
113F PHE 4.0 1.3 - - - +
115F VAL* 1.3 75.2 - - - +
117F ASP* 1.3 66.8 + - - +
119F ILE* 3.2 16.7 + - + +
120F MET* 3.1 28.3 + - + +
143F ILE* 6.2 1.3 - - - -
146F ALA* 4.3 11.6 - - + +
401F YS4 3.9 26.7 - - + -
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Residues in contact with ASP 117 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113F PHE 2.8 22.6 + - - +
114F LEU* 3.9 4.7 - - - +
116F ALA* 1.3 74.5 - - - +
118F ASP* 1.3 56.2 + - - +
120F MET* 3.1 9.7 + - - +
121F ASP* 2.7 32.6 + - - +
126F ARG* 3.8 4.0 + - - -
185F GLN* 3.1 16.2 + - - +
401F YS4 2.9 35.1 + - + -
402F MG 2.2 25.3 - - - -
403F MG 2.1 27.9 - - - -
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Residues in contact with ASP 118 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F LEU* 2.9 22.5 + - - +
115F VAL* 4.0 4.7 - - - +
117F ASP* 1.3 78.4 - - - +
119F ILE* 1.3 61.3 + - - +
122F SER 3.1 2.3 + - - -
123F SER* 3.0 42.4 + - - -
125F THR 5.0 0.7 - - - +
126F ARG* 2.8 55.0 + - - +
131F CYS* 3.5 27.9 - - + +
133F TYR* 3.3 10.4 - - + -
401F YS4 4.3 0.2 + - - -
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Residues in contact with ILE 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115F VAL 3.4 17.0 + - - +
116F ALA* 3.2 13.2 + - + +
117F ASP 3.2 0.6 - - - -
118F ASP* 1.3 77.5 - - - +
120F MET* 1.3 67.3 + - + +
122F SER* 3.2 15.8 + - - -
133F TYR* 3.6 34.4 + - + -
139F GLY 5.1 0.2 - - - +
140F LEU* 3.8 25.6 - - + -
142F ALA* 4.1 20.0 - - + -
143F ILE* 3.9 29.4 - - + +
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Residues in contact with MET 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F ALA* 3.1 26.7 + - + +
117F ASP* 3.8 4.0 - - - +
119F ILE* 1.3 83.3 - - + +
121F ASP* 1.3 66.8 + - - +
122F SER* 3.7 2.6 + - - -
185F GLN* 3.7 13.2 - - - +
189F LEU* 4.3 36.0 - - + +
278F ASP* 5.6 0.5 - - - -
401F YS4 2.8 39.9 - - + -
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Residues in contact with ASP 121 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117F ASP* 2.7 21.9 + - - +
120F MET* 1.3 78.9 - - - +
122F SER* 1.3 72.5 + - - +
123F SER* 3.3 14.9 + - - +
185F GLN* 5.1 0.2 + - - -
189F LEU* 4.6 6.4 - - - +
274F THR* 3.7 8.6 + - - +
275F ASP* 5.8 0.2 - - - +
278F ASP* 2.6 28.8 - - - +
280F LYS* 2.7 27.0 + - - +
401F YS4 2.8 0.5 + - - -
402F MG 2.2 20.7 - - - -
403F MG 2.2 29.5 - - - -
----------------------------------------------------------
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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