Contacts of the helix formed by residues 126 - 150 (chain L) in PDB entry 1QGH
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 126 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LYS* 2.5 36.8 + - - +
117B ILE* 3.6 19.5 - - + +
133B ILE* 3.7 29.4 - - + +
136B LYS* 5.2 4.5 - - - +
124L GLY* 3.0 9.7 + - - +
125L ASP* 1.3 71.8 + - - +
127L VAL* 1.3 65.2 + - + +
129L ASN* 3.2 9.9 - - - +
130L ASP* 3.0 24.3 + - - +
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Residues in contact with VAL 127 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ILE* 5.7 0.2 - - + -
133B ILE* 3.7 18.6 - - + +
136B LYS* 3.7 25.2 - - + +
137B ALA* 3.5 44.2 - - + +
140B ASP* 4.1 2.0 - - - +
63L ARG* 3.2 41.3 - - - +
125L ASP* 3.2 1.2 + - - -
126L ASP* 1.3 78.6 - - + +
128L THR* 1.3 62.9 + - - +
130L ASP* 3.1 5.9 + - - +
131L MET* 3.1 23.5 + - + +
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Residues in contact with THR 128 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9L THR* 4.0 5.2 - - + +
13L LEU* 3.7 37.5 - - + +
63L ARG* 2.8 21.5 + - - +
67L ILE* 4.6 0.2 - - - +
120L THR* 3.5 14.4 - - - +
125L ASP* 2.5 31.2 + - - -
127L VAL* 1.3 75.6 - - - +
129L ASN* 1.3 64.1 + - - +
131L MET* 3.0 22.4 + - + +
132L LEU* 3.0 20.8 + - + +
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Residues in contact with ASN 129 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117L ILE* 3.1 27.5 + - - +
120L THR* 2.9 37.0 + - + +
121L ASP* 4.0 15.0 + - - +
125L ASP 3.0 10.9 + - - +
126L ASP* 3.2 15.1 - - - +
128L THR* 1.3 77.7 - - - +
130L ASP* 1.3 66.6 + - - +
132L LEU* 3.4 3.4 + - - +
133L ILE* 3.0 39.9 + - - +
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Residues in contact with ASP 130 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ASP* 3.5 24.8 - - - +
133B ILE* 3.8 26.0 - - + +
134B ALA* 5.4 0.9 + - - +
130G ASP* 3.4 27.0 - - - +
126L ASP 3.0 10.3 + - - +
127L VAL 3.1 6.5 + - - +
129L ASN* 1.3 83.0 - - - +
131L MET* 1.3 67.6 + - - +
133L ILE* 3.3 7.4 + - - +
134L ALA* 3.0 21.8 + - - +
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Residues in contact with MET 131 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13L LEU* 4.3 4.0 - - + -
59L GLU* 3.8 17.7 - - - +
60L VAL* 4.1 18.6 - - + -
63L ARG* 3.8 32.5 - - + -
127L VAL* 3.1 18.8 + - + +
128L THR* 3.0 20.8 + - + +
130L ASP* 1.3 75.9 - - - +
132L LEU* 1.3 87.4 + - + +
134L ALA* 3.1 8.7 + - - +
135L PHE* 2.9 44.4 + - + -
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Residues in contact with LEU 132 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12L PHE* 4.0 32.5 - - + -
13L LEU* 4.3 3.8 - - + -
16L GLN* 6.0 0.7 - - + -
60L VAL* 5.2 2.7 - - + -
113L TYR* 4.0 18.4 - - + +
116L GLY 4.0 20.0 - - - +
117L ILE* 3.8 15.7 - - + +
120L THR* 4.4 4.0 - - + +
128L THR* 3.0 30.4 + - + +
129L ASN 3.6 4.3 - - - +
131L MET* 1.3 104.2 - - + +
133L ILE* 1.3 62.4 + - - +
135L PHE* 3.2 16.0 + - + +
136L LYS* 2.8 24.1 + - - +
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Residues in contact with ILE 133 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126G ASP* 3.6 40.6 - - + +
127G VAL* 3.5 15.5 - - + +
130G ASP* 3.9 21.8 - - + +
117L ILE* 3.8 25.1 - - + -
129L ASN* 3.0 35.3 + - - +
130L ASP* 3.7 16.6 - - - +
131L MET 3.2 0.2 - - - -
132L LEU* 1.3 73.7 - - - +
134L ALA* 1.3 58.7 + - - +
136L LYS* 3.0 4.2 + - - +
137L ALA* 2.8 27.5 + - + +
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Residues in contact with ALA 134 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130G ASP* 5.5 0.4 + - - -
130L ASP 3.0 13.4 + - - +
131L MET* 3.4 9.6 - - - +
133L ILE* 1.3 77.7 - - - +
135L PHE* 1.3 69.9 + - + +
137L ALA* 3.2 17.9 + - - +
138L SER* 3.3 10.7 + - - -
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Residues in contact with PHE 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56L GLN* 3.5 47.6 + - + +
59L GLU* 3.7 34.5 - - + -
60L VAL* 3.5 26.9 - - + -
113L TYR* 3.4 28.0 - + + -
131L MET* 2.9 37.2 + - + -
132L LEU* 3.6 8.1 - - + +
134L ALA* 1.3 82.4 - - + +
136L LYS* 1.3 65.3 + - - +
138L SER* 3.0 6.8 + - - -
139L ILE* 2.9 25.1 + - - +
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Residues in contact with LYS 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G ARG* 4.6 5.6 - - - +
125G ASP* 5.5 1.3 + - - -
126G ASP* 5.1 4.0 - - - +
127G VAL* 3.7 20.8 - - + +
110L ARG* 4.1 34.1 - - + +
113L TYR* 4.2 6.0 - - + -
114L LYS* 4.6 15.9 - - + +
117L ILE* 4.0 22.0 - - + -
132L LEU 2.8 13.5 + - - +
133L ILE 3.0 8.5 + - - +
135L PHE* 1.3 76.3 - - - +
137L ALA* 1.3 64.2 + - - +
139L ILE* 3.1 9.8 + - + +
140L ASP* 2.9 54.5 + - - +
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Residues in contact with ALA 137 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G ARG* 5.0 1.0 + - - -
127G VAL* 3.6 30.3 - - + +
131G MET* 6.4 0.9 - - + -
133L ILE* 2.8 11.3 + - + +
134L ALA* 3.4 13.9 - - - +
135L PHE 3.1 0.4 - - - -
136L LYS* 1.3 76.4 - - - +
138L SER* 1.3 63.2 + - - +
140L ASP* 3.5 4.7 + - - +
141L LYS* 3.3 18.2 + - - +
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Residues in contact with SER 138 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52L GLU* 2.6 28.9 + - - -
56L GLN* 4.8 1.9 + - - -
134L ALA 3.3 6.8 + - - -
135L PHE* 3.0 11.0 + - - -
137L ALA* 1.3 78.9 - - - +
139L ILE* 1.3 67.7 + - - +
141L LYS* 3.1 9.8 + - - +
142L HIS* 2.9 36.8 + - - -
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Residues in contact with ILE 139 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53L PHE* 3.9 28.9 - - + -
56L GLN* 4.4 2.0 - - - +
106L LEU* 3.7 29.2 - - + +
109L LEU* 4.2 16.2 - - + -
110L ARG* 3.9 13.2 - - + +
113L TYR* 3.9 31.6 - - + -
135L PHE 2.9 15.0 + - - +
136L LYS* 3.6 7.4 - - - +
138L SER* 1.3 75.1 - - - +
140L ASP* 1.3 54.1 + - - +
142L HIS* 3.0 11.2 + - - +
143L ILE* 2.7 51.8 + - + +
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Residues in contact with ASP 140 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G ARG* 2.9 32.8 + - - +
66G ALA* 4.0 15.9 - - + +
67G ILE* 6.1 0.2 - - - -
127G VAL* 4.2 1.7 - - - +
110L ARG* 3.1 34.7 + - - +
136L LYS* 2.9 42.1 + - - +
137L ALA 3.6 3.8 - - - +
139L ILE* 1.3 76.3 - - - +
141L LYS* 1.3 57.8 + - - +
143L ILE* 3.2 7.6 + - - +
144L TRP* 2.9 27.4 + - - +
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Residues in contact with LYS 141 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E HIS* 5.4 1.8 + - - -
62G GLU* 2.9 32.0 + - + +
66G ALA* 4.8 4.5 - - - -
137L ALA 3.3 8.9 + - - +
138L SER* 3.1 11.9 + - - +
140L ASP* 1.3 78.2 - - - +
142L HIS* 1.3 66.2 + - + +
144L TRP* 3.1 24.0 + - + +
145L MET* 3.0 45.2 + - + +
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Residues in contact with HIS 142 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45L LYS* 4.5 5.3 + - - -
49L LEU* 3.7 21.9 - - + +
52L GLU* 2.8 28.7 + - - -
53L PHE* 4.0 22.4 - + - -
106L LEU* 4.0 17.5 - - + -
138L SER* 2.9 35.5 + - - -
139L ILE* 3.2 7.0 - - - +
141L LYS* 1.3 77.0 - - + +
143L ILE* 1.3 59.4 + - - +
145L MET* 3.1 21.3 + - + +
146L PHE* 2.8 44.8 + + + +
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Residues in contact with ILE 143 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66G ALA 6.1 0.4 - - - +
103L VAL* 4.9 4.9 - - + +
106L LEU* 3.8 22.2 - - + -
107L GLU* 3.9 26.7 - - + +
110L ARG* 3.8 35.7 - - - +
139L ILE* 2.7 40.4 + - + +
140L ASP* 3.5 7.2 - - - +
142L HIS* 1.3 74.1 - - - +
144L TRP* 1.3 64.2 + - - +
146L PHE* 4.6 1.3 - - - +
147L LYS* 3.1 30.1 + - + +
154L PRO* 3.9 23.8 - - + +
155L LEU* 5.3 1.3 - - + -
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Residues in contact with TRP 144 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E HIS 4.6 0.4 - - - -
32E TRP* 4.0 12.7 + - - -
34E MET 5.5 0.6 + - - -
39E PHE* 4.0 17.0 - + - -
43E HIS* 3.6 27.4 - + - -
62G GLU* 3.7 40.2 - - + -
65G LEU* 3.7 34.5 - - + +
66G ALA* 4.0 19.5 - - + -
140L ASP 2.9 13.4 + - - +
141L LYS* 3.1 20.4 + - + +
143L ILE* 1.3 77.5 - - - +
145L MET* 1.3 80.4 + - + +
147L LYS* 3.9 1.4 - - - +
148L ALA* 3.0 33.5 + - + +
152L LYS 5.2 0.2 - - - +
154L PRO* 3.9 28.5 - - + +
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Residues in contact with MET 145 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E PHE* 3.6 33.5 - - + -
40E PHE* 3.8 17.7 - - + -
43E HIS* 4.6 11.2 - - - -
45L LYS* 4.1 14.4 - - - +
141L LYS* 3.0 41.4 + - + +
142L HIS* 3.8 25.1 - - + +
144L TRP* 1.3 104.5 - - + +
146L PHE* 1.3 62.8 + - + +
148L ALA* 3.3 2.8 + - - +
149L PHE* 3.0 21.5 + - - +
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Residues in contact with PHE 146 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E PHE* 3.4 32.1 - + - -
42L LEU* 4.6 1.3 - - + -
45L LYS* 3.8 21.5 - - + -
46L MET* 3.5 33.7 - - + -
49L LEU* 4.0 10.5 - - + -
99L MET* 3.7 26.7 - - + +
102L LEU* 3.8 16.6 - - + -
103L VAL* 3.4 24.2 - - + -
106L LEU* 4.3 5.8 - - + -
142L HIS* 2.8 42.7 + - + +
145L MET* 1.3 73.6 - - + +
147L LYS* 1.3 63.3 + - - +
149L PHE* 3.2 6.0 + - + +
150L LEU* 3.0 26.3 + - + +
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Residues in contact with LYS 147 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103L VAL* 3.7 21.8 - - + -
107L GLU* 3.3 17.4 + - - -
143L ILE* 3.1 23.2 + - + +
144L TRP 3.9 2.2 - - - +
146L PHE* 1.3 72.6 - - - +
148L ALA* 1.3 68.0 + - - +
150L LEU* 2.9 22.0 + - + +
152L LYS* 2.9 34.6 + - + +
153L ALA 3.1 29.4 - - - +
154L PRO* 3.3 11.9 - - + +
156L GLU* 2.9 49.3 + - - +
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Residues in contact with ALA 148 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E MET 3.9 9.9 - - - +
35E ARG* 3.3 11.5 - - + +
36E GLY 2.8 29.4 + - - -
39E PHE* 3.7 27.6 - - + -
144L TRP* 3.0 25.1 + - + +
145L MET 3.6 5.2 - - - +
146L PHE 3.3 0.2 - - - -
147L LYS* 1.3 76.8 - - - +
149L PHE* 1.3 52.6 + - - +
151L GLY 2.9 10.1 + - - +
152L LYS 3.6 10.0 + - - +
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Residues in contact with PHE 149 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E GLY 3.2 27.5 - - - -
37E HIS* 3.2 62.0 + - + -
39E PHE* 4.1 3.5 - - + +
40E PHE* 3.7 28.7 - + + -
38L ASN* 4.0 4.7 - - + -
42L LEU* 3.4 28.7 - - + -
95L MET* 3.9 7.9 - - + -
96L ASP* 3.7 17.3 - - - -
99L MET* 3.5 30.5 - - + -
145L MET 3.0 13.7 + - - +
146L PHE* 3.3 10.1 - + - +
148L ALA* 1.3 77.6 - - - +
150L LEU* 1.3 65.4 + - + +
151L GLY 3.2 0.4 + - - -
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Residues in contact with LEU 150 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E HIS* 5.2 3.1 - - - -
96L ASP* 3.8 47.5 - - + +
99L MET* 4.0 13.2 - - + -
100L GLU* 3.8 37.9 - - + +
103L VAL* 4.4 12.8 - - + -
146L PHE 3.0 15.4 + - - +
147L LYS* 2.9 16.1 + - + +
149L PHE* 1.3 82.5 - - + +
151L GLY* 1.3 60.0 + - - +
152L LYS* 3.5 18.7 + - + +
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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