Contacts of the helix formed by residues 114 - 139 (chain B) in PDB entry 1HPL
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 TYR 114 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B THR 3.6 1.6 + - - -
113B ALA* 1.3 70.3 - - - +
115B SER* 1.3 57.7 + - - +
117B ALA* 3.3 2.6 + - - +
118B SER* 2.8 50.3 + - - -
153B LEU* 3.3 29.7 - - + +
178B ALA* 3.3 12.8 - - - +
180B PRO* 2.7 43.1 + - + +
181B CYS* 4.0 10.1 - - - -
215B PHE* 3.7 23.8 - + - -
248B ILE* 4.1 23.3 - - + +
249B ASP* 3.0 16.3 + - - +
252B TRP* 3.7 43.5 - + + -
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Residues in contact with SER 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 4.1 29.8 - - - +
27B ILE* 4.2 7.3 - - - +
113B ALA* 4.1 11.3 - - - +
114B TYR* 1.3 78.0 - - - +
116B GLN* 1.3 63.3 + - - +
118B SER* 3.6 7.9 - - - -
119B GLN* 3.3 25.8 + - - +
181B CYS* 4.8 10.3 - - - -
249B ASP* 4.4 4.0 + - - -
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Residues in contact with GLN 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ILE* 4.4 16.8 - - + +
28B LEU 2.9 28.4 + - - +
29B PRO* 3.5 3.0 - - - +
30B TRP* 3.4 43.6 + - + +
112B THR* 4.3 9.6 - - + +
113B ALA* 3.0 13.8 + - + +
115B SER* 1.3 79.2 + - - +
117B ALA* 1.3 59.7 + - - +
119B GLN* 3.2 5.1 + - - +
120B ASN* 2.9 50.3 + - - +
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Residues in contact with ALA 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B TRP* 3.9 3.4 - - + -
109B GLY 3.8 12.3 - - - +
110B SER* 3.8 30.7 - - - +
112B THR* 4.1 1.8 + - - +
113B ALA 3.0 10.1 + - - +
114B TYR 3.8 4.9 - - - +
116B GLN* 1.3 73.9 - - - +
118B SER* 1.3 57.0 + - - +
120B ASN* 3.0 15.6 + - - +
121B VAL* 3.2 15.9 + - - +
153B LEU* 3.6 20.6 - - + -
252B TRP* 3.8 9.4 - - + +
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Residues in contact with SER 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ARG* 4.5 8.3 + - - -
114B TYR* 2.8 51.1 + - - -
115B SER* 3.6 9.2 - - - -
117B ALA* 1.3 71.0 - - - +
119B GLN* 1.3 66.8 + - - +
121B VAL* 3.1 23.1 - - - +
122B ARG* 4.8 1.4 - - - +
153B LEU* 4.1 4.6 - - - +
181B CYS* 4.0 9.4 - - - +
182B PHE* 3.8 25.1 - - - -
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Residues in contact with GLN 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B TRP 2.8 27.9 + - - +
18B ALA* 4.1 6.3 - - - +
23B ARG* 3.5 15.2 + - - +
25B LEU 4.9 1.8 + - - -
27B ILE* 3.6 34.5 + - + +
29B PRO* 3.4 22.3 - - - +
115B SER 3.3 12.5 + - - +
116B GLN* 3.2 13.9 + - - +
118B SER* 1.3 81.3 - - - +
120B ASN* 1.3 59.8 + - - +
122B ARG* 3.2 55.2 + - - +
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Residues in contact with ASN 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B PRO* 4.4 4.0 - - - -
30B TRP* 2.9 56.2 + - - -
34B VAL* 3.9 14.4 - - + -
106B TRP* 4.3 6.1 - - + -
109B GLY* 2.8 29.7 + - - +
112B THR* 4.3 0.2 + - - -
116B GLN* 2.9 29.6 + - - +
117B ALA 3.0 8.4 + - - +
119B GLN* 1.3 72.5 - - - +
121B VAL* 1.3 64.5 + - - +
122B ARG 3.1 0.9 + - - -
123B ILE* 3.2 14.2 + - - +
124B VAL* 3.3 15.7 + - - +
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B TRP* 4.0 10.1 - - + -
117B ALA 3.2 13.1 + - - +
118B SER* 3.1 20.9 - - - +
120B ASN* 1.3 76.1 - - - +
122B ARG* 1.4 62.0 + - + +
124B VAL* 3.4 10.4 + - - +
125B GLY* 2.9 27.5 + - - -
153B LEU* 3.5 38.6 - - + +
156B HIS* 4.5 4.3 - - + +
157B ALA* 3.9 24.0 - - + +
160B GLU* 4.4 2.7 - - + +
182B PHE* 4.2 17.3 - - + -
189B VAL 5.7 1.3 - - - +
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Residues in contact with ARG 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 3.9 30.9 - - + +
12B SER 2.8 40.2 + - - +
13B ASP* 4.7 2.0 - - - +
17B TRP* 3.4 62.2 - - + +
23B ARG* 5.8 2.2 - - - +
27B ILE 5.3 0.4 + - - -
28B LEU* 5.0 0.2 - - - +
29B PRO* 4.0 17.7 - - + +
118B SER 4.8 0.7 - - - +
119B GLN* 3.3 41.8 + - - +
120B ASN 3.1 0.2 - - - -
121B VAL* 1.4 84.0 - - + +
123B ILE* 1.3 56.0 - - - +
125B GLY 3.5 0.2 + - - -
126B ALA* 3.1 27.7 + - - +
160B GLU* 3.8 20.2 - - - +
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Residues in contact with ILE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B TYR* 4.9 2.0 - - + -
8B LEU* 4.2 8.5 - - + -
11B PHE* 3.7 32.5 - - + -
29B PRO* 3.7 19.7 - - + -
30B TRP 3.5 25.4 - - - +
31B PRO* 4.0 25.1 - - + -
34B VAL* 3.9 30.1 - - + -
120B ASN* 3.2 9.2 + - - +
122B ARG* 1.3 73.5 - - - +
124B VAL* 1.3 65.6 + - - +
126B ALA* 3.2 6.5 + - - +
127B GLU* 3.0 33.1 + - + +
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Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B VAL* 4.0 9.2 - - + -
36B THR* 4.0 23.8 - - + +
74B ILE* 4.2 14.1 - - + -
104B VAL* 4.1 15.3 - - + -
106B TRP* 3.6 42.2 - - + -
120B ASN 3.3 16.5 + - - +
121B VAL* 3.7 7.4 - - - +
123B ILE* 1.3 72.9 - - - +
125B GLY* 1.3 63.1 + - - +
127B GLU* 3.3 3.1 + - - +
128B VAL* 3.2 29.8 + - + +
157B ALA* 4.2 9.2 - - + -
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Residues in contact with GLY 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B VAL 2.9 15.7 + - - -
124B VAL* 1.3 75.8 - - - +
126B ALA* 1.3 63.4 + - - +
128B VAL* 3.4 1.2 + - - -
129B ALA* 3.1 20.1 + - - +
157B ALA 3.4 25.0 + - - -
160B GLU* 3.8 12.3 - - - -
161B ALA* 3.5 16.9 - - - +
164B ARG* 4.3 0.4 - - - -
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Residues in contact with ALA 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 3.6 25.5 - - + +
11B PHE* 4.1 4.3 - - + -
122B ARG 3.1 17.8 + - - +
123B ILE 3.2 6.9 + - - +
125B GLY* 1.3 77.6 - - - +
127B GLU* 1.3 55.1 + - - +
129B ALA* 3.9 1.6 - - - +
130B TYR* 3.0 29.8 + - - +
164B ARG* 3.6 35.7 + - - +
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Residues in contact with GLU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ARG* 2.7 34.8 + - - -
8B LEU* 3.9 20.8 - - + +
31B PRO* 4.1 14.9 - - - +
36B THR* 3.9 28.9 + - + +
38B PHE* 3.8 25.1 - - + -
123B ILE* 3.0 20.9 + - + +
124B VAL 3.3 7.4 + - - +
126B ALA* 1.3 72.9 - - - +
128B VAL* 1.3 59.7 + - - +
130B TYR* 3.3 4.0 + - - +
131B LEU* 3.0 28.2 + - - +
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Residues in contact with VAL 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B PHE* 3.9 23.1 - - + -
72B PHE* 4.2 19.3 - - + -
74B ILE* 4.3 20.2 - - + -
104B VAL* 4.5 11.4 - - + -
124B VAL* 3.2 15.1 + - + +
125B GLY* 3.9 6.1 - - - +
127B GLU* 1.3 72.2 - - - +
129B ALA* 1.4 59.5 + - - +
131B LEU* 3.1 6.1 + - - +
132B VAL* 2.9 39.6 + - + +
148B ILE* 4.0 28.3 - - + -
161B ALA* 4.0 7.4 - - + -
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B GLY 3.1 14.3 + - - +
126B ALA 4.0 2.9 - - - +
128B VAL* 1.4 76.9 - - - +
130B TYR* 1.3 63.3 + - - +
132B VAL* 3.2 13.7 + - - +
133B GLY* 2.9 21.3 + - - -
161B ALA* 3.6 23.7 - - - +
164B ARG* 3.7 21.5 - - + +
165B THR* 3.8 6.5 - - - +
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Residues in contact with TYR 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ARG* 3.4 71.2 - - + +
8B LEU* 4.1 8.5 - - + -
54B ALA* 3.8 28.8 + - + -
126B ALA 3.0 20.8 + - - +
127B GLU* 3.4 6.1 - - - +
128B VAL 3.2 0.2 - - - -
129B ALA* 1.3 76.9 - - - +
131B LEU* 1.3 61.0 + - - +
133B GLY* 3.3 1.4 + - - -
134B VAL* 3.1 34.6 + - + +
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Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B PHE* 3.9 38.6 - - + -
52B ILE* 4.4 16.8 - - + -
53B VAL 4.5 1.1 - - - +
54B ALA* 3.6 35.9 - - + +
59B ILE* 3.8 21.5 - - + -
72B PHE* 4.0 19.5 - - + -
102B ILE* 4.6 2.9 - - + -
127B GLU 3.0 14.1 + - - +
128B VAL* 3.6 8.1 - - - +
130B TYR* 1.3 75.7 - - - +
132B VAL* 1.4 61.0 + - - +
134B VAL* 3.1 4.4 + - + +
135B LEU* 3.1 27.8 + - + +
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PHE* 4.2 18.6 - - + -
128B VAL* 2.9 40.3 + - + +
129B ALA* 3.2 9.8 + - - +
131B LEU* 1.4 69.8 - - - +
133B GLY* 1.3 65.3 + - - +
135B LEU* 3.2 11.6 + - - +
136B GLN* 3.0 24.6 + - - +
141B TYR 5.0 0.5 - - - +
143B PRO* 5.1 12.2 - - + +
146B VAL* 4.4 20.0 - - + -
148B ILE* 5.4 0.4 - - + -
165B THR* 3.8 28.0 - - + +
169B VAL* 4.8 6.7 - - + -
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Residues in contact with GLY 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ALA 2.9 14.2 + - - -
130B TYR* 3.8 4.0 - - - -
131B LEU 3.3 0.2 - - - -
132B VAL* 1.3 79.5 - - - +
134B VAL* 1.3 60.5 + - - +
136B GLN* 3.3 13.5 + - - +
137B SER* 2.9 29.7 + - - -
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Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ALA* 4.0 37.5 - - + +
56B PRO* 4.3 24.0 - - + -
59B ILE* 4.4 12.1 - - + -
130B TYR* 3.1 28.3 + - + +
131B LEU* 3.1 9.7 + - + +
133B GLY* 1.3 76.0 - - - +
135B LEU* 1.4 62.0 + - - +
137B SER* 4.6 4.7 - - - -
138B SER* 2.9 26.4 + - - +
139B PHE* 4.6 2.7 - - + -
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ILE* 6.4 0.9 - - + -
59B ILE* 3.8 37.7 - - + -
64B PHE* 4.0 31.0 - - + -
70B THR* 5.2 1.8 - - + +
72B PHE* 4.9 10.5 - - + -
102B ILE* 5.8 0.9 - - + -
131B LEU* 3.1 26.3 + - + +
132B VAL* 3.2 15.0 + - + +
134B VAL* 1.4 73.1 - - - +
136B GLN* 1.3 63.7 + - - +
139B PHE* 3.0 35.0 + - + +
141B TYR* 3.2 36.2 + - + +
146B VAL* 5.2 3.8 - - + -
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Residues in contact with GLN 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B VAL* 3.0 11.8 + - - +
133B GLY* 3.4 16.9 - - - +
135B LEU* 1.3 79.4 - - - +
137B SER* 1.3 63.3 + - - +
140B ASP* 3.2 20.3 + - - +
141B TYR 3.3 19.4 + - - +
142B SER* 5.4 0.6 - - - +
143B PRO* 3.5 32.9 - - + +
168B ALA* 6.1 0.2 - - - +
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Residues in contact with SER 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLY 2.9 20.4 + - - -
134B VAL* 4.0 4.7 - - - -
136B GLN* 1.3 76.3 - - - +
138B SER* 1.3 65.3 + - - +
140B ASP* 4.7 4.7 + - - +
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Residues in contact with SER 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B PRO* 3.5 25.8 - - - +
134B VAL* 2.9 21.1 + - - +
137B SER* 1.3 77.3 - - - +
139B PHE* 1.3 81.8 + - - +
140B ASP 3.7 0.7 - - - -
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Residues in contact with PHE 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B PRO* 3.4 35.0 - - + -
59B ILE* 3.7 37.7 - - + -
60B GLN* 4.4 21.5 - - + -
64B PHE* 5.5 2.0 - + - -
66B THR* 4.0 30.3 - - + +
134B VAL* 4.4 2.9 - - + -
135B LEU* 3.0 31.5 + - + +
138B SER* 1.3 97.4 - - - +
140B ASP* 1.3 71.8 + - - +
141B TYR* 3.2 4.7 + - + -
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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