Contacts of the helix formed by residues 54 - 80 (chain B) in PDB entry 4G1U
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 ILE 54 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B HIS* 4.4 13.9 - - + +
50B ILE* 2.9 29.8 + - + +
53B ASN* 1.3 89.5 - - - +
55B ARG* 1.3 65.0 + - + +
57B PRO* 3.4 6.7 - - - +
58B ARG* 3.1 34.9 + - + +
187B GLY 6.2 0.2 - - - +
189B ALA* 4.5 14.8 - - + +
190B GLN* 6.2 1.3 - - + -
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Residues in contact with ARG 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B SER 3.9 3.0 + - - +
26B ALA* 2.8 36.3 + - + +
27B ASN 3.7 3.6 + - - -
28B MET 3.1 34.6 + - - -
50B ILE* 2.9 29.6 + - + +
51B TRP* 4.0 26.5 - - + +
54B ILE* 1.3 76.9 - - + +
56B LEU* 1.3 67.7 + - - +
58B ARG* 3.8 7.2 - - - +
59B VAL* 2.9 31.7 + - + +
299B ARG* 3.6 28.7 - - - +
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Residues in contact with LEU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ALA* 5.8 6.3 - - + -
51B TRP* 3.2 38.2 + - + +
52B LEU* 3.9 17.3 - - + +
55B ARG* 1.3 78.2 - - - +
57B PRO* 1.4 63.8 - - + +
59B VAL* 3.8 7.2 - - + +
60B LEU* 2.9 47.3 + - + +
191B TRP* 3.7 27.6 - - + -
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Residues in contact with PRO 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU 3.6 12.8 - - - +
53B ASN 3.6 11.9 - - - +
54B ILE* 3.4 17.9 - - - +
56B LEU* 1.4 95.0 - - + +
58B ARG* 1.3 55.6 + - - -
60B LEU* 4.2 0.4 - - + -
61B LEU* 2.9 27.9 + - - +
189B ALA* 4.0 9.8 - - - +
190B GLN* 4.2 12.3 - - - +
191B TRP* 3.6 31.4 - - + +
194B LEU* 3.8 24.4 - - + +
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Residues in contact with ARG 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ILE* 3.1 25.0 + - + +
55B ARG* 3.2 8.3 + - - +
57B PRO* 1.3 75.1 - - - +
59B VAL* 1.3 64.6 + - - +
60B LEU 3.3 0.2 - - - -
61B LEU* 3.2 2.4 + - - +
62B ALA* 2.9 27.5 + - - +
186B LEU* 3.0 36.3 + - + +
187B GLY* 3.2 19.0 + - - +
189B ALA* 3.6 15.3 - - + -
295B ASP* 2.7 30.7 + - - +
298B ALA* 5.3 1.6 - - - +
299B ARG* 3.3 50.6 - - - +
306B GLU* 4.9 11.7 + - - +
307B MET 5.6 2.2 + - - -
309B VAL* 5.6 0.8 - - - +
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Residues in contact with VAL 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ALA* 3.8 37.2 - - + +
25B SER* 4.1 25.8 - - - +
26B ALA* 4.5 5.8 - - + +
55B ARG* 2.9 21.3 + - + +
56B LEU* 3.8 7.4 - - + +
58B ARG* 1.3 79.2 - - + +
60B LEU* 1.3 69.8 + - + +
62B ALA* 3.1 5.9 + - - +
63B VAL* 3.0 22.8 + - + +
292B LEU* 3.7 22.1 - - + +
296B THR* 5.0 1.1 - - - +
299B ARG* 5.1 6.1 - - - +
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ALA* 5.8 3.8 - - + -
56B LEU* 2.9 40.3 + - + +
59B VAL* 1.3 85.2 - - + +
61B LEU* 1.3 56.7 + - - +
63B VAL* 3.3 12.7 + - + +
64B VAL* 2.9 34.4 + - + +
191B TRP* 4.5 11.9 - - + -
194B LEU* 3.8 26.0 - - + -
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Residues in contact with LEU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PRO 2.9 21.7 + - - +
58B ARG* 3.7 6.5 - - - +
59B VAL 3.2 0.6 - - - -
60B LEU* 1.3 73.6 - - - +
62B ALA* 1.3 60.4 + - - +
64B VAL* 4.5 2.2 - - + +
65B VAL* 2.9 41.0 + - + +
186B LEU* 3.5 31.6 - - + -
188B GLN 5.4 1.1 - - - +
189B ALA* 4.0 22.7 - - + -
193B THR* 5.2 0.4 - - - +
194B LEU* 3.6 30.3 - - + +
197B ALA* 4.8 6.1 - - + -
253B VAL* 3.6 33.2 - - + +
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Residues in contact with ALA 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ARG 2.9 12.2 + - - +
59B VAL 3.1 8.5 + - - +
61B LEU* 1.3 75.6 - - - +
63B VAL* 1.3 57.7 + - - +
66B GLY* 2.9 28.1 + - - -
186B LEU* 3.5 15.8 - - + +
288B ALA* 4.3 3.1 - - - -
291B LEU* 3.6 12.0 - - + +
292B LEU* 3.6 34.5 - - + +
295B ASP* 4.4 10.5 - - + -
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Residues in contact with VAL 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 3.6 37.5 - - + -
22B ALA* 5.3 3.4 - - + -
59B VAL* 3.0 20.1 + - + +
60B LEU* 3.5 17.9 - - + +
62B ALA* 1.3 77.0 - - - +
64B VAL* 1.3 64.2 + - + +
67B CYS* 3.0 28.4 + - + +
288B ALA* 3.3 22.5 - - + +
292B LEU* 3.9 14.1 - - + -
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Residues in contact with VAL 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 2.9 22.7 + - + +
61B LEU* 4.2 3.6 - - + +
63B VAL* 1.3 80.9 - - + +
65B VAL* 1.3 59.8 + - + +
67B CYS* 3.5 6.8 + - - +
68B ALA* 2.9 25.6 + - - +
194B LEU* 4.2 15.7 - - + -
197B ALA* 4.7 3.1 - - + -
198B SER* 4.0 29.2 - - - +
201B ILE* 3.6 30.1 - - + +
202B LEU* 4.3 12.1 - - + -
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Residues in contact with VAL 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 2.9 39.7 + - + +
64B VAL* 1.3 73.7 - - + +
66B GLY* 1.3 61.2 + - - +
68B ALA* 3.0 7.4 + - - +
69B LEU* 2.9 35.8 + - + +
186B LEU* 4.8 1.6 - - + -
197B ALA* 6.0 1.6 - - + -
201B ILE* 5.3 3.6 - - + -
250B ALA* 4.2 21.8 - - + +
253B VAL* 5.0 4.7 - - + -
254B SER* 3.7 34.8 - - - +
257B ILE* 4.7 0.7 - - + -
291B LEU* 3.5 19.7 - - + -
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Residues in contact with GLY 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ALA 2.9 17.5 + - - -
65B VAL* 1.3 75.7 - - - +
67B CYS* 1.3 56.9 + - - +
70B ALA* 3.0 31.9 + - - +
260B ILE* 3.6 6.6 - - - +
287B GLY* 3.5 27.2 - - - -
291B LEU* 3.3 13.4 - - - +
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Residues in contact with CYS 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B VAL* 3.0 20.5 + - + +
64B VAL* 3.6 8.3 - - - +
66B GLY* 1.3 75.9 - - - +
68B ALA* 1.3 56.8 + - - +
71B VAL* 3.0 36.2 + - - +
201B ILE* 4.9 3.6 - - - -
202B LEU* 6.3 3.1 - - - -
205B CYS* 3.5 26.0 - - - -
284B ALA* 3.5 39.7 - - - +
288B ALA* 3.8 2.7 - - + +
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Residues in contact with ALA 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B VAL 2.9 16.6 + - - +
65B VAL 3.0 8.3 + - - +
67B CYS* 1.3 76.7 - - - +
69B LEU* 1.3 57.6 + - - +
72B SER* 2.9 31.8 + - - -
201B ILE* 3.6 24.4 - - + +
246B LEU* 3.5 24.5 - - + +
250B ALA* 3.7 17.3 - - + -
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B VAL* 2.9 26.6 + - + +
68B ALA* 1.3 71.1 - - - +
70B ALA* 1.3 60.4 + - - +
72B SER* 4.0 2.6 - - - -
73B GLY 2.9 22.9 + - - -
87B PRO* 4.2 21.8 - - + +
93B SER* 5.2 3.4 - - - +
247B ILE* 5.2 7.6 - - + -
250B ALA* 3.8 20.9 - - + -
251B VAL* 5.6 2.7 - - + -
254B SER* 5.5 1.6 - - - +
257B ILE* 3.7 48.5 - - + +
260B ILE* 3.5 32.8 - - + -
261B GLY* 3.3 13.5 - - - +
291B LEU* 5.1 1.1 - - + -
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B GLY 3.0 18.8 + - - +
67B CYS 3.8 3.4 - - - +
69B LEU* 1.3 78.0 - - - +
71B VAL* 1.3 58.4 + - - +
73B GLY* 3.8 0.7 - - - -
74B THR* 2.9 33.4 + - - -
260B ILE 3.3 11.4 + - - -
264B VAL* 3.4 16.4 - - + -
265B PRO* 4.1 3.1 - - - +
283B ALA* 3.2 31.9 - - - +
284B ALA* 4.1 0.9 - - - +
287B GLY* 3.7 3.4 - - - -
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Residues in contact with VAL 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B CYS 3.0 18.0 + - - +
70B ALA* 1.3 78.5 - - - +
72B SER* 1.3 59.0 + - - +
74B THR* 3.1 7.3 + - - +
75B ILE* 2.9 41.1 + - + +
205B CYS* 3.7 30.5 - - + +
208B GLY* 5.4 0.7 - - - -
246B LEU* 3.6 18.4 - - + -
280B LEU* 4.2 21.8 - - + +
283B ALA* 5.1 1.6 - - - -
284B ALA* 3.5 29.2 - - + -
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Residues in contact with SER 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ALA 2.9 21.9 + - - -
69B LEU* 4.0 4.3 - - - -
71B VAL* 1.3 77.9 - - - +
73B GLY* 1.3 58.0 + - - +
75B ILE* 3.9 1.8 - - - +
76B MET* 2.9 42.4 + - - +
87B PRO* 4.0 1.7 - - - +
243B SER* 3.5 7.3 - - - -
246B LEU* 3.6 23.1 - - - +
247B ILE* 3.1 28.9 - - - +
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Residues in contact with GLY 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU 2.9 18.5 + - - -
70B ALA 3.8 0.4 - - - -
72B SER* 1.3 76.5 + - - +
74B THR* 1.3 57.3 + - - +
77B GLN* 2.9 36.6 + - - +
85B ALA 3.4 2.0 - - - +
87B PRO* 3.6 17.7 - - - +
261B GLY 3.6 20.9 - - - -
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Residues in contact with THR 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ALA 2.9 14.3 + - - -
71B VAL* 3.1 6.5 + - - -
73B GLY* 1.3 75.9 - - - +
75B ILE* 1.3 65.4 + - - +
77B GLN* 3.5 4.8 + - - +
78B GLY* 3.0 20.3 + - - -
265B PRO* 3.1 31.1 - - - +
269B ARG* 5.2 1.5 + - - +
276B HIS* 4.1 14.1 + - + -
279B LEU* 3.9 29.5 - - + +
280B LEU* 4.2 20.2 - - + -
283B ALA* 3.7 11.2 - - - +
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Residues in contact with ILE 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL* 2.9 40.2 + - + +
72B SER 3.9 3.1 - - - +
74B THR* 1.3 72.2 - - - +
76B MET* 1.3 59.0 + - - +
78B GLY* 3.2 1.7 + - - -
79B LEU* 2.9 28.5 + - + +
208B GLY* 4.4 5.8 - - - -
215B LEU* 4.3 15.6 - - + +
239B LEU* 3.7 45.1 - - + +
242B LEU* 3.7 29.8 - - + -
243B SER* 4.2 7.0 - - - +
246B LEU* 3.8 9.4 - - + -
280B LEU* 4.0 15.5 - - + -
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Residues in contact with MET 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B SER* 2.9 41.2 + - - +
73B GLY 3.6 0.9 - - - +
75B ILE* 1.3 77.1 - - - +
77B GLN* 1.3 64.7 + - - +
79B LEU* 3.0 17.2 + - - -
80B PHE* 3.0 45.0 + - + -
85B ALA* 3.2 22.4 - - + +
87B PRO* 3.8 8.7 - - + -
90B LEU* 3.9 4.9 - - + -
92B ILE* 3.6 25.4 - - - -
131B SER* 4.3 2.5 - - - -
240B LEU* 6.0 0.2 - - - -
243B SER* 3.5 18.6 - - - -
247B ILE* 3.4 17.5 - - + -
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Residues in contact with GLN 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLY 2.9 18.3 + - - +
74B THR 3.8 3.6 - - - +
76B MET* 1.3 72.6 - - - +
78B GLY* 1.3 61.9 + - - +
81B ARG 3.2 1.2 + - - -
82B ASN 3.0 44.6 + - - +
83B PRO 3.6 4.4 + - - +
85B ALA* 3.6 20.4 + - - +
261B GLY 2.9 28.1 + - - -
262B LEU* 3.7 14.5 + - - +
265B PRO* 3.6 12.6 - - - +
266B HIS* 3.0 21.9 + - - -
269B ARG* 2.9 25.6 + - - +
98C PHE* 3.4 13.3 - - + -
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Residues in contact with GLY 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B THR 3.0 12.2 + - - -
75B ILE 3.6 3.1 - - - -
77B GLN* 1.3 77.1 - - - +
79B LEU* 1.3 64.3 + - - +
81B ARG* 3.0 11.6 + - - +
215B LEU* 3.6 18.6 - - - -
218B LEU* 5.4 2.6 - - - +
219B GLN* 2.8 32.7 + - - -
269B ARG* 5.7 0.4 - - - +
276B HIS* 4.3 4.5 - - - -
98C PHE* 4.5 2.2 - - - -
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Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ILE* 2.9 20.8 + - + +
76B MET* 3.0 6.0 + - - +
78B GLY* 1.3 73.3 - - - +
80B PHE* 1.3 80.4 + - + +
81B ARG* 3.4 2.8 + - - -
135B PHE* 4.3 5.4 - - + -
139B ARG* 2.3 49.6 + - - +
215B LEU* 4.4 1.9 - - - +
218B LEU* 4.8 7.2 - - + -
236B LYS* 3.8 30.5 - - + +
239B LEU* 3.8 22.4 - - + -
240B LEU* 3.6 38.6 - - + +
243B SER* 5.5 2.0 - - - +
----------------------------------------------------------
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Residues in contact with PHE 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B MET* 3.0 39.1 + - + +
79B LEU* 1.3 91.0 - - + +
81B ARG* 1.3 72.5 + - - +
82B ASN* 3.1 17.5 + - + +
85B ALA* 3.5 21.1 - - + -
90B LEU* 3.5 16.6 - - + -
92B ILE* 5.3 0.2 - - + -
131B SER* 4.4 7.0 - - - -
134B ILE* 4.1 4.7 - - + -
135B PHE* 3.5 46.4 - + + -
138B SER* 3.6 25.0 + - - +
139B ARG* 5.0 0.9 - - - -
148B LEU* 4.2 14.4 - - + +
240B LEU* 4.8 3.4 - - + -
----------------------------------------------------------
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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