Contacts of the helix formed by residues 62 - 86 (chain F) in PDB entry 1MA1
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 62 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ALA* 4.4 7.1 - - - +
69C GLU* 4.6 10.6 - - - +
50F LYS* 5.8 4.5 - - - +
61F VAL* 1.3 72.4 - - - +
63F ILE* 1.3 58.3 + - - +
64F LYS* 3.4 13.7 + - - +
65F ALA* 3.2 32.0 + - + +
66F ALA* 3.0 25.5 + - - +
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Residues in contact with ILE 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D GLU* 2.9 34.5 - - + +
121D GLN* 3.3 33.3 - - + +
122D ALA* 2.8 44.6 - - + +
125D SER* 4.6 1.3 - - - +
145D ILE* 6.1 0.4 - - + -
51F LEU* 5.5 2.2 - - + -
61F VAL* 3.1 26.1 + - + -
62F ASP* 1.3 70.7 + - - +
64F LYS* 1.3 65.4 + - - +
66F ALA* 3.8 7.9 - - + -
67F LEU* 2.8 47.7 + - + +
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Residues in contact with LYS 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C GLU* 2.9 35.7 + - - +
73C HIS* 5.2 3.6 - - - -
125D SER* 3.4 37.5 + - - +
127D GLU* 2.7 40.5 + - + +
147D GLN* 3.4 28.7 - - - +
62F ASP* 3.4 10.3 + - - +
63F ILE* 1.3 82.2 - - - +
65F ALA* 1.3 65.5 + - - +
67F LEU* 4.1 1.3 - - - +
68F LYS* 3.1 39.6 + - + +
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Residues in contact with ALA 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ASP* 4.5 6.7 - - - +
65C ALA* 3.5 26.9 - - + +
62F ASP* 3.2 29.5 + - + +
64F LYS* 1.3 82.6 - - - +
66F ALA* 1.3 63.5 + - - +
68F LYS* 3.4 7.5 + - - +
69F GLU* 3.0 24.8 + - - +
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Residues in contact with ALA 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F LEU* 3.1 28.4 - - + +
50F LYS* 5.5 7.2 - - - +
51F LEU* 4.0 25.8 - - + -
61F VAL* 5.2 0.9 - - + -
62F ASP 3.0 18.7 + - - +
63F ILE* 3.6 9.6 - - + +
64F LYS 3.2 0.2 - - - -
65F ALA* 1.3 77.1 - - - +
67F LEU* 1.3 61.4 + - + +
69F GLU* 3.3 2.7 + - - +
70F LEU* 2.8 25.1 + - - +
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Residues in contact with LEU 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D GLU* 6.1 0.9 - - - +
122D ALA* 3.9 18.2 - - + -
145D ILE* 3.2 55.7 - - + +
146D MET* 5.4 1.2 - - - +
147D GLN* 4.1 24.2 + - + +
154D ASN 5.4 0.3 - - - +
51F LEU* 4.8 14.8 - - + -
55F ARG* 6.3 0.2 - - - +
63F ILE* 2.8 37.2 + - + +
64F LYS 4.2 0.9 - - - +
66F ALA* 1.3 72.0 - - + +
68F LYS* 1.3 61.2 + - - +
70F LEU* 3.6 14.8 - - + +
71F SER* 2.9 30.3 + - - -
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Residues in contact with LYS 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C LYS* 5.3 26.5 - - + +
150C LYS* 4.1 3.4 - - - +
127D GLU* 3.5 20.2 + - - -
147D GLN* 3.9 20.2 - - + +
149D GLU* 3.2 28.2 + - - -
154D ASN* 3.8 29.5 - - + +
127E GLU* 4.8 3.7 - - - +
64F LYS* 3.1 30.6 + - + +
65F ALA* 3.7 7.0 - - - +
67F LEU* 1.3 77.0 - - - +
69F GLU* 1.3 61.5 + - - +
71F SER* 2.9 22.1 + - - -
72F PHE* 3.2 8.3 + - - +
152F ASN* 4.0 2.6 + - - -
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Residues in contact with GLU 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ASP* 4.6 9.5 - - - +
64C LYS* 3.0 37.6 + - - +
127E GLU* 4.0 10.3 - - - +
43F GLY 4.8 1.9 - - - +
46F ALA* 6.1 0.7 - - - +
47F LEU* 3.9 21.2 - - + +
65F ALA 3.0 16.6 + - - +
66F ALA* 3.6 5.2 - - - +
68F LYS* 1.3 75.2 - - - +
70F LEU* 1.3 66.1 + - - +
72F PHE* 3.1 4.3 + - - +
73F HIS* 3.0 45.5 + - + +
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Residues in contact with LEU 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D PHE* 4.2 30.7 - - + -
145D ILE 4.4 15.7 - - - +
156D ILE* 5.1 3.8 - - + -
44F ALA* 4.4 9.4 - - - +
47F LEU* 3.2 28.9 - - + +
48F LEU* 4.4 18.8 - - + -
51F LEU* 5.1 10.1 - - + -
66F ALA 2.8 16.5 + - - +
67F LEU* 3.6 13.7 - - + +
68F LYS 3.3 0.2 - - - -
69F GLU* 1.3 72.6 - - - +
71F SER* 1.3 64.4 + - - +
73F HIS* 5.1 1.8 - - - -
74F VAL* 3.0 53.6 + - + +
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Residues in contact with SER 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D MET* 5.2 4.5 - - - -
154D ASN* 3.6 30.9 - - - +
156D ILE* 3.7 25.9 - - - +
67F LEU 2.9 15.8 + - - -
68F LYS 2.9 10.2 + - - -
70F LEU* 1.3 77.3 - - - +
72F PHE* 1.3 60.6 + - - +
75F GLY* 3.1 20.6 + - - -
152F ASN* 2.8 31.3 + - - +
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Residues in contact with PHE 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127E GLU* 3.4 56.3 - - + +
128E GLY 4.3 0.4 - - - -
40F TYR* 3.9 15.5 - + - -
68F LYS 3.2 8.5 + - - +
69F GLU 3.1 8.5 + - - +
71F SER* 1.3 83.2 + - - +
73F HIS* 1.3 87.2 + + - +
76F GLY 2.9 22.5 + - - -
150F LYS* 3.8 15.7 - - + -
151F HIS* 3.5 27.1 - + - +
152F ASN* 3.7 14.8 - - - +
168F TRP* 3.9 26.2 - + - -
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Residues in contact with HIS 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C LYS* 5.1 3.4 - - - -
39F ALA* 4.0 4.1 + - - +
40F TYR* 3.5 46.0 - + - +
43F GLY* 3.6 28.4 + - - -
44F ALA* 3.6 20.2 - - - +
47F LEU* 5.6 0.4 - - - +
69F GLU* 3.0 41.9 + - + +
70F LEU* 4.3 2.2 - - - +
72F PHE* 1.3 96.2 - + - +
74F VAL* 1.3 61.6 + - - +
76F GLY 3.2 0.7 + - - -
77F TYR* 2.7 26.7 + - - +
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Residues in contact with VAL 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D PHE* 4.1 5.2 - - + -
156D ILE* 3.8 16.8 - - + -
159D PHE* 3.8 23.8 - - + -
8F TYR* 3.5 28.9 - - + +
44F ALA* 4.0 13.9 - - + -
70F LEU* 3.0 43.8 + - + +
73F HIS* 1.3 73.6 - - - +
75F GLY* 1.3 61.9 + - - +
77F TYR* 3.5 5.9 - - - +
78F VAL* 2.8 39.0 + - + +
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Residues in contact with GLY 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D ILE* 4.1 11.9 - - - +
157D PRO* 4.3 4.7 - - - -
71F SER 3.1 19.8 + - - -
72F PHE 3.9 0.2 - - - -
74F VAL* 1.3 74.6 - - - +
76F GLY* 1.3 64.4 + - - +
78F VAL* 4.0 1.5 - - - +
79F LEU* 2.9 30.5 + - - +
151F HIS* 3.5 20.9 - - - -
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Residues in contact with GLY 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F TYR* 3.9 10.3 - - - -
72F PHE 2.9 12.1 + - - -
73F HIS 3.2 4.4 + - - -
75F GLY* 1.3 74.1 - - - +
77F TYR* 1.3 61.2 + - - +
79F LEU* 4.2 0.4 - - - -
80F HIS* 2.8 32.7 + - - +
151F HIS* 3.2 34.5 - - - +
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Residues in contact with TYR 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D ARG* 3.3 36.7 + - + +
8F TYR* 3.7 41.2 - + + -
9F GLU 3.5 27.1 + - - -
11F PRO* 4.1 13.7 - - + +
37F HIS* 3.5 16.9 + - - -
40F TYR* 3.7 10.1 - - + +
41F VAL* 3.8 21.8 - - + -
44F ALA* 5.6 0.4 - - + -
73F HIS 2.7 19.6 + - - +
74F VAL* 3.3 7.4 + - - +
76F GLY* 1.3 72.5 - - - +
78F VAL* 1.3 76.2 + - + +
81F LEU* 3.1 37.4 + - + +
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Residues in contact with VAL 78 (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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137D CYS* 6.4 0.2 - - - -
156D ILE* 4.5 1.3 - - + -
157D PRO* 4.0 19.3 - - + +
158D HIS* 4.3 4.9 - - + +
159D PHE* 3.7 27.8 - - + -
8F TYR* 5.9 0.7 - - + -
74F VAL* 2.8 28.0 + - + +
75F GLY* 4.0 4.5 - - - +
77F TYR* 1.3 87.2 - - + +
79F LEU* 1.3 64.1 + - + +
81F LEU* 3.2 9.2 + - + +
82F PHE* 3.1 40.3 + - + -
161F ILE* 4.1 10.5 - - + -
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Residues in contact with LEU 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D PRO* 3.9 15.5 - - + -
75F GLY 2.9 19.7 + - - +
76F GLY 4.3 0.2 - - - +
78F VAL* 1.3 74.5 - - - +
80F HIS* 1.3 60.3 + - - +
82F PHE* 3.3 1.3 + - - +
83F PHE* 2.9 29.6 + - - +
131F TRP* 3.5 48.7 - - + +
133F VAL* 4.2 11.7 - - + -
148F VAL* 4.7 4.0 - - + -
151F HIS* 3.7 22.7 - - + +
161F ILE* 3.9 18.4 - - + -
164F VAL* 3.6 30.7 - - + +
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Residues in contact with HIS 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F HIS* 3.2 20.0 + + - -
37F HIS* 3.6 32.4 + + + +
40F TYR* 3.3 28.8 - + - -
76F GLY 2.8 28.4 + - - +
79F LEU* 1.3 77.5 - - - +
81F LEU* 1.3 63.3 + - - +
83F PHE* 3.4 6.5 - + - +
84F TRP* 3.0 46.5 + + - +
131F TRP* 3.6 19.0 - + - -
151F HIS* 3.7 5.4 - + - -
166F ASP* 4.1 1.6 - - - -
170F HIS* 3.7 1.2 + - - -
206F FE 2.1 30.7 - - - -
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Residues in contact with LEU 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D ARG* 3.5 46.9 - - - +
11F PRO* 3.8 27.1 - - + -
37F HIS* 4.0 6.2 - - + -
77F TYR* 3.1 29.3 + - + +
78F VAL* 3.2 11.7 - - + +
79F LEU 3.1 0.2 - - - -
80F HIS* 1.3 79.8 - - - +
82F PHE* 1.3 76.6 + - + +
84F TRP* 3.7 5.5 + - + +
85F GLY* 3.4 14.7 + - - -
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Residues in contact with PHE 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D HIS* 3.6 32.1 - + - -
78F VAL* 3.1 31.5 + - + +
79F LEU 3.3 4.9 + - - +
81F LEU* 1.3 93.0 - - + +
83F PHE* 1.3 65.6 + - - +
86F ASN* 3.0 14.3 + - - +
161F ILE* 3.6 47.1 - - + -
164F VAL* 4.5 4.3 - - + -
199F ARG* 2.9 55.7 + - + +
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Residues in contact with PHE 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F ILE* 4.9 3.8 - - + -
32F HIS* 3.8 18.2 - + - -
79F LEU 2.9 18.9 + - - +
80F HIS* 3.2 6.0 + - - +
82F PHE* 1.3 73.6 - - - +
84F TRP* 1.3 97.5 + + - +
86F ASN* 3.1 21.1 + - - +
87F MET* 3.4 41.5 + - + +
131F TRP* 3.8 7.4 - + + -
164F VAL* 3.2 29.6 - - + +
165F LEU* 3.8 9.6 - - + -
166F ASP* 3.3 27.1 - - + -
183F TYR* 3.3 22.4 - + - -
187F PHE* 4.1 1.6 - + - -
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Residues in contact with TRP 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F PRO* 4.7 6.1 - - + -
12F GLU 5.7 1.3 - - - +
13F LEU* 3.8 15.5 - - + -
14F PRO* 4.1 18.1 - - + +
15F TYR* 2.9 30.5 + - - +
24F ILE* 6.2 1.1 - - + -
29F LEU* 3.8 23.3 - - + -
32F HIS* 3.4 34.1 - + + -
33F HIS* 3.5 28.5 - + + -
37F HIS* 2.8 33.0 + + - -
80F HIS* 3.0 34.5 + + + +
81F LEU* 4.0 6.7 - - + +
83F PHE* 1.3 97.6 - + - +
85F GLY* 1.3 61.8 + - - +
87F MET* 3.3 22.1 + - + +
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Residues in contact with GLY 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F PRO* 4.6 11.3 - - - +
81F LEU 3.4 7.1 + - - -
82F PHE 3.2 6.6 + - - -
83F PHE 3.0 0.8 - - - -
84F TRP* 1.3 82.5 - - - +
86F ASN* 1.3 55.2 + - - +
87F MET 3.3 6.9 + - - +
192F ASN* 4.0 5.9 + - - -
195F GLU* 3.3 20.7 - - - +
199F ARG* 3.5 13.2 - - - -
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Residues in contact with ASN 86 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F PHE 3.0 13.6 + - - +
83F PHE 3.1 13.9 + - - -
85F GLY* 1.3 77.0 - - - +
87F MET* 1.3 63.9 + - - +
163F LEU* 3.6 11.7 - - + +
164F VAL* 3.0 38.7 + - - +
187F PHE* 4.3 2.1 - - - -
191F VAL* 3.5 8.1 - - - +
192F ASN* 2.9 23.5 + - - -
195F GLU* 4.4 0.9 - - + -
196F VAL* 3.8 20.9 - - + -
199F ARG* 2.9 29.3 + - - +
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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