Contacts of the helix formed by residues 28 - 50 (chain C) in PDB entry 1FTA
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 GLY 28 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A MET* 3.7 19.9 - - - +
22A ARG* 4.3 6.1 - - - -
26C GLY 3.2 4.2 + - - -
27C THR* 1.3 80.2 - - - +
29C GLU* 1.3 59.2 + - - +
30C LEU 3.5 1.6 - - - -
31C THR* 3.8 11.0 - - - -
32C GLN* 3.0 35.2 + - - +
338C AMP 2.8 4.8 + - - -
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Residues in contact with GLU 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ARG* 3.8 23.9 + - - +
27C THR* 3.6 5.1 - - - +
28C GLY* 1.3 74.0 - - - +
30C LEU* 1.3 68.7 + - - +
32C GLN* 3.2 3.9 + - - +
33C LEU 2.9 17.7 + - - -
89C PHE 4.3 4.2 - - - +
90C ALA* 3.4 31.8 - - + +
111C GLY* 4.0 8.2 - - - -
112C LYS* 3.0 49.9 + - - +
113C TYR* 3.8 3.0 - - + -
338C AMP 3.0 16.1 + - - +
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Residues in contact with LEU 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C GLU* 1.3 79.9 - - - +
31C THR* 1.3 64.3 + - - +
33C LEU* 2.9 28.3 + - + +
34C LEU* 2.8 35.9 + - + +
113C TYR* 3.8 25.8 - - + +
138C ILE* 4.1 18.8 - - + -
160C VAL* 3.8 23.3 - - + -
161C ALA* 5.3 3.4 - - + -
177C MET* 5.3 3.8 - - - -
338C AMP 3.4 51.0 + - + +
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Residues in contact with THR 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A MET* 3.9 25.6 - - + -
17C VAL* 3.9 22.1 + - + +
18C MET* 4.2 17.6 - - + +
21C GLY* 4.0 6.6 - - - -
28C GLY* 3.5 16.4 + - - -
29C GLU 3.3 0.6 - - - -
30C LEU* 1.3 76.4 - - - +
32C GLN* 1.3 57.4 + - - +
34C LEU* 3.3 1.9 + - - +
35C ASN* 2.9 39.3 + - - +
338C AMP 2.9 27.0 + - - -
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Residues in contact with GLN 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG* 3.4 42.4 - - - +
18A MET* 3.2 34.0 - - + +
19A GLU* 3.8 19.1 - - - +
22A ARG* 3.8 15.9 - - - +
28C GLY 3.0 21.4 + - - +
29C GLU* 3.5 4.9 - - - +
31C THR* 1.3 74.4 - - - +
33C LEU* 1.3 58.0 + - - +
35C ASN* 3.3 12.3 + - - +
36C SER* 3.0 32.4 + - - +
88C SER* 4.1 19.6 - - - +
90C ALA* 5.1 0.2 - - + -
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Residues in contact with LEU 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C GLU 2.9 11.1 + - - +
30C LEU* 2.9 21.8 + - + +
32C GLN* 1.3 76.4 - - - +
34C LEU* 1.3 56.3 + - - +
36C SER* 3.3 2.3 + - - -
37C LEU* 3.0 32.6 + - + +
85C LEU* 3.4 26.9 - - + -
88C SER* 4.2 9.8 - - - +
90C ALA* 3.9 7.6 - - + -
91C THR* 4.1 9.0 - - + -
113C TYR* 3.5 39.5 - - + -
115C VAL* 4.0 15.9 - - + -
138C ILE* 4.2 15.5 - - + -
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Residues in contact with LEU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 4.7 5.5 - - + +
17C VAL* 3.8 37.2 - - + -
30C LEU* 2.8 35.6 + - + +
31C THR 3.8 3.8 - - - +
33C LEU* 1.3 69.3 - - - +
35C ASN* 1.3 66.6 + - - +
37C LEU* 3.4 14.9 + - + +
38C CYS* 3.0 23.7 + - - +
136C PHE* 5.0 1.8 - - + -
138C ILE* 3.8 28.5 - - + -
161C ALA* 5.1 2.5 - - + -
175C LEU* 4.6 19.3 - - + -
177C MET* 4.5 20.0 - - - -
338C AMP 4.5 3.8 - - - +
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Residues in contact with ASN 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A THR* 4.2 20.5 - - + +
15A ARG* 5.5 5.4 - - + -
18A MET* 4.1 5.5 - - - +
13C LEU* 5.8 2.2 - - - +
14C THR* 4.0 31.3 + - - +
17C VAL* 4.9 7.1 - - - +
31C THR* 2.9 33.5 + - - +
32C GLN* 3.6 25.0 + - - +
34C LEU* 1.3 77.3 - - - +
36C SER* 1.3 61.1 + - - +
38C CYS* 3.2 18.0 + - - +
39C THR* 3.2 16.9 + - - -
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Residues in contact with SER 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG* 3.0 27.0 + - - +
32C GLN 3.0 15.0 + - - -
33C LEU* 3.5 8.7 - - - -
35C ASN* 1.3 76.0 - - - +
37C LEU* 1.3 62.0 + - - +
39C THR* 3.3 3.3 + - - -
40C ALA* 3.1 18.2 + - - +
84C MET* 3.3 41.4 - - - +
85C LEU* 4.5 4.5 - - - -
88C SER* 3.2 12.8 - - - -
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Residues in contact with LEU 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 3.0 20.8 + - + +
34C LEU* 3.7 17.7 - - + +
35C ASN 3.3 0.2 - - - -
36C SER* 1.3 73.7 - - - +
38C CYS* 1.3 67.9 + - - +
40C ALA* 3.3 5.9 + - + +
41C VAL* 3.0 36.4 + - + +
81C VAL* 3.9 28.3 - - + -
85C LEU* 4.1 14.8 - - + +
115C VAL* 5.6 2.7 - - + -
117C PHE* 6.2 0.4 - - + -
134C THR* 6.0 2.5 - - + -
136C PHE* 3.7 52.0 - - + -
138C ILE* 4.6 6.5 - - + -
173C LEU* 6.1 1.6 - - + -
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Residues in contact with CYS 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A GLU* 5.1 1.6 - - - -
13C LEU* 3.6 28.9 - - + -
14C THR* 4.7 11.9 - - - -
34C LEU 3.0 13.9 + - - +
35C ASN* 3.3 14.1 - - - +
37C LEU* 1.3 76.7 - - - +
39C THR* 1.3 62.9 + - - +
41C VAL* 3.2 6.0 + - - +
42C LYS* 3.1 38.2 + - - +
173C LEU* 5.7 3.8 - - - -
193C PHE* 3.8 23.2 - - - -
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Residues in contact with THR 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A THR* 4.2 10.4 + - + +
190A ILE* 4.4 1.9 - - + +
192A GLU* 2.7 43.8 + - + +
59B ILE* 4.0 20.6 - - + -
35C ASN 3.2 10.8 + - - -
36C SER 3.3 6.9 + - - -
38C CYS* 1.3 75.6 - - - +
40C ALA* 1.3 64.8 + - - +
42C LYS* 3.0 9.2 + - - +
43C ALA* 2.9 20.1 + - - +
84C MET* 3.8 23.3 - - + +
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Residues in contact with ALA 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ILE* 6.1 0.2 - - - -
36C SER 3.1 14.4 + - - +
37C LEU* 3.5 11.7 - - + +
39C THR* 1.3 73.7 - - - +
41C VAL* 1.3 53.9 + - + +
43C ALA* 3.0 11.6 + - - +
44C ILE* 2.8 38.0 + - - +
80C LEU* 3.9 24.4 - - + +
81C VAL* 4.0 23.3 - - + -
84C MET* 4.2 9.1 - - + +
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Residues in contact with VAL 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LEU* 3.0 29.5 + - + +
38C CYS* 3.5 5.2 - - - +
39C THR 3.1 0.2 - - - -
40C ALA* 1.3 74.8 - - + +
42C LYS* 1.3 66.4 + - - +
43C ALA 3.2 0.3 + - - -
44C ILE* 3.2 5.0 + - + +
45C SER* 2.9 22.9 + - - -
81C VAL* 6.0 0.2 - - + -
134C THR* 4.8 13.2 - - + -
136C PHE* 5.6 2.7 - - + -
165C ALA* 3.8 27.8 - - + -
167C TYR* 3.9 19.0 + - + +
171C THR* 5.1 1.6 - - + -
173C LEU* 4.2 10.5 - - + -
193C PHE* 3.6 25.4 - - + -
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Residues in contact with LYS 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LYS* 4.5 1.6 - - - +
189A ALA 4.9 0.9 - - - +
190A ILE* 3.3 33.3 + - + +
191A GLY 3.5 7.3 + - - -
192A GLU* 3.0 29.3 + - - -
38C CYS* 3.1 18.6 + - - +
39C THR* 3.0 11.7 + - - +
41C VAL* 1.3 74.1 - - - +
43C ALA* 1.3 61.7 + - - +
45C SER* 3.5 8.4 - - - -
46C SER* 3.2 22.0 + - - -
186C LEU* 4.0 21.3 - - + +
191C GLY* 2.9 29.7 + - - +
193C PHE* 3.7 24.9 - - + -
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Residues in contact with ALA 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A ILE* 3.8 17.8 - - + +
55B HIS* 5.4 7.2 - - + -
59B ILE* 4.6 11.0 - - + -
39C THR 2.9 12.4 + - - +
40C ALA* 3.0 10.1 + - - +
42C LYS* 1.3 72.9 - - - +
44C ILE* 1.3 65.8 + - - +
46C SER* 3.4 5.1 + - - -
47C ALA* 3.1 21.0 + - - +
80C LEU* 3.6 32.0 - - + +
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Residues in contact with ILE 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C ALA* 2.8 25.7 + - + +
41C VAL* 3.2 7.2 + - + +
43C ALA* 1.3 70.8 - - - +
45C SER* 1.3 64.2 + - - +
47C ALA* 3.1 6.1 + - + +
48C VAL* 2.8 29.8 + - + +
77C SER* 3.2 34.1 - - - +
80C LEU* 4.0 15.9 - - + -
81C VAL* 3.6 30.7 - - + -
119C PRO 4.2 1.6 - - - +
120C LEU* 3.6 23.6 - - + -
134C THR* 3.9 16.2 - - + +
167C TYR* 3.8 11.0 - - - +
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Residues in contact with SER 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C VAL 2.9 17.5 + - - -
42C LYS* 3.5 10.1 - - - -
44C ILE* 1.3 72.5 - - - +
46C SER* 1.3 63.7 + - - +
48C VAL* 3.0 6.8 + - - +
49C ARG* 2.9 31.8 + - - +
167C TYR* 3.7 24.0 - - - -
171C THR* 3.2 28.0 + - - +
186C LEU* 3.8 11.7 - - - +
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Residues in contact with SER 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ALA* 3.1 33.3 + - - +
190A ILE* 4.5 6.1 - - - -
42C LYS 3.2 10.3 + - - -
43C ALA 3.6 8.7 - - - -
45C SER* 1.3 76.0 - - - +
47C ALA* 1.3 63.4 + - - +
49C ARG* 3.1 15.4 + - - +
50C LYS 3.4 0.2 + - - -
51C ALA* 3.3 32.7 + - - +
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Residues in contact with ALA 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B HIS* 6.4 1.3 - - + -
43C ALA 3.1 9.4 + - - +
44C ILE* 3.1 13.5 + - + +
46C SER* 1.3 78.5 - - - +
48C VAL* 1.3 63.4 + - + +
50C LYS* 3.2 18.9 + - - +
51C ALA 5.1 4.5 - - - +
73C LEU* 3.7 29.7 - - + +
76C LEU* 3.8 22.0 - - + -
77C SER* 5.5 0.9 - - - +
80C LEU* 5.4 0.9 - - + -
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Residues in contact with VAL 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ILE* 2.8 22.7 + - + +
45C SER* 3.3 9.4 - - - +
47C ALA* 1.3 71.7 - - - +
49C ARG* 1.3 58.0 + - - +
50C LYS* 2.8 24.2 + - - +
73C LEU* 3.9 17.1 - - + +
120C LEU* 3.8 29.6 - - + -
126C ILE* 4.1 7.1 - - + +
132C VAL* 3.6 22.9 - - + -
167C TYR* 4.1 12.6 - - + -
169D SER* 3.8 26.8 + - - +
170D ALA* 3.9 3.6 - - - +
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Residues in contact with ARG 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C SER* 2.9 28.4 + - - +
46C SER* 3.1 7.8 + - - +
48C VAL* 1.3 73.9 - - - +
50C LYS* 1.3 68.7 + - - +
51C ALA* 3.3 2.9 + - + +
167C TYR* 4.0 6.8 - - - +
168C GLY 2.7 37.0 + - - +
170C ALA* 3.7 7.5 + - - +
171C THR* 3.1 30.0 + - - +
186C LEU* 5.6 1.8 - - - +
188C PRO* 6.1 3.6 - - - +
49D ARG* 3.6 41.3 + - + +
169D SER* 3.0 21.7 + - - +
170D ALA* 4.2 6.8 - - - +
171D THR 5.3 0.9 + - - -
186D LEU 4.1 1.4 - - - +
188D PRO* 3.3 26.8 - - + +
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Residues in contact with LYS 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ALA 3.2 15.9 + - - +
48C VAL 2.8 23.3 + - - +
49C ARG* 1.3 79.7 - - - +
51C ALA* 1.3 68.3 + - - +
52C GLY 3.2 0.3 + - - -
53C ILE* 3.1 49.5 + - + +
73C LEU* 4.3 21.7 - - - +
126C ILE* 5.4 7.4 - - + -
129C LEU* 6.2 1.6 - - + -
170D ALA* 4.3 8.7 - - + -
185D MET* 4.0 35.7 - - + -
186D LEU 4.3 2.0 - - - +
187D ASP* 4.0 4.7 - - - +
188D PRO* 4.3 1.1 - - - -
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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