Contacts of the helix formed by residues 28 - 50 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B MET* 3.8 20.6 - - - +
22B ARG* 4.0 6.3 - - - -
21D GLY* 6.5 0.2 - - - -
26D GLY* 3.2 4.9 - - - -
27D THR* 1.3 80.3 - - - +
29D GLU* 1.3 58.6 + - - +
30D LEU 3.5 1.6 - - - -
31D THR* 3.3 13.7 + - - -
32D GLN* 3.0 30.7 + - - +
338D AMP 2.9 4.1 + - - -
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Residues in contact with GLU 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ARG* 3.8 15.2 - - - +
27D THR* 3.5 10.4 + - - +
28D GLY* 1.3 74.9 - - - +
30D LEU* 1.3 64.8 + - - +
32D GLN* 3.0 5.9 + - - +
33D LEU 2.9 19.1 + - - -
88D SER 5.5 0.7 - - - +
89D PHE 3.7 7.1 - - - +
90D ALA* 3.5 27.8 - - + +
111D GLY* 3.4 14.9 - - - -
112D LYS* 3.1 50.9 + - - +
113D TYR* 3.4 7.4 - - - -
338D AMP 2.8 8.6 + - - +
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Residues in contact with LEU 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D GLU* 1.3 77.8 - - - +
31D THR* 1.3 55.9 + - - +
33D LEU* 3.4 14.7 + - + -
34D LEU* 2.9 48.7 + - + +
113D TYR* 4.1 29.1 - - + +
138D ILE* 4.5 13.5 - - + -
160D VAL* 3.8 16.4 - - + -
161D ALA* 5.5 3.6 - - + -
177D MET* 5.5 3.4 - - - -
338D AMP 3.2 64.0 + - + +
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Residues in contact with THR 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B MET* 4.4 8.5 - - - +
17D VAL* 3.7 24.5 - - + -
18D MET* 4.2 28.3 - - + -
21D GLY* 4.1 6.9 - - - -
28D GLY* 3.3 17.9 + - - -
29D GLU 3.1 0.4 - - - -
30D LEU* 1.3 74.7 - - - +
32D GLN* 1.3 64.6 + - - +
34D LEU* 3.9 0.5 - - - +
35D ASN* 3.0 39.0 + - - +
338D AMP 3.2 24.3 + - - -
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Residues in contact with GLN 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ARG* 3.2 42.6 - - + +
18B MET* 3.4 26.4 - - + +
19B GLU* 3.2 30.6 + - - +
22B ARG* 4.3 8.3 - - - +
28D GLY 3.0 18.5 + - - +
29D GLU* 3.0 7.8 + - - +
31D THR* 1.3 75.6 - - - +
33D LEU* 1.3 58.4 + - - +
35D ASN* 3.1 17.2 + - - +
36D SER* 2.7 33.2 + - - +
88D SER* 3.8 21.5 - - - +
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Residues in contact with LEU 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D GLU 2.9 7.5 + - - +
30D LEU* 3.6 10.5 - - + +
32D GLN* 1.3 77.0 - - - +
34D LEU* 1.3 67.7 + - + +
36D SER* 3.0 3.6 + - - -
37D LEU* 3.0 27.9 + - + +
85D LEU* 3.9 23.1 - - + +
88D SER* 4.0 12.2 - - - -
90D ALA* 3.7 17.5 - - + -
91D THR* 4.0 11.7 - - + -
113D TYR* 3.6 37.7 - - + -
115D VAL* 4.2 3.8 - - + -
138D ILE* 3.4 37.9 - - + -
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Residues in contact with LEU 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D LEU* 5.4 2.1 - - - +
17D VAL* 4.2 23.8 - - + -
30D LEU* 2.9 43.3 + - + +
31D THR 4.1 2.7 - - - +
33D LEU* 1.3 75.4 - - + +
35D ASN* 1.3 57.3 + - - +
37D LEU* 3.6 7.6 + - + +
38D CYS* 3.1 25.8 + - - +
136D PHE* 4.9 5.6 - - + -
138D ILE* 4.4 18.8 - - + -
161D ALA* 4.8 4.3 - - + -
175D LEU* 4.1 26.9 - - + -
177D MET* 4.3 16.6 - - - -
338D AMP 4.2 16.4 - - - +
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Residues in contact with ASN 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B THR* 3.7 30.5 - - + +
15B ARG* 5.6 4.0 - - + +
18B MET* 4.5 3.1 - - - +
14D THR* 4.5 14.6 + - - +
17D VAL* 3.8 19.4 - - - +
31D THR* 3.0 33.2 + - - +
32D GLN* 3.4 23.2 + - - +
34D LEU* 1.3 75.1 - - - +
36D SER* 1.3 63.8 + - - +
38D CYS* 3.4 8.3 + - - +
39D THR* 3.2 24.6 + - - -
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Residues in contact with SER 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ARG* 3.1 22.5 + - - +
32D GLN 2.7 17.1 + - - -
33D LEU 3.2 8.1 - - - -
35D ASN* 1.3 72.7 - - - +
37D LEU* 1.3 66.0 + - - +
39D THR* 3.3 5.2 + - - -
40D ALA* 3.0 21.5 + - - +
84D MET* 3.5 40.1 - - - +
85D LEU* 4.7 2.9 - - - -
88D SER* 3.2 13.7 - - - -
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Residues in contact with LEU 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D LEU* 3.0 30.9 + - + +
34D LEU* 3.6 10.5 - - + +
36D SER* 1.3 74.4 - - - +
38D CYS* 1.3 64.7 + - - +
40D ALA* 3.1 10.1 + - + +
41D VAL* 2.9 38.3 + - + +
81D VAL* 4.3 25.6 - - + -
85D LEU* 4.4 12.3 - - + +
115D VAL* 5.4 2.5 - - + -
117D PHE* 6.4 0.2 - - + -
134D THR* 5.6 3.6 - - + -
136D PHE* 3.6 53.2 - - + -
138D ILE* 4.5 2.0 - - + -
173D LEU* 5.9 1.3 - - + -
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Residues in contact with CYS 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D LEU* 3.5 34.3 - - + -
14D THR* 5.2 8.1 - - - -
34D LEU 3.1 14.9 + - - +
35D ASN* 3.4 13.5 - - - +
37D LEU* 1.3 73.5 - - - +
39D THR* 1.3 65.2 + - - +
41D VAL* 3.2 7.4 + - - +
42D LYS* 3.0 35.9 + - - +
173D LEU* 4.8 5.4 - - - -
193D PHE* 3.6 17.8 - - - -
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Residues in contact with THR 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ILE* 4.4 17.3 - - + -
12B THR* 4.1 10.7 + - + +
14B THR* 6.2 0.2 - - - -
190B ILE* 4.5 3.7 - - + +
192B GLU* 3.1 42.1 + - + +
194B ILE* 6.2 0.2 - - + -
35D ASN 3.2 12.2 + - - -
36D SER* 3.5 8.7 - - - -
37D LEU 3.2 0.2 - - - -
38D CYS* 1.3 77.5 - - - +
40D ALA* 1.3 58.1 + - - +
42D LYS* 2.9 24.2 + - - +
43D ALA* 2.9 11.8 + - - +
84D MET* 3.8 21.9 - - + +
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Residues in contact with ALA 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D SER 3.0 13.7 + - - +
37D LEU* 3.1 13.2 + - + +
39D THR* 1.3 75.3 - - - +
41D VAL* 1.3 56.8 + - + +
43D ALA* 3.2 8.4 + - - +
44D ILE* 3.0 36.8 + - - +
80D LEU* 4.1 11.4 - - - +
81D VAL* 4.0 32.5 - - + +
84D MET* 4.1 10.5 - - + +
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Residues in contact with VAL 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D LEU* 2.9 30.8 + - + +
38D CYS 3.6 7.6 - - - +
39D THR 3.2 0.2 - - - -
40D ALA* 1.3 75.6 - - + +
42D LYS* 1.3 57.6 + - - +
44D ILE* 3.6 2.2 + - + -
45D SER* 3.0 26.3 + - - -
81D VAL* 6.3 0.2 - - + -
134D THR* 4.8 10.5 - - + -
136D PHE* 5.7 4.9 - - + -
165D ALA* 3.6 29.6 - - + -
167D TYR* 3.7 20.6 - - + +
171D THR* 4.8 2.2 - - + -
173D LEU* 4.2 12.8 - - + -
193D PHE* 3.8 22.2 - - + -
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Residues in contact with LYS 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LYS* 4.3 2.4 - - - +
189B ALA 5.0 0.2 - - - +
190B ILE* 3.3 28.0 + - + +
191B GLY 3.0 23.0 + - - -
192B GLU* 2.8 30.3 + - - -
38D CYS* 3.0 22.0 + - - +
39D THR* 2.9 14.3 + - - +
41D VAL* 1.3 72.7 - - - +
43D ALA* 1.3 64.7 + - - +
45D SER* 3.5 6.6 + - - +
46D SER* 3.3 21.3 + - - -
186D LEU* 3.8 22.0 - - + +
191D GLY* 3.2 20.6 + - - +
193D PHE* 3.7 20.9 - - + -
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Residues in contact with ALA 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A HIS* 5.4 7.0 + - - +
59A ILE* 3.6 32.3 - - + -
190B ILE* 3.9 14.9 - - + +
39D THR 2.9 8.7 + - - +
40D ALA* 3.5 9.0 - - - +
42D LYS* 1.3 73.4 - - - +
44D ILE* 1.3 65.2 + - - +
46D SER* 3.4 6.6 + - - -
47D ALA* 3.3 19.2 + - - +
80D LEU* 3.7 18.7 - - + +
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Residues in contact with ILE 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ALA 3.0 23.6 + - - +
41D VAL* 3.8 5.6 - - + +
43D ALA* 1.3 73.4 - - - +
45D SER* 1.3 67.1 + - - +
47D ALA* 3.0 7.8 + - + +
48D VAL* 2.9 35.1 + - + +
77D SER* 3.9 24.7 - - - +
80D LEU* 3.9 18.4 - - + +
81D VAL* 4.0 25.4 - - + -
119D PRO 4.1 5.6 - - - +
120D LEU* 4.3 3.8 - - + -
134D THR* 3.8 17.9 - - + +
167D TYR* 3.6 22.7 - - + +
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Residues in contact with SER 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D VAL 3.0 18.3 + - - -
42D LYS* 3.9 5.6 - - - -
43D ALA 3.4 0.2 - - - -
44D ILE* 1.3 73.3 - - - +
46D SER* 1.3 64.2 + - - +
48D VAL* 3.4 1.7 + - - -
49D ARG* 3.0 38.5 + - - -
167D TYR* 3.7 19.8 - - - -
171D THR* 2.7 32.2 + - - -
186D LEU* 4.2 11.2 - - - +
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Residues in contact with SER 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ALA* 3.9 30.6 + - - +
190B ILE* 4.1 6.5 - - - +
42D LYS 3.3 10.7 + - - -
43D ALA 3.5 10.8 - - - -
44D ILE 3.2 0.4 - - - -
45D SER* 1.3 79.3 - - - +
47D ALA* 1.3 64.0 + - - +
49D ARG* 3.2 10.5 + - - +
50D LYS 3.3 0.2 + - - -
51D ALA* 3.3 36.5 + - - +
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Residues in contact with ALA 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A HIS* 6.2 1.6 - - - +
43D ALA 3.3 8.6 + - - +
44D ILE* 3.0 12.0 + - - +
46D SER* 1.3 81.1 - - - +
48D VAL* 1.3 62.3 + - - +
50D LYS* 3.1 20.8 + - - +
51D ALA 5.0 5.8 - - - +
73D LEU* 4.1 20.7 - - + +
76D LEU* 4.3 20.0 - - + -
80D LEU* 5.5 1.1 - - + -
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Residues in contact with VAL 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C SER* 3.1 39.1 + - - +
170C ALA* 3.8 1.2 - - - +
44D ILE* 2.9 38.4 + - + +
45D SER* 3.8 6.7 - - - +
47D ALA* 1.3 74.0 - - - +
49D ARG* 1.3 58.5 + - - +
50D LYS* 3.0 22.2 + - - +
73D LEU* 4.4 18.2 - - + +
120D LEU* 4.1 15.9 - - + -
126D ILE* 4.5 5.6 - - + +
132D VAL* 3.8 14.8 - - + -
167D TYR* 4.0 13.2 - - + -
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Residues in contact with ARG 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ARG* 3.6 32.7 + - + +
168C GLY 3.3 8.5 + - - -
169C SER* 3.3 25.7 + - - +
170C ALA* 3.9 8.1 - - - +
171C THR 4.9 0.7 + - - -
186C LEU 3.9 2.9 - - - +
188C PRO* 3.5 22.4 - - + +
45D SER* 3.0 40.6 + - - +
46D SER* 3.7 5.6 - - - +
47D ALA 3.2 0.4 - - - -
48D VAL* 1.3 79.5 - - - +
50D LYS* 1.3 67.6 + - - +
51D ALA 3.4 1.1 - - - -
167D TYR* 3.9 10.1 + - - +
168D GLY 2.9 29.5 + - - +
169D SER 3.6 4.6 + - - -
170D ALA* 3.3 21.4 + - - +
171D THR* 3.2 17.7 + - - +
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Residues in contact with LYS 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C ALA* 4.0 9.6 - - + -
185C MET* 3.9 34.9 - - + +
186C LEU 4.1 2.0 - - - +
187C ASP* 3.8 2.4 - - - +
188C PRO* 3.8 3.7 - - - +
46D SER 3.3 0.2 + - - -
47D ALA 3.1 14.1 + - - +
48D VAL 3.0 28.0 + - - +
49D ARG* 1.3 77.9 - - - +
51D ALA* 1.3 66.6 + - - +
52D GLY 2.9 4.2 + - - -
53D ILE* 3.1 47.4 + - + +
56D LEU* 5.9 1.8 - - - +
71D LYS* 5.7 6.2 - - - +
73D LEU* 4.7 17.2 - - - +
126D ILE* 5.8 6.5 - - - -
129D LEU* 5.4 4.5 - - - -
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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