Contacts of the helix formed by residues 20 - 42 (chain A) in PDB entry 3LKB
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 THR 20 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ALA* 4.3 0.2 - - + -
19A PRO* 1.3 74.7 - - - +
21A SER* 1.3 58.7 + - - +
22A ASP 3.2 3.1 - - - -
23A ALA* 3.0 21.3 + - - +
58A TYR* 3.8 16.8 + - + -
82A TYR* 2.4 51.6 + - + +
151A HIS* 4.2 9.2 + - - -
155A PHE* 4.1 11.3 - - - -
207A VAL* 3.8 12.8 - - + +
393A VAL 3.6 20.5 + - - +
4571A IPA 3.2 20.1 - - - +
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Residues in contact with SER 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ALA 3.5 21.3 - - - -
16A ILE 3.5 16.2 - - - -
17A THR* 3.6 8.2 - - - -
18A GLY 2.8 23.9 + - - -
19A PRO 3.2 0.8 + - - -
20A THR* 1.3 73.7 - - - +
22A ASP* 1.3 67.4 + - - +
23A ALA 2.9 2.8 + - - -
24A GLY 3.7 0.2 - - - -
25A ALA* 3.0 24.8 + - - +
4571A IPA 3.5 11.6 + - - +
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Residues in contact with ASP 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A THR 3.1 0.6 + - - -
21A SER* 1.3 77.2 + - - +
23A ALA* 1.3 57.3 + - + +
26A PRO* 3.3 18.9 - - - +
207A VAL* 4.0 13.1 - - + +
208A ALA* 4.6 8.1 - - + +
209A GLY* 3.1 31.3 + - - -
237A ASP* 4.5 13.7 - - + +
241A LEU* 4.5 14.4 - - + +
286A ASN* 4.7 1.4 + - - -
4571A IPA 2.8 33.0 + - - +
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Residues in contact with ALA 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A THR* 3.0 8.3 + - + +
21A SER 3.0 0.2 - - - -
22A ASP* 1.3 79.5 - - + +
24A GLY* 1.3 65.6 + - - +
25A ALA 3.3 2.1 + - - -
26A PRO* 3.3 3.9 - - - +
27A TYR* 3.1 25.1 + - - +
82A TYR* 3.9 5.6 - - + +
207A VAL* 4.0 11.9 - - + -
232A TYR* 3.5 36.6 - - + +
286A ASN* 3.6 16.7 - - - +
393A VAL 5.5 0.4 - - - +
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Residues in contact with GLY 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A TRP* 3.6 8.7 - - - -
15A ALA 3.2 20.2 - - - -
16A ILE* 4.3 1.0 - - - -
20A THR 3.2 3.2 + - - -
21A SER 3.4 0.4 + - - -
23A ALA* 1.3 78.8 - - - +
25A ALA* 1.3 55.7 + - - +
27A TYR* 4.1 1.6 - - - -
28A GLY* 2.8 27.5 + - - -
82A TYR* 3.0 32.2 + - - -
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Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ALA 3.6 2.4 + - - -
16A ILE* 3.7 27.4 - - - +
21A SER* 3.0 15.5 + - - +
24A GLY* 1.3 75.8 - - - +
26A PRO* 1.3 65.5 - - + +
28A GLY* 3.2 0.7 + - - -
29A ALA* 2.9 29.5 + - - +
281A PHE* 3.7 11.6 - - + -
17B THR* 3.8 20.4 - - + -
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Residues in contact with PRO 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ASP 3.3 24.9 - - - +
23A ALA 3.3 10.3 - - - +
25A ALA* 1.3 96.1 - - + +
27A TYR* 1.3 54.4 + - - +
29A ALA* 3.2 0.3 + - - +
30A ALA* 2.9 25.6 + - - +
237A ASP* 4.9 1.3 - - - +
281A PHE* 3.6 29.2 - - + -
284A SER* 3.9 23.6 - - - +
286A ASN* 4.0 7.2 - - + -
287A TYR* 3.4 27.0 - - + +
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Residues in contact with TYR 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A TRP* 3.1 40.4 - + - -
23A ALA 3.1 20.7 + - - +
24A GLY* 3.7 7.6 - - - +
26A PRO* 1.3 74.9 - - - +
28A GLY* 1.3 66.0 + - - +
30A ALA* 3.2 4.3 + - - +
31A VAL* 3.2 23.7 + - + +
80A LEU* 5.8 0.8 - - + +
81A SER 4.3 1.2 + - - -
82A TYR* 4.9 2.5 - + - -
102A ILE 4.7 1.0 + - - -
103A PRO 4.0 2.8 + - - -
104A ALA* 3.3 41.6 + - + +
122A PRO* 5.4 0.7 - - - +
232A TYR* 4.5 2.7 - + - -
286A ASN* 3.4 15.1 + - + +
289A ASN* 3.5 34.5 + - + -
290A GLY* 3.5 25.1 - - - -
293A ALA* 3.3 22.1 - - + +
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Residues in contact with GLY 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A TRP* 3.8 31.0 - - - -
16A ILE* 4.8 3.1 - - - -
24A GLY 2.8 20.6 + - - -
25A ALA 3.8 0.9 - - - -
27A TYR* 1.3 73.4 - - - +
29A ALA* 1.3 63.2 + - - +
31A VAL* 3.1 14.2 + - - +
32A GLU* 3.1 13.4 + - - +
53A VAL* 4.2 9.7 - - - +
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ILE* 5.8 0.2 - - - +
25A ALA 2.9 17.1 + - - +
26A PRO 3.5 5.4 - - - +
28A GLY* 1.3 77.2 - - - +
30A ALA* 1.3 56.4 + - - +
32A GLU* 3.3 2.8 + - - -
33A ASP* 2.9 33.3 + - - -
277A ARG* 3.4 34.9 + - - +
281A PHE* 3.9 18.6 - - + -
287A TYR* 3.9 4.9 - - + -
57B GLN* 5.3 0.2 - - - +
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Residues in contact with ALA 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A PRO 2.9 11.1 + - - +
27A TYR 3.2 4.2 + - - +
29A ALA* 1.3 77.1 - - - +
31A VAL* 1.3 62.6 + - - +
33A ASP* 3.8 0.8 - - - +
34A TYR* 2.9 27.4 + - - +
287A TYR* 3.1 51.5 - - + +
290A GLY* 3.8 2.2 - - - -
291A MET* 3.5 19.0 - - + +
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Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU* 5.1 9.4 - - + +
12A TRP* 4.1 25.4 - - + +
27A TYR* 3.2 31.5 + - + +
28A GLY 3.1 7.9 + - - +
30A ALA* 1.3 76.4 - - - +
32A GLU* 1.3 62.9 + - - +
34A TYR* 3.9 1.2 - - - +
35A CYS* 3.0 23.7 + - - +
51A CYS* 5.2 2.7 - - - -
53A VAL* 4.4 8.1 - - + -
80A LEU* 3.8 27.6 - - + -
290A GLY 3.9 14.8 - - - +
293A ALA* 5.4 0.4 - - + -
294A ALA* 4.0 11.4 - - + +
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Residues in contact with GLU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A GLY 3.1 8.9 + - - +
29A ALA* 3.7 7.6 - - - +
31A VAL* 1.3 79.7 - - - +
33A ASP* 1.3 62.3 + - - +
35A CYS* 3.4 2.8 + - - +
36A LYS* 3.0 54.2 + - - +
51A CYS* 3.6 21.9 - - - -
53A VAL* 4.0 24.1 - - + +
277A ARG* 4.4 11.3 + - - +
54B ARG* 4.7 9.7 + - - -
66B PHE* 6.2 0.3 - - - -
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Residues in contact with ASP 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ALA 2.9 17.9 + - - +
30A ALA* 3.8 2.9 - - - +
32A GLU* 1.3 76.8 - - - +
34A TYR* 1.3 61.1 + - - +
36A LYS* 3.1 11.8 - - - +
37A TRP* 2.8 25.5 + - - +
271A ILE* 3.7 13.0 - - + +
275A TYR* 3.5 25.9 - - + +
277A ARG* 2.7 41.3 + - - +
287A TYR* 2.7 28.7 + - + +
291A MET* 5.1 0.2 - - + -
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Residues in contact with TYR 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ALA 2.9 18.0 + - - +
31A VAL 3.9 2.5 - - - +
33A ASP* 1.3 76.6 - - - +
35A CYS* 1.3 52.6 + - - +
37A TRP* 3.1 14.2 + + - +
38A ALA* 2.7 32.1 + - - +
43A LEU* 3.8 20.8 - - + +
267A LEU* 4.1 23.5 - - + +
271A ILE* 4.0 12.7 - - + +
291A MET* 3.6 27.3 - - + +
294A ALA* 3.8 15.3 - - + -
295A ALA* 3.5 41.7 + - + +
298A VAL* 4.0 24.9 - - + +
329A PHE* 5.4 2.9 - - - -
333A PHE* 5.2 1.6 - + - -
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Residues in contact with CYS 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU* 3.7 32.1 - - + -
31A VAL* 3.0 18.6 + - + +
32A GLU 3.7 3.6 - - - +
34A TYR* 1.3 78.8 - - - +
36A LYS* 1.3 61.9 + - - +
38A ALA* 3.4 8.8 + - - +
39A ASN* 3.3 23.7 + - - -
49A PHE* 3.2 35.4 - - - -
51A CYS* 3.7 29.6 - - + -
294A ALA* 5.2 0.4 - - - +
298A VAL* 5.3 0.2 - - - -
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Residues in contact with LYS 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A GLU* 3.0 45.2 + - + +
33A ASP* 3.1 13.7 - - - +
35A CYS* 1.3 78.6 - - - +
37A TRP* 1.4 60.7 + - - +
39A ASN* 3.3 11.5 + - - +
40A GLU* 3.0 32.0 + - - +
51A CYS* 5.3 9.6 - - - +
275A TYR* 3.4 33.0 - - + +
54B ARG* 4.4 15.4 - - - +
65B ARG* 6.0 3.8 - - - +
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Residues in contact with TRP 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ASP 2.8 12.9 + - - +
34A TYR* 3.5 16.4 - + - +
36A LYS* 1.4 74.3 - - - +
38A ALA* 1.3 65.0 + - - +
40A GLU* 3.3 2.6 + - + -
41A ARG* 3.0 66.6 + - + +
43A LEU* 3.5 41.5 - - + -
267A LEU* 3.5 38.7 - - + +
270A GLU* 4.6 13.6 + - + +
271A ILE* 3.5 36.4 - - + +
274A LYS* 5.0 15.1 - - + +
275A TYR* 3.2 14.5 + + + +
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Residues in contact with ALA 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A TYR* 2.7 17.2 + - + +
35A CYS* 3.5 13.9 - - - +
36A LYS 3.4 0.2 - - - -
37A TRP* 1.3 72.1 - - - +
39A ASN* 1.3 58.6 + - - +
42A LYS* 3.0 24.9 + - - -
43A LEU* 3.1 33.4 + - + -
44A VAL 4.8 0.7 + - - -
49A PHE* 3.9 27.0 - - + -
298A VAL* 4.3 11.0 - - + -
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Residues in contact with ASN 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A CYS* 3.3 14.5 + - - -
36A LYS* 3.3 11.2 + - - +
37A TRP 3.2 1.0 - - - -
38A ALA* 1.3 79.0 - - - +
40A GLU* 1.3 63.2 + - + +
42A LYS* 3.4 22.1 + - - +
47A VAL 4.0 3.6 - - - +
48A VAL* 3.5 13.6 - - - +
49A PHE* 2.7 53.9 + - - +
51A CYS* 6.1 0.2 - - - +
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Residues in contact with GLU 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LYS* 3.0 23.3 + - - +
37A TRP* 3.9 4.3 - - + +
39A ASN* 1.3 76.8 - - + +
41A ARG* 1.3 73.8 + - + +
42A LYS* 3.7 8.3 + - - +
274A LYS* 3.6 26.6 + - - -
275A TYR* 3.2 29.9 + - - +
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Residues in contact with ARG 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A TRP* 3.0 58.0 + - + +
40A GLU* 1.3 85.2 + - + +
42A LYS* 1.3 71.8 + - - +
43A LEU* 3.2 22.0 + - + +
270A GLU* 6.0 0.4 - - - -
274A LYS* 6.3 1.8 - - - +
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Residues in contact with LYS 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ALA 3.0 9.9 + - - -
39A ASN* 3.4 14.3 + - - +
40A GLU 3.4 9.1 + - - +
41A ARG* 1.3 80.9 - - - +
43A LEU* 1.3 65.6 + - - +
44A VAL* 3.2 14.2 + - - +
45A PRO* 4.1 11.7 - - + +
46A GLY 6.1 0.9 - - - +
47A VAL 5.9 3.6 - - - +
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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
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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) + - + + + + + -
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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