Contacts of the helix formed by residues 38 - 64 (chain A) in PDB entry 3J41
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 PRO 38 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ALA* 4.2 5.6 - - + -
36A PRO* 3.4 28.9 - - + +
37A GLY* 1.3 92.6 - - - +
39A LEU* 1.3 63.4 + - + +
42A LEU* 4.2 0.5 - - - +
177A TYR* 3.6 5.3 - - - +
33B ARG* 5.7 2.7 - - - +
39B LEU* 3.3 38.8 - - + +
43B GLN* 2.3 36.2 + - - +
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Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ARG* 5.2 5.4 - - - +
35A ALA* 5.4 4.9 - - + -
38A PRO* 1.3 81.5 - - + +
40A HIS* 1.3 75.0 - - + +
41A VAL 3.3 0.2 - - - -
42A LEU* 3.5 10.0 + - + +
43A GLN* 3.0 26.7 + - - +
39B LEU* 3.3 24.8 - - + +
38D PRO* 3.3 45.8 - - + +
39D LEU* 3.3 33.7 - - + +
42D LEU* 5.0 6.1 - - + +
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Residues in contact with HIS 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A SER* 3.8 16.4 - - - -
33A ARG* 2.7 44.9 + - + +
34A TRP* 2.8 25.2 + - - +
35A ALA* 3.3 29.6 - - + -
37A GLY* 4.3 13.2 - - - -
38A PRO* 3.3 0.4 - - - +
39A LEU* 1.3 84.9 - - + +
41A VAL* 1.3 60.7 + - + +
44A VAL* 2.9 42.1 + - + +
176A MET* 3.8 19.4 - - + +
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Residues in contact with VAL 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLY* 2.7 39.4 + - - +
39A LEU 3.3 0.2 - - - -
40A HIS* 1.3 77.9 - - + +
42A LEU* 1.3 55.9 + - - +
45A ALA* 2.7 38.8 + - - +
172A HIS 3.8 9.9 - - - +
173A LEU* 3.8 34.1 - - + +
176A MET* 3.9 22.7 - - + +
177A TYR* 3.6 18.2 - - + -
43B GLN* 3.4 11.7 - - - +
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Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PRO 4.2 1.1 - - - +
39A LEU* 3.5 13.4 + - + +
40A HIS 3.4 0.6 - - - -
41A VAL* 1.3 78.0 - - - +
43A GLN* 1.3 57.7 + - - +
45A ALA* 3.7 0.7 - - - +
46A LEU* 3.0 58.9 + - + +
169A THR* 6.2 0.2 - - + -
173A LEU* 4.0 13.7 - - + -
39B LEU* 4.9 5.8 - - + +
42B LEU* 3.6 38.4 - - + -
43B GLN* 3.3 29.2 - - + +
46B LEU* 3.7 20.4 - - + -
42D LEU* 3.6 16.2 - - + -
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Residues in contact with GLN 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA* 4.9 5.3 - - + +
33A ARG* 3.4 18.1 + - - +
39A LEU* 3.0 18.2 + - - +
40A HIS 3.5 3.8 - - - +
42A LEU* 1.3 75.2 - - - +
44A VAL* 1.3 61.3 + - - +
46A LEU* 3.5 3.3 + - - +
47A ALA* 2.9 28.8 + - - +
37D GLY 3.4 5.0 + - - -
38D PRO* 2.3 33.1 + - - +
41D VAL* 3.4 7.7 - - - +
42D LEU* 3.3 30.0 - - + +
173D LEU* 3.9 24.1 - - + +
177D TYR* 3.3 22.2 + - - -
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Residues in contact with VAL 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLY 5.1 0.2 - - - +
30A ALA 3.6 22.0 - - - +
31A SER* 3.2 28.9 - - - +
33A ARG* 4.0 2.5 - - - +
40A HIS* 2.9 34.0 + - + +
43A GLN* 1.3 73.9 - - - +
45A ALA* 1.3 64.5 + - - +
47A ALA* 3.7 5.1 - - + +
48A PHE* 3.1 39.1 + - + -
172A HIS* 4.3 1.3 - - + -
176A MET* 3.3 31.0 - - + -
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Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A VAL 2.7 23.0 + - - +
42A LEU 3.7 1.3 - - - +
44A VAL* 1.3 73.5 - - - +
46A LEU* 1.3 56.8 + - - +
48A PHE* 4.1 1.6 - - - +
49A GLY 3.0 15.6 + - - -
169A THR* 2.8 45.3 + - + +
172A HIS* 3.5 20.4 - - + -
173A LEU* 3.6 21.1 - - + +
176A MET* 4.3 0.2 - - - -
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Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 3.0 42.1 + - + +
43A GLN* 3.8 3.8 - - - +
45A ALA* 1.3 75.1 - - - +
47A ALA* 1.3 56.4 + - - +
50A LEU* 2.7 50.6 + - + +
166A PHE* 4.2 21.1 - - + -
169A THR* 3.9 17.5 - - + +
46B LEU* 5.0 9.0 - - + -
50B LEU* 5.5 1.6 - - + -
42D LEU* 3.7 24.5 - - + -
46D LEU* 5.1 9.4 - - + -
173D LEU* 4.0 11.7 - - + -
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Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE 4.8 2.7 - - - +
27A GLY* 5.2 1.3 - - - -
30A ALA* 3.6 30.1 - - + -
43A GLN 2.9 19.0 + - - +
44A VAL* 3.7 5.6 - - - +
46A LEU* 1.3 76.0 - - - +
48A PHE* 1.3 61.3 + - + +
51A ALA* 2.7 32.6 + - - +
170D LEU* 3.6 12.8 - - + +
173D LEU* 3.6 17.0 - - + +
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Residues in contact with PHE 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TYR* 4.0 28.9 - + - -
24A VAL* 5.6 0.2 - - - -
27A GLY* 3.4 33.4 - - - -
28A LEU* 4.0 2.2 - - + -
31A SER* 3.4 21.3 - - - -
44A VAL* 3.1 33.7 + - + +
45A ALA 4.1 1.6 - - - +
47A ALA* 1.3 76.7 - - + +
49A GLY* 1.3 59.0 + - - +
51A ALA* 3.1 6.4 + - - +
52A LEU 2.9 25.6 + - - -
168A LEU* 3.5 13.9 - - + +
172A HIS* 3.4 36.1 - + + +
187A ARG* 3.8 47.3 - - + -
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Residues in contact with GLY 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ALA 3.0 10.7 + - - -
48A PHE* 1.3 77.7 - - - +
50A LEU* 1.3 59.2 + - - +
52A LEU 3.3 0.2 + - - -
53A ALA* 2.9 25.1 + - - +
165A GLY* 3.1 36.9 - - - -
166A PHE* 5.8 0.2 - - - -
168A LEU* 4.2 3.9 - - - +
169A THR* 3.2 15.7 - - - -
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Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 2.7 36.3 + - + +
47A ALA* 4.1 2.5 - - - +
49A GLY* 1.3 72.9 - - - -
51A ALA* 1.3 57.8 + - - +
53A ALA* 4.0 3.8 - - + +
54A THR* 2.6 38.4 + - - -
162A LEU* 4.3 14.1 - - + -
166A PHE* 4.3 13.7 - - + -
46D LEU* 5.6 1.8 - - + -
166D PHE* 3.7 54.7 - - + +
169D THR* 3.7 30.1 - - + -
170D LEU* 4.0 8.1 - - + +
173D LEU* 4.5 6.1 - - + -
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Residues in contact with ALA 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PHE 5.3 0.2 - - - +
23A TYR* 4.6 16.6 - - + +
26A PHE* 4.6 10.8 - - + -
27A GLY 5.1 1.6 - - - +
47A ALA 2.7 19.7 + - - +
48A PHE* 3.1 8.7 + - - +
50A LEU* 1.3 76.8 - - - +
52A LEU* 1.3 58.7 + - - +
54A THR* 3.5 1.4 - - - -
55A LEU* 2.9 40.2 + - + +
170D LEU* 3.8 24.6 - - + +
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Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TYR* 4.1 19.2 - - + -
48A PHE 2.9 16.3 + - - +
49A GLY 3.6 3.8 - - - +
51A ALA* 1.3 71.9 - - - +
53A ALA* 1.3 56.5 + - - +
54A THR 3.1 1.3 - - - -
55A LEU* 3.0 5.8 + - + -
56A VAL* 2.7 54.7 + - + +
65A ALA 4.9 7.0 - - - +
66A HIS 5.2 3.1 - - - +
67A VAL* 5.1 11.4 - - + -
141A PHE* 3.3 36.6 - - + -
164A VAL* 3.6 21.1 - - + +
165A GLY* 4.2 2.2 - - - -
168A LEU* 3.5 21.5 - - + -
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Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLY 2.9 20.1 + - - +
50A LEU* 4.0 8.1 - - + +
52A LEU* 1.3 73.4 - - - +
54A THR* 1.3 60.9 + - - +
57A GLN* 3.2 30.2 + - + +
161A ALA* 3.1 33.9 + - + +
162A LEU* 3.8 23.3 - - + +
165A GLY* 4.2 1.1 - - - -
166D PHE* 6.1 2.2 - - + -
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Residues in contact with THR 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU 2.6 22.5 + - - -
51A ALA* 3.5 7.4 - - - +
53A ALA* 1.3 78.6 - - - +
55A LEU* 1.3 64.3 + - + +
57A GLN* 3.2 5.6 + - - +
58A ALA* 2.9 27.0 + - + +
140D GLN* 3.5 29.6 - - + +
144D CYS* 4.0 21.4 - - + -
163D ALA* 4.7 2.9 + - - -
166D PHE* 4.4 2.9 + - - +
167D SER* 3.6 27.2 + - - +
170D LEU* 4.6 3.8 - - + +
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Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA* 3.2 39.5 - - + +
22A PHE* 3.8 31.6 - - + -
23A TYR* 3.5 29.4 - - + +
26A PHE* 6.2 0.4 - - + -
51A ALA* 2.9 22.0 + - + +
52A LEU* 3.7 5.4 - - + +
54A THR* 1.3 80.2 - - + +
56A VAL* 1.3 61.6 + - - +
58A ALA* 3.9 10.5 - - + -
59A VAL* 2.8 35.9 + - + +
65A ALA* 4.4 2.0 - - - -
67A VAL* 5.1 5.6 - - + -
140D GLN* 5.5 4.5 - - + -
143D LEU* 5.4 2.5 - - + -
170D LEU* 6.5 0.4 - - + -
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Residues in contact with VAL 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 2.7 48.3 + - + +
55A LEU* 1.3 72.6 - - - +
57A GLN* 1.3 59.1 + - - +
60A GLY* 2.9 25.8 + - - -
65A ALA* 3.6 20.4 - - + +
149A TYR* 4.0 21.5 - - + +
160A VAL* 4.6 9.6 - - + +
161A ALA* 3.6 29.8 - - + +
164A VAL* 4.5 9.4 - - + -
153D ARG* 4.3 3.6 + - - -
154D ASN* 5.5 0.3 + - - -
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Residues in contact with GLN 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ALA 3.2 18.1 + - - +
54A THR* 3.2 9.7 + - - +
56A VAL* 1.3 76.9 - - - +
58A ALA* 1.3 62.6 + - - +
59A VAL 3.6 0.2 + - - -
61A HIS* 3.8 0.3 - - - -
159A SER* 3.6 6.0 + - - +
161A ALA* 3.4 17.0 - - + +
144D CYS* 4.4 3.6 - - - -
147D ALA* 3.6 2.4 - - - +
148D THR* 3.8 15.1 - - + +
153D ARG* 2.7 36.7 + - - +
154D ASN* 4.4 2.9 + - - -
156D ARG 4.8 1.2 - - - +
157D LEU* 2.9 55.0 + - - +
159D SER 4.7 0.4 + - - -
160D VAL* 5.3 1.0 - - - +
163D ALA* 3.8 29.2 - - + +
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Residues in contact with ALA 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A THR* 2.9 18.3 + - + +
55A LEU* 3.2 13.2 + - + +
57A GLN* 1.3 79.2 - - - +
59A VAL* 1.3 67.4 + - + +
61A HIS* 3.1 16.1 + - - -
62A ILE* 4.4 1.0 - - - +
143D LEU* 3.7 36.0 - - + +
144D CYS* 4.6 3.1 - - - +
147D ALA* 3.4 17.1 - - - +
219D TYR* 4.0 6.4 - - - -
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Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ALA* 3.8 29.2 - - + +
16A GLU* 5.1 0.2 - - - +
18A PHE* 6.3 1.6 - - + -
19A ALA* 4.0 22.9 - - + +
55A LEU* 2.8 20.1 + - + +
58A ALA* 1.3 86.7 - - + +
60A GLY* 1.3 60.0 + - - +
61A HIS* 3.2 6.7 - - - -
62A ILE* 3.1 11.1 + - + -
63A SER* 3.0 35.8 + - - +
65A ALA* 3.9 12.6 - - + -
143D LEU* 5.0 11.2 - - + -
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Residues in contact with GLY 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A VAL* 2.9 27.3 + - - -
59A VAL* 1.3 78.3 - - - +
61A HIS* 1.3 59.3 + - - +
64A GLY* 3.0 24.8 + - - -
65A ALA* 3.7 16.8 - - - -
149A TYR* 5.5 0.7 - - - -
153D ARG* 4.8 0.9 - - - -
154D ASN* 5.7 1.1 - - - -
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Residues in contact with HIS 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLN 3.8 0.2 - - - -
58A ALA 3.1 25.6 + - - -
60A GLY* 1.3 79.4 - - - +
62A ILE* 1.3 79.5 + - + +
147D ALA* 4.0 0.8 - - - +
150D ASP* 4.6 0.9 - - - -
153D ARG* 3.5 48.9 + - + +
154D ASN* 3.4 21.5 - - - +
219D TYR* 3.1 29.7 + + - -
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Residues in contact with ILE 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ARG* 4.1 16.8 - - + +
12A ALA* 3.5 29.3 - - - +
15A ALA* 4.2 4.7 - - + -
58A ALA 4.4 8.1 - - - +
59A VAL* 3.1 15.7 + - + +
61A HIS* 1.3 111.8 - - + +
63A SER* 1.3 57.0 + - - +
85A ARG* 5.6 0.9 + - - -
219D TYR* 4.5 13.5 - - + +
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Residues in contact with SER 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ALA* 3.5 25.1 - - - -
15A ALA* 3.6 9.5 - - - +
16A GLU* 2.6 25.8 + - - -
59A VAL* 3.0 9.0 + - - +
62A ILE* 1.3 75.3 - - - +
64A GLY* 1.3 61.2 + - - +
65A ALA* 3.2 5.9 + - - -
66A HIS* 3.7 4.9 - - - -
89A TYR* 2.9 40.9 + - - -
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Residues in contact with GLY 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLY* 3.0 22.3 + - - -
63A SER* 1.3 78.2 - - - +
65A ALA* 1.3 63.0 + - - +
66A HIS* 3.5 11.2 + - - -
149A TYR* 2.7 41.8 + - - -
----------------------------------------------------------
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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