Contacts of the helix formed by residues 35 - 66 (chain A) in PDB entry 5ID6
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 ARG 35 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ILE 3.0 4.2 + - - -
32A ASP* 2.9 39.4 + - - +
33A ASN 3.0 6.5 - - - +
34A LYS* 1.3 80.6 - - - +
36A LEU* 1.3 63.7 + - - +
37A LEU* 3.2 3.8 - - - -
38A VAL* 3.2 50.3 - - + +
39A GLU* 4.5 1.9 + - - +
526A GLN* 4.5 5.2 + - - -
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Residues in contact with LEU 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ILE* 3.1 15.1 + - + +
34A LYS* 3.0 24.7 + - + +
35A ARG* 1.3 78.5 - - - +
37A LEU* 1.3 62.5 + - - +
39A GLU* 3.9 14.7 - - - +
40A ASP* 4.5 7.1 - - - +
525A PHE* 3.5 43.3 - - + +
526A GLN* 4.0 31.5 - - + +
559A ASP* 5.3 3.4 - - - +
700A TYR* 3.3 42.4 - - + +
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLN* 5.7 1.3 - - - +
31A ILE* 3.6 29.0 + - + +
32A ASP* 5.3 7.4 - - - +
35A ARG* 3.2 1.0 - - - -
36A LEU* 1.3 76.7 - - - +
38A VAL* 1.3 58.8 + - + +
39A GLU 3.1 2.7 - - - -
40A ASP* 2.7 34.1 + - - +
41A GLU* 3.2 9.0 + - - +
521A PHE* 4.5 2.8 - - + -
523A LEU* 4.1 31.2 - - + -
525A PHE* 4.9 6.3 - - + -
746A MSE 3.7 18.6 - - + -
748A ARG* 3.4 41.1 - - - +
794A TYR* 4.0 10.5 - - + +
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Residues in contact with VAL 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG* 3.2 53.4 - - + +
37A LEU* 1.3 79.6 - - + +
39A GLU* 1.3 65.7 + - + +
41A GLU* 3.7 16.8 - - + +
42A LYS* 3.0 27.5 + - - +
748A ARG* 5.6 1.8 - - - +
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Residues in contact with GLU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG 4.7 4.3 - - - +
36A LEU 3.9 9.2 - - - +
37A LEU 3.0 0.2 + - - -
38A VAL* 1.3 82.7 - - + +
40A ASP* 1.3 63.5 + - - +
42A LYS* 3.8 2.4 + - - +
43A ARG* 3.5 41.3 + - - +
526A GLN* 3.9 39.1 + - + +
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Residues in contact with ASP 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU 4.5 4.4 - - - +
37A LEU* 2.7 13.1 + - - +
39A GLU* 1.3 75.6 - - - +
41A GLU* 1.3 60.9 + - - +
43A ARG* 3.0 38.5 + - - +
44A ALA* 3.4 18.2 + - - +
521A PHE* 3.9 7.7 - - - +
522A LYS 3.2 23.3 - - - +
523A LEU* 3.3 16.6 - - + +
524A TYR* 2.8 29.9 + - - +
525A PHE* 3.3 11.6 + - - -
526A GLN 5.0 1.7 + - - -
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Residues in contact with GLU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 3.2 7.2 + - - +
38A VAL* 3.1 21.0 + - + +
40A ASP* 1.3 78.0 - - - +
42A LYS* 1.3 65.7 + - - +
44A ALA* 3.1 18.3 - - - +
45A GLU* 3.1 23.8 + - + +
521A PHE* 3.5 30.3 - - + -
748A ARG* 2.5 48.0 + - - +
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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
----------------------------------------------------------
38A VAL 3.0 15.1 + - - +
39A GLU* 4.5 2.5 - - - +
41A GLU* 1.3 74.0 - - - +
43A ARG* 1.3 55.5 + - - +
45A GLU* 2.8 30.2 + - - +
46A ASP* 2.8 59.6 + - - +
140A LEU* 5.0 6.7 - - - -
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Residues in contact with ARG 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLU* 3.5 35.0 + - - +
40A ASP* 3.0 36.0 + - - +
41A GLU 3.3 0.2 - - - -
42A LYS* 1.3 76.8 - - - +
44A ALA* 1.3 57.1 + - - +
46A ASP* 4.5 2.7 - - - +
47A TYR* 2.8 28.6 + - - +
143A SER 4.2 13.8 + - - +
144A PHE* 3.4 46.2 - - + -
147A PHE* 3.3 58.6 - - - +
522A LYS 5.5 0.2 + - - -
524A TYR* 3.7 9.3 - - - -
526A GLN* 5.4 4.4 - - - +
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Residues in contact with ALA 44 (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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40A ASP 3.4 4.7 + - - +
41A GLU* 3.1 15.0 + - + +
43A ARG* 1.3 80.2 - - - +
45A GLU* 1.3 58.5 + - + +
47A TYR* 3.7 16.1 - - - +
48A LYS* 4.7 1.4 + - - +
520A LYS 5.3 1.6 - - - +
521A PHE* 3.6 33.9 - - + -
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Residues in contact with GLU 45 (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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41A GLU* 3.2 22.8 - - + +
42A LYS* 2.8 37.7 + - - +
44A ALA* 1.3 80.4 - - + +
46A ASP* 1.3 65.6 + - - +
47A TYR 3.4 0.9 + - - -
48A LYS* 3.9 12.3 + - - +
49A GLY 4.5 0.9 + - - -
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Residues in contact with ASP 46 (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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42A LYS* 2.8 52.3 + - - +
43A ARG* 3.7 4.0 - - - +
45A GLU* 1.3 76.4 - - - +
47A TYR* 1.3 65.6 + - - +
48A LYS 3.2 1.3 - - - -
49A GLY* 2.9 6.8 + - - +
50A VAL* 2.8 24.4 + - - +
140A LEU* 3.4 37.8 - - + +
143A SER* 5.6 1.0 + - - -
144A PHE* 4.3 12.1 - - + -
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Residues in contact with TYR 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ARG 2.8 18.2 + - - +
44A ALA* 3.7 13.7 - - - +
45A GLU 3.2 1.0 - - - -
46A ASP* 1.3 77.9 - - - +
48A LYS* 1.3 67.8 + - + +
50A VAL* 3.2 2.4 + - - +
51A LYS* 3.0 60.3 + - + +
144A PHE* 3.7 9.6 - - + -
150A ALA* 3.1 39.2 + - + -
151A PHE* 3.7 26.9 - + - -
154A PHE* 4.1 11.3 + - - +
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Residues in contact with LYS 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ALA 4.7 1.0 + - - +
45A GLU 3.9 9.2 + - - +
46A ASP 3.2 0.4 - - - -
47A TYR* 1.3 83.1 - - + +
49A GLY* 1.3 63.4 + - - +
51A LYS* 3.5 19.2 + - + +
52A LYS* 3.4 49.3 + - + +
294A TYR* 5.9 2.2 - - - -
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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 GLU 4.5 0.8 + - - -
46A ASP* 2.9 12.0 + - - +
48A LYS* 1.3 76.8 - - - +
50A VAL* 1.3 64.9 + - - +
52A LYS* 3.1 17.3 + - - +
53A LEU* 3.4 14.8 + - - +
140A LEU* 4.9 13.2 - - - -
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Residues in contact with VAL 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ASP 2.8 15.7 + - - +
47A TYR 3.8 3.8 - - - +
49A GLY* 1.3 71.4 - - - +
51A LYS* 1.3 57.8 + - - +
53A LEU* 3.0 10.8 + - - +
54A LEU* 2.8 36.0 + - + +
124A ILE* 5.2 2.0 - - + -
128A LEU* 4.5 2.0 - - + -
140A LEU* 3.7 25.3 - - + +
141A VAL* 3.9 21.5 - - + -
144A PHE* 3.4 31.6 - - + -
151A PHE* 3.4 28.0 - - + -
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Residues in contact with LYS 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A TYR* 3.0 60.6 + - + +
48A LYS* 3.5 18.5 - - + +
49A GLY 3.2 0.4 - - - -
50A VAL* 1.3 75.3 - - - +
52A LYS* 1.3 60.0 + - + +
54A LEU* 3.3 10.0 + - - +
55A ASP* 3.0 32.7 + - - +
151A PHE* 4.2 9.4 - - + -
154A PHE* 3.7 42.1 - - + -
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Residues in contact with LYS 52 (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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48A LYS* 3.4 33.8 + - - +
49A GLY* 3.1 12.6 + - - +
51A LYS* 1.3 80.9 - - + +
53A LEU* 1.3 59.7 + - + +
55A ASP* 3.3 21.3 + - + +
56A ARG* 3.0 24.7 + - - +
158A ARG* 5.8 1.6 - - - +
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Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLY 3.4 13.0 + - - +
50A VAL* 3.0 10.2 + - - +
52A LYS* 1.3 78.4 - - + +
54A LEU* 1.3 63.9 + - - +
56A ARG* 3.1 47.5 + - - +
57A TYR 3.2 10.2 + - - -
128A LEU* 3.6 22.4 - - + +
137A GLU* 3.5 51.1 - - + +
140A LEU* 5.1 7.0 - - + -
141A VAL* 3.8 14.4 - - + -
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A VAL* 2.8 19.8 + - + +
51A LYS* 3.6 7.6 - - - +
53A LEU* 1.3 75.3 - - - +
55A ASP* 1.3 60.1 + - - +
56A ARG 3.2 0.2 + - - -
57A TYR* 3.4 2.6 + - - +
58A TYR* 3.0 47.9 + - + +
123A ILE* 3.7 31.9 - - + -
124A ILE* 4.1 11.0 - - + -
128A LEU* 3.8 22.7 - - + -
151A PHE* 3.9 30.3 - - + -
154A PHE* 3.9 26.5 - - + -
155A PHE* 4.6 4.9 - - + -
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Residues in contact with ASP 55 (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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51A LYS* 3.0 16.9 + - - +
52A LYS* 3.3 27.5 + - + +
54A LEU* 1.3 72.7 - - - +
56A ARG* 1.3 64.6 + - - +
58A TYR* 3.7 11.5 - - - +
59A LEU* 3.1 25.6 + - - +
154A PHE* 3.4 9.5 - - - -
158A ARG* 2.9 42.6 + - - -
161A MSE 5.5 1.5 - - - +
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Residues in contact with ARG 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LYS 3.0 13.7 + - - +
53A LEU* 3.3 26.4 - - - +
54A LEU 3.1 0.8 - - - -
55A ASP* 1.3 76.5 - - - +
57A TYR* 1.3 59.3 + - - +
59A LEU* 2.9 21.3 + - - +
60A SER* 3.0 12.9 + - - -
132A ALA* 3.9 27.2 - - - +
137A GLU* 2.8 42.2 + - - -
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Residues in contact with TYR 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU 3.2 3.0 + - - -
54A LEU* 4.0 2.9 - - - +
56A ARG* 1.3 80.2 - - - +
58A TYR* 1.3 67.9 + + - +
60A SER* 3.4 11.5 + - - -
61A PHE* 2.9 45.2 + - + +
64A ASP* 6.1 1.1 - - - -
117A SER 4.8 1.8 + - - -
118A LEU* 3.6 25.6 - - + +
123A ILE* 3.7 23.3 - - + -
127A ILE* 3.8 23.6 - - + +
128A LEU* 3.8 24.2 - - + -
130A GLU* 5.0 4.5 - - - -
131A ALA* 4.4 19.3 - - + -
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Residues in contact with TYR 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 3.0 34.0 + - + +
55A ASP* 3.7 14.8 - - - +
56A ARG 3.2 0.2 - - - -
57A TYR* 1.3 88.1 - + - +
59A LEU* 1.3 56.9 + - - +
61A PHE* 3.4 6.9 + - - +
62A ILE* 2.9 41.7 + - + +
118A LEU* 3.4 38.8 + - + -
119A PHE* 3.8 9.6 - + - -
123A ILE* 4.9 0.9 - - + -
154A PHE* 4.2 11.9 - + - -
155A PHE* 3.2 33.3 - - - -
158A ARG* 3.8 35.7 - - + -
161A MSE 5.6 5.6 - - + -
162A PHE* 5.5 8.3 - + + -
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Residues in contact with LEU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ASP 3.1 16.9 + - - +
56A ARG* 2.9 8.0 + - - +
58A TYR* 1.3 75.9 - - - +
60A SER* 1.3 64.0 + - - +
62A ILE* 4.0 7.1 - - - +
63A ASN* 3.2 25.3 + - - +
231A GLN* 4.3 19.7 - - + +
279A GLN 5.0 0.2 - - - +
280A VAL* 3.4 46.0 - - + +
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Residues in contact with SER 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ARG* 3.0 12.5 + - - -
57A TYR* 3.7 16.4 - - - -
59A LEU* 1.3 76.1 - - - +
61A PHE* 1.3 64.7 + - - +
63A ASN* 3.2 6.7 + - - +
64A ASP* 3.1 32.6 + - - +
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Residues in contact with PHE 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TYR* 2.9 40.8 + - + +
58A TYR* 3.4 9.6 - + - +
60A SER* 1.3 72.2 - - - +
62A ILE* 1.3 61.3 + - - +
63A ASN 3.0 1.1 - - - -
64A ASP* 2.6 36.9 + - + +
65A VAL* 3.2 28.6 + - + +
109A PHE* 4.0 30.3 - + - -
112A ALA 4.9 1.1 - - - -
113A ALA* 4.0 22.7 - - + -
115A TYR* 4.0 33.9 - + + -
118A LEU* 4.7 10.3 - - + -
162A PHE* 4.1 21.1 - + - -
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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
----------------------------------------------------------
58A TYR* 2.9 30.8 + - + +
59A LEU* 4.0 5.4 - - - +
61A PHE* 1.3 75.8 - - - +
63A ASN* 1.3 59.4 + - - +
65A VAL* 3.7 1.9 + - - +
66A LEU* 3.1 46.5 + - + +
109A PHE* 4.2 9.4 - - + -
161A MSE 4.6 7.2 - - - -
162A PHE* 3.6 25.1 - - + -
171A ILE* 3.5 31.0 - - + -
279A GLN* 5.0 1.8 - - - +
280A VAL* 3.6 33.2 - - + -
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Residues in contact with ASN 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU* 3.2 22.3 + - + +
60A SER* 3.4 7.9 - - - +
61A PHE 3.0 1.2 - - - -
62A ILE* 1.3 88.1 + - - +
64A ASP* 1.3 61.4 + - - +
66A LEU* 4.1 5.8 - - - +
67A HIS* 3.0 33.1 + - - +
230A THR* 3.4 20.0 - - - +
231A GLN* 2.3 52.2 + - - +
232A GLU* 3.5 2.9 - - - +
279A GLN* 5.5 3.4 - - - +
280A VAL* 5.6 0.8 - - - +
----------------------------------------------------------
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Residues in contact with ASP 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TYR* 6.1 1.0 - - - -
60A SER* 3.1 24.0 + - - +
61A PHE* 2.6 25.1 + - + +
63A ASN* 1.3 77.7 - - - +
65A VAL* 1.3 65.4 + - + +
66A LEU 3.3 0.6 + - - -
67A HIS* 3.7 6.7 + - - +
68A SER* 3.6 19.9 + - - -
113A ALA* 5.8 6.7 - - + -
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Residues in contact with VAL 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PHE* 3.2 33.3 + - + +
62A ILE 4.1 0.2 - - - +
64A ASP* 1.3 79.8 - - + +
66A LEU* 1.3 59.6 + - + +
68A SER* 2.9 22.0 + - - +
69A ILE* 3.1 20.5 - - + +
105A ILE 5.2 0.4 - - - +
108A ALA* 3.3 42.2 - - + +
109A PHE* 3.6 37.0 - - + +
112A ALA 5.6 0.4 - - - +
113A ALA* 5.5 7.6 - - + -
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ILE* 3.1 38.9 + - + +
63A ASN* 4.5 3.8 - - - +
64A ASP 3.3 0.4 - - - -
65A VAL* 1.3 78.1 - - + +
67A HIS* 1.3 60.1 + - - +
68A SER 3.0 5.8 + - - -
69A ILE* 3.7 17.4 + - + +
105A ILE* 5.2 10.3 - - + -
109A PHE* 4.4 14.8 - - + -
171A ILE* 4.6 13.0 - - + -
175A CYS* 4.7 8.7 - - - -
226A ASN 4.4 10.9 - - - +
229A LEU* 3.3 46.7 - - + +
230A THR* 3.6 23.3 - - + +
279A GLN* 4.8 5.4 - - - +
----------------------------------------------------------
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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