Contacts of the helix formed by residues 41 - 65 (chain A) in PDB entry 5DYE
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 41 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU 3.4 6.1 + - - +
40A PRO* 1.3 75.3 - - - +
42A ILE* 1.3 67.4 + - - +
43A LEU* 4.4 5.7 - - - +
44A GLN* 3.2 29.0 + - - +
45A ILE* 3.0 22.4 + - - +
41C THR* 6.6 0.7 - - - -
43C LEU* 5.2 4.9 - - - +
41D THR* 6.0 7.6 - - + -
44D GLN* 5.5 1.8 - - - -
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Residues in contact with ILE 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PRO 5.5 1.1 - - - +
41A THR* 1.3 74.0 - - - +
43A LEU* 1.3 57.3 + - - +
45A ILE* 3.2 11.5 + - + -
46A ALA* 2.9 28.3 + - - +
173A HIS 4.0 9.0 - - - +
174A LEU* 4.4 5.2 - - - +
177A ILE* 3.5 39.8 - - + +
178A TYR* 3.6 36.1 - - + +
37D SER* 6.2 1.1 - - - -
38D ALA* 4.4 18.4 - - + -
44D GLN* 3.4 26.8 + - - +
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Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR* 4.4 5.6 + - - +
42A ILE* 1.3 79.6 - - - +
44A GLN* 1.3 61.6 + - - +
46A ALA* 3.3 4.9 + - + +
47A LEU* 3.0 35.5 + - + +
170A THR* 5.3 1.1 - - + -
174A LEU* 4.0 21.5 - - + -
43C LEU* 3.8 17.9 - - + -
41D THR* 4.7 3.6 - - - +
43D LEU* 3.6 40.4 - - + -
44D GLN* 3.8 27.5 + - + +
47D LEU* 3.5 23.1 - - + -
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Residues in contact with GLN 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A SER* 4.2 5.1 + - - +
39A LEU 4.8 0.9 - - - +
40A PRO* 3.8 25.5 - - + +
41A THR* 3.2 24.7 + - - +
42A ILE 3.3 0.6 - - - -
43A LEU* 1.3 79.7 - - - +
45A ILE* 1.3 63.7 + - - +
47A LEU* 3.3 1.7 + - - +
48A ALA* 3.0 25.3 + - + +
42C ILE* 3.5 21.4 + - - +
43C LEU* 4.2 23.1 + - + +
174C LEU* 3.8 31.2 + - + +
178C TYR* 3.1 32.7 + - - -
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Residues in contact with ILE 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A SER* 4.4 2.7 - - - +
32A ALA* 3.9 22.9 - - + +
40A PRO* 3.5 34.1 - - + +
41A THR 3.0 24.2 + - - +
42A ILE* 3.2 13.0 + - + +
44A GLN* 1.3 76.2 - - - +
46A ALA* 1.3 62.6 + - - +
48A ALA* 3.6 4.9 + - - +
49A PHE* 3.1 48.0 + - + -
177A ILE* 3.7 25.8 - - + -
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Residues in contact with ALA 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ILE 2.9 16.9 + - - +
43A LEU 3.5 6.3 - - - +
45A ILE* 1.3 78.7 - - - +
47A LEU* 1.3 63.7 + - - +
49A PHE* 3.6 2.4 - - - +
50A GLY 3.0 18.2 + - - -
170A THR* 3.3 37.0 + - + +
173A HIS* 3.5 22.4 - - + +
174A LEU* 4.0 13.7 - - + +
177A ILE* 4.0 0.4 - - - +
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Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 3.0 31.9 + - + +
44A GLN 3.9 2.9 - - - +
46A ALA* 1.3 74.9 - - - +
48A ALA* 1.3 55.6 + - - +
50A GLY 3.1 0.7 + - - -
51A LEU* 2.7 65.5 + - + +
167A LEU* 4.6 13.5 - - + -
170A THR* 3.6 24.2 - - + +
43C LEU* 3.7 32.3 - - + -
47C LEU* 4.8 14.4 - - + -
167C LEU* 6.1 0.7 - - + -
170C THR* 6.2 0.2 - - + -
174C LEU* 4.6 1.1 - - + -
47D LEU* 5.1 7.6 - - + -
51D LEU* 6.2 0.2 - - + -
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Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE 4.7 4.3 - - - +
31A SER* 3.4 34.5 - - - +
44A GLN 3.0 17.2 + - - +
45A ILE 4.0 0.9 - - - +
47A LEU* 1.3 76.8 - - - +
49A PHE* 1.3 60.5 + - - +
51A LEU* 4.8 1.1 - - - -
52A ALA* 3.3 22.9 + - - +
171C LEU* 3.4 15.4 - - + +
174C LEU* 3.7 24.5 - - + +
175C VAL* 5.8 0.7 - - + -
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Residues in contact with PHE 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 3.3 37.4 - + - -
25A VAL* 6.0 0.7 - - - -
28A GLY* 3.1 42.0 - - - -
29A LEU* 3.9 4.0 - - + -
31A SER* 4.4 0.7 - - - -
32A ALA* 4.0 4.3 - - + -
45A ILE* 3.1 39.8 + - + +
46A ALA 3.6 3.6 - - - +
48A ALA* 1.3 76.2 - - - +
50A GLY* 1.3 62.1 + - - +
52A ALA* 3.3 16.9 + - - +
53A ILE* 3.4 3.1 + - - +
169A VAL* 4.0 2.2 - - + -
173A HIS* 3.2 35.2 - + + +
181A GLY 5.3 0.9 - - - -
188A ARG* 3.3 53.2 - - + -
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Residues in contact with GLY 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ALA 3.0 10.7 + - - -
49A PHE* 1.3 73.8 - - - +
51A LEU* 1.3 60.0 + - - +
52A ALA 3.1 1.8 - - - -
53A ILE* 3.2 2.6 + - - +
54A GLY 2.9 24.9 + - - -
166A GLY* 3.3 31.3 - - - -
169A VAL* 3.6 15.2 - - - +
170A THR* 3.4 8.7 - - - -
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Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 2.7 54.8 + - + +
48A ALA* 4.6 1.8 - - - +
50A GLY* 1.3 71.0 - - - -
52A ALA* 1.3 56.5 + - - +
54A GLY* 4.0 3.4 - - - +
55A THR* 2.8 35.8 + - - +
163A LEU* 5.4 4.7 - - + -
166A GLY* 5.3 3.4 - - - -
167A LEU* 5.4 9.4 - - + -
170A THR* 4.1 1.1 + - - +
47C LEU* 5.7 0.2 - - + -
167C LEU* 3.8 45.1 - - + +
170C THR* 4.2 26.7 - - + -
171C LEU* 3.8 16.9 - - + +
174C LEU* 5.0 2.5 - - + -
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Residues in contact with ALA 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 6.3 0.4 - - + -
24A PHE* 3.8 19.5 - - + +
27A PHE* 4.1 15.7 - - + -
48A ALA 3.3 16.6 + - - +
49A PHE* 3.3 12.6 - - - +
50A GLY 3.1 0.6 - - - -
51A LEU* 1.3 74.6 - - - +
53A ILE* 1.3 64.2 + - - +
55A THR* 4.1 1.0 - - - -
56A LEU* 3.1 34.4 + - + +
171C LEU* 3.8 19.6 - - + +
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Residues in contact with ILE 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 3.4 48.0 - - + -
49A PHE 3.4 4.0 + - - +
50A GLY 3.2 7.0 + - - +
52A ALA* 1.3 76.9 - - - +
54A GLY* 1.3 54.9 + - - +
56A LEU* 3.0 3.8 + - - +
57A ALA* 2.8 35.6 + - + +
67A HIS 5.2 3.8 - - - +
68A ILE* 3.7 34.2 - - + +
165A ILE* 4.3 19.5 - - + +
169A VAL* 4.0 27.8 - - + -
185A ASN* 5.1 0.7 - - - +
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Residues in contact with GLY 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLY 2.9 15.0 + - - -
51A LEU* 4.1 3.8 - - - -
53A ILE* 1.3 76.3 - - - +
55A THR* 1.3 58.8 + - - +
57A ALA* 4.1 4.3 - - - -
58A GLN* 3.7 5.0 + - - +
162A ALA* 3.1 47.2 - - - +
163A LEU* 4.6 11.1 - - - +
165A ILE* 5.7 0.2 - - - -
166A GLY* 3.9 6.0 - - - -
164C SER* 4.8 0.3 + - - -
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Residues in contact with THR 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU* 2.8 25.1 + - - +
52A ALA 4.1 2.7 - - - -
54A GLY* 1.3 75.5 - - - +
56A LEU* 1.3 63.1 + - + +
57A ALA 3.2 0.4 - - - -
58A GLN* 3.2 8.7 + - - +
59A ALA* 2.9 26.3 + - + +
163A LEU* 6.1 0.2 - - - +
141C GLN* 3.5 26.5 - - + +
145C CYS* 3.8 26.1 - - + +
164C SER* 4.6 4.5 + - - -
167C LEU* 4.6 3.5 - - - +
168C SER* 3.8 22.2 + - - +
171C LEU* 4.2 5.8 - - + +
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Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA* 3.2 41.7 - - + +
23A ILE* 4.1 25.6 - - + -
24A PHE* 3.5 27.8 - - + +
52A ALA* 3.1 24.8 + - - +
53A ILE 3.0 1.2 + - - -
55A THR* 1.3 76.5 - - + +
57A ALA* 1.3 60.9 + - - +
59A ALA* 4.2 7.9 - - + -
60A LEU* 2.8 39.3 + - + +
61A GLY 3.6 1.0 + - - -
66A GLY* 5.5 0.7 - - - -
68A ILE* 3.3 22.2 - - + +
141C GLN* 5.7 4.9 - - + -
144C LEU* 6.0 1.6 - - + -
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Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ILE* 2.8 23.7 + - + +
54A GLY* 4.2 1.8 - - - +
56A LEU* 1.3 72.5 - - - +
58A GLN* 1.3 59.1 + - - +
61A GLY* 2.9 33.1 + - - +
62A PRO* 3.6 3.8 - - - +
65A GLY 6.0 0.4 - - - +
66A GLY* 5.2 10.3 - - - +
68A ILE* 4.3 4.2 - - + +
162A ALA* 3.8 22.7 - - + -
165A ILE* 5.2 10.5 - - + -
154C ARG* 5.5 0.3 + - - -
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Residues in contact with GLN 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLY 3.7 12.3 + - - +
55A THR* 3.2 11.3 + - - +
57A ALA* 1.3 79.2 - - - +
59A ALA* 1.3 58.8 + - - +
62A PRO* 4.1 0.7 - - - +
160A SER* 5.7 1.2 + - - -
161A PRO* 5.3 0.9 - - - +
162A ALA* 3.8 15.8 + - + +
163A LEU* 5.9 1.4 - - - +
145C CYS* 4.9 5.2 - - - +
148C ALA* 3.3 17.7 - - - +
149C SER* 3.3 21.8 + - - +
154C ARG* 3.3 35.8 + - - +
157C PRO 4.4 2.1 - - - +
158C VAL* 3.0 38.0 + - - +
161C PRO* 4.5 0.4 - - - +
164C SER* 3.1 31.0 + - - +
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Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A THR* 2.9 17.1 + - + +
56A LEU* 3.9 11.2 - - + +
57A ALA 3.2 0.4 - - - -
58A GLN* 1.3 80.7 - - - +
60A LEU* 1.3 72.7 + - + +
61A GLY 3.6 0.4 + - - -
62A PRO* 4.0 7.5 - - - +
63A VAL* 4.6 4.7 - - - +
141C GLN 5.5 0.7 - - - +
144C LEU* 4.0 31.6 - - + +
145C CYS* 4.4 4.9 - - + +
148C ALA* 3.6 19.2 - - - +
221C TYR* 5.2 4.3 - - - -
226C PHE* 5.9 0.2 - - - -
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Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ALA* 3.6 36.6 - - + +
19A LEU* 4.0 25.1 - - + -
20A ALA* 4.0 16.4 - - + +
23A ILE* 5.6 0.2 - - + -
56A LEU* 2.8 22.3 + - + +
59A ALA* 1.3 77.0 - - + +
61A GLY* 1.3 59.5 + - - +
62A PRO 3.4 2.0 - - - -
63A VAL* 3.3 24.7 + - + +
64A SER* 3.1 32.1 + - - +
66A GLY* 4.8 2.5 - - - -
144C LEU* 4.0 21.1 - - + -
221C TYR* 6.4 0.4 - - + -
225C LEU* 4.0 17.3 - - + -
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Residues in contact with GLY 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU 3.6 2.4 + - - -
57A ALA* 2.9 19.0 + - - -
60A LEU* 1.3 76.1 - - - +
62A PRO* 1.3 61.5 - - - +
65A GLY* 2.8 45.6 + - - -
66A GLY* 3.9 4.5 - - - -
156C GLU* 5.9 1.1 - - - -
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Residues in contact with PRO 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ALA 3.6 9.0 - - - +
58A GLN 4.1 2.7 - - - +
59A ALA 4.0 12.1 - - - +
60A LEU 3.8 1.8 - - - -
61A GLY* 1.3 88.7 - - - +
63A VAL* 1.3 59.9 - - + +
65A GLY 4.9 0.2 - - - -
148C ALA* 5.5 1.8 - - + -
154C ARG* 3.5 34.1 - - + +
156C GLU* 4.6 20.2 - - + -
226C PHE* 4.4 21.8 - - + -
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Residues in contact with VAL 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ALA 4.8 1.2 - - - +
12A LYS* 3.8 13.9 - - + +
13A ALA* 3.5 15.5 + - - +
16A ALA* 3.4 23.8 - - + -
59A ALA 4.6 4.0 - - - +
60A LEU* 3.3 31.5 + - + +
61A GLY 3.2 1.0 - - - -
62A PRO* 1.3 78.6 - - + +
64A SER* 1.3 57.8 + - - +
65A GLY 3.9 0.2 - - - -
221C TYR* 5.9 0.4 - - + -
225C LEU* 3.7 24.9 - - + -
226C PHE* 3.7 28.7 - - + -
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Residues in contact with SER 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ALA* 3.1 26.7 - - - -
16A ALA* 3.8 12.9 + - - +
17A GLU* 3.4 23.5 + - - +
20A ALA* 5.6 1.0 - - - +
60A LEU* 3.1 14.5 + - - +
63A VAL* 1.3 75.8 - - - +
65A GLY* 1.3 58.2 + - - +
66A GLY* 3.2 5.4 + - - -
67A HIS* 4.0 3.5 + - - -
90A TYR* 2.7 34.3 + - - -
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Residues in contact with GLY 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ALA* 6.0 0.5 - - - +
61A GLY* 2.8 29.3 + - - +
63A VAL 3.9 0.2 - - - -
64A SER* 1.3 69.6 - - - +
66A GLY* 1.3 62.5 + - - +
67A HIS* 3.8 11.8 - - - -
150A THR* 5.1 10.7 - - - +
----------------------------------------------------------
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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