Contacts of the helix formed by residues 23 - 51 (chain A) in PDB entry 2IMT
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 SER 23 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A SER 3.1 4.9 + - - -
22A ALA* 1.3 75.2 - - - +
24A GLU* 1.3 59.0 + - - +
25A GLU* 3.6 12.1 + - - +
26A GLN* 3.0 37.3 + - - +
27A VAL* 2.9 29.1 + - - +
172A ALA* 4.0 1.6 - - - -
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Residues in contact with GLU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A SER* 1.3 72.8 - - - +
25A GLU* 1.3 57.5 + - + +
27A VAL* 3.5 2.3 + - - +
28A ALA* 3.0 27.6 + - - +
163A LEU* 4.0 27.2 - - + +
166A CYS* 5.0 3.5 - - - -
168A ALA* 3.8 6.4 - - + +
169A ARG* 3.7 53.7 + - + +
172A ALA* 3.9 13.6 - - + +
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Residues in contact with GLU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A SER* 3.2 11.5 + - - +
24A GLU* 1.3 77.4 - - + +
26A GLN* 1.3 59.7 + - + +
28A ALA* 3.2 8.6 + - - +
29A GLN* 3.0 41.8 + - - +
163A LEU* 5.6 4.0 - - + -
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Residues in contact with GLN 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A SER 4.2 2.6 - - - +
22A ALA* 3.7 16.7 - - + +
23A SER* 3.0 38.9 + - - +
25A GLU* 1.3 80.1 - - + +
27A VAL* 1.3 58.5 + - - +
29A GLN* 3.2 16.7 + - - +
30A ASP* 2.9 38.6 + - - +
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Residues in contact with VAL 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA* 3.8 17.5 - - + -
23A SER 2.9 22.2 + - - +
24A GLU 3.8 4.5 - - - +
26A GLN* 1.3 76.9 - - - +
28A ALA* 1.3 61.5 + - - +
30A ASP* 3.1 17.1 + - - +
31A THR* 3.1 15.7 + - - +
168A ALA* 3.6 24.9 - - + +
171A ILE* 3.6 17.7 - - + -
172A ALA* 3.7 23.1 - - + +
176A GLY* 4.2 8.1 - - - -
177A TRP* 3.3 21.3 + - + +
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Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLU 3.0 19.1 + - - +
25A GLU* 3.4 7.6 - - - +
27A VAL* 1.3 77.8 - - - +
29A GLN* 1.3 62.6 + - + +
31A THR* 3.4 18.7 - - - -
159A VAL* 3.5 18.9 - - + +
162A MET* 6.3 0.2 - - - -
163A LEU* 3.8 36.6 - - + -
168A ALA* 3.9 10.7 - - + +
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Residues in contact with GLN 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLU* 3.0 23.7 + - - +
26A GLN* 3.2 24.5 + - - +
28A ALA* 1.3 78.3 - - + +
30A ASP* 1.3 63.1 + - - +
31A THR 3.2 0.9 + - - -
32A GLU* 3.3 20.1 + - - +
33A GLU* 4.5 0.9 + - - +
159A VAL* 5.4 1.7 - - - +
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Residues in contact with ASP 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA* 5.0 6.9 - - - +
26A GLN* 2.9 24.5 + - - +
27A VAL* 3.4 12.0 - - - +
29A GLN* 1.3 76.6 - - - +
31A THR* 1.3 64.4 + - - +
32A GLU 3.1 0.4 - - - -
33A GLU* 3.2 9.5 + - - +
34A VAL* 3.0 24.0 + - - +
71A MET* 3.7 33.8 - - - +
177A TRP* 3.5 15.2 + - + +
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Residues in contact with THR 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 3.1 15.6 + - - +
28A ALA* 3.4 15.7 + - - -
29A GLN 3.2 0.8 + - - -
30A ASP* 1.3 76.8 - - - +
32A GLU* 1.3 57.0 + - - +
34A VAL* 4.2 4.0 - - - -
35A PHE* 2.8 31.5 + - + +
132A LEU* 5.4 1.3 - - + -
158A VAL* 4.2 9.2 - - + -
159A VAL* 3.9 24.2 - - + -
162A MET* 3.7 32.6 - - + +
168A ALA* 5.3 0.5 - - - +
177A TRP* 3.3 20.7 + - + +
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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
----------------------------------------------------------
29A GLN 3.3 13.0 + - - +
30A ASP 3.1 1.0 - - - -
31A THR* 1.3 79.1 - - - +
33A GLU* 1.3 57.0 + - - +
35A PHE* 3.8 1.2 - - - +
36A ARG* 3.0 76.4 + - - +
155A THR* 4.0 15.2 - - + +
156A ARG* 5.9 3.3 - - - +
159A VAL* 3.7 19.3 - - + +
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Residues in contact with GLU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLN 4.5 0.6 + - - +
30A ASP* 3.2 10.3 + - - +
32A GLU* 1.3 77.2 - - - +
34A VAL* 1.3 59.5 + - - +
36A ARG* 3.9 9.7 - - + +
37A SER* 2.9 34.9 + - - -
65A LEU* 6.3 2.2 - - + -
66A GLN* 3.4 30.8 + - - +
69A SER* 2.6 30.6 + - - -
71A MET* 3.6 22.4 - - + +
72A GLY* 3.9 5.4 + - - +
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Residues in contact with VAL 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASP 3.0 16.8 + - - +
31A THR* 3.7 7.6 - - - +
33A GLU* 1.3 75.9 - - - +
35A PHE* 1.3 58.9 + - - +
38A TYR* 2.8 27.4 + - - +
71A MET* 3.6 39.7 - - + +
74A VAL* 4.2 6.1 - - + -
75A GLY* 3.6 16.1 - - - -
78A LEU* 4.3 5.6 - - + -
132A LEU* 4.4 7.4 - - + -
177A TRP* 3.8 44.4 - - + -
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Residues in contact with PHE 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A THR* 2.8 17.8 + - + +
32A GLU 3.9 2.0 - - - +
34A VAL* 1.3 75.2 - - - +
36A ARG* 1.3 66.0 + - - +
38A TYR* 3.2 6.2 + + - +
39A VAL* 2.9 48.1 + - + +
132A LEU* 3.4 50.4 - - + +
135A GLY* 3.8 25.6 - - - -
136A TYR* 4.0 0.9 - - - -
151A LEU* 4.6 6.5 - - + -
154A VAL* 4.0 7.4 - - + -
155A THR* 3.3 49.1 - - + +
158A VAL* 4.2 17.0 - - + -
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Residues in contact with ARG 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A GLU* 3.0 63.3 + - - +
33A GLU* 3.9 7.6 - - + +
35A PHE* 1.3 73.5 - - - +
37A SER* 1.3 57.1 + - - +
39A VAL* 3.3 1.1 + - - -
40A PHE* 2.9 26.7 + - - +
63A LEU* 3.4 29.2 - - + +
64A PRO* 3.6 51.5 - - - +
65A LEU* 4.5 2.7 - - + -
152A GLY* 6.1 3.2 - - - -
155A THR* 4.6 16.7 + - + +
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Residues in contact with SER 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLU* 2.9 20.7 + - - -
34A VAL 3.7 3.4 - - - -
36A ARG* 1.3 74.5 - - - +
38A TYR* 1.3 65.4 + - - +
40A PHE* 3.3 0.9 + - - +
41A TYR* 2.9 42.5 + - - -
65A LEU* 3.7 17.4 - - - +
71A MET 4.1 0.4 - - - -
72A GLY* 2.8 38.4 + - - -
75A GLY* 4.1 3.4 - - - -
76A ARG 3.5 3.1 + - - -
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Residues in contact with TYR 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL 2.8 18.5 + - - +
35A PHE* 3.2 9.8 + + - +
37A SER* 1.3 75.8 - - - +
39A VAL* 1.3 64.9 + - + +
42A ARG* 2.8 69.0 + - - +
75A GLY* 3.6 13.8 - - - +
78A LEU* 3.8 14.8 - - + -
79A ALA* 3.5 36.1 - - - +
82A GLY* 5.3 3.1 - - - -
86A ASN* 4.3 4.9 + - - +
129A VAL* 4.0 12.7 + - + +
132A LEU* 3.5 44.9 - - + -
133A GLY* 3.3 14.2 + - - -
136A TYR* 4.0 10.5 - - + -
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Residues in contact with VAL 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PHE* 2.9 56.0 + - + +
36A ARG 3.6 3.8 - - - +
38A TYR* 1.3 76.9 - - + +
40A PHE* 1.3 58.0 + - - +
43A HIS* 2.8 33.1 + - - +
60A MET* 3.6 38.4 - - + -
63A LEU* 4.1 14.8 - - + -
136A TYR* 3.7 20.6 - - + -
151A LEU* 4.5 7.6 - - + -
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Residues in contact with PHE 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ARG 2.9 17.5 + - - +
37A SER 3.7 3.6 - - - +
39A VAL* 1.3 79.2 - - - +
41A TYR* 1.3 82.2 + + - +
43A HIS* 3.7 2.4 - - - +
44A GLN* 2.9 53.6 + - + +
60A MET 3.5 21.5 - - - -
61A VAL* 3.5 34.5 - - + -
63A LEU* 4.1 13.0 - - + -
65A LEU* 3.7 28.0 - - + -
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Residues in contact with TYR 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A SER* 2.9 44.3 + - - +
40A PHE* 1.3 100.5 - + - +
42A ARG* 1.3 61.4 + - - +
44A GLN* 3.5 23.3 - - - +
45A GLN* 2.8 38.4 + - - +
65A LEU* 3.8 12.8 - - + +
67A PRO* 3.3 31.4 + - + +
72A GLY 4.2 4.3 - - - -
76A ARG* 3.5 36.6 - - + -
79A ALA* 3.9 17.7 - - + -
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Residues in contact with ARG 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A TYR* 2.8 57.9 + - + +
39A VAL 3.9 2.0 - - - +
41A TYR* 1.3 72.3 - - - +
43A HIS* 1.3 58.4 + - - +
45A GLN* 3.2 8.4 + - + +
46A GLU* 2.8 35.6 + - - +
79A ALA* 3.7 16.2 - - + +
82A GLY 6.5 1.1 - - - -
83A ASP 6.4 0.2 - - - +
86A ASN* 3.8 10.4 - - - +
90A ASP* 2.7 28.8 + - - -
133A GLY* 3.4 24.5 + - - -
136A TYR* 3.5 24.8 - - + -
137A ARG* 3.2 26.9 - - - +
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Residues in contact with HIS 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL 2.8 19.0 + - - +
40A PHE 3.7 4.0 - - - +
42A ARG* 1.3 78.6 - - - +
44A GLN* 1.3 55.2 + - - +
46A GLU* 3.3 4.7 + - + +
47A GLN* 3.0 61.1 + - + +
54A ALA* 6.0 0.4 - - + -
55A PRO 3.4 25.6 - - - -
56A ALA* 5.1 0.6 - - - -
57A ASP* 3.6 26.6 + - + -
60A MET* 3.6 24.8 - - + +
61A VAL* 3.8 17.6 - - + +
136A TYR* 3.0 28.1 + - + +
140A LEU* 4.9 1.6 - - + -
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Residues in contact with GLN 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PHE* 2.9 46.0 + - + +
41A TYR* 3.5 24.9 - - - +
43A HIS* 1.3 75.2 - - - +
45A GLN* 1.3 58.7 + - - +
47A GLN* 3.2 17.5 + - - +
48A GLU* 2.8 51.9 + - + +
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Residues in contact with GLN 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TYR* 2.8 22.8 + - - +
42A ARG* 3.4 9.0 - - + +
44A GLN* 1.3 78.3 - - - +
46A GLU* 1.3 57.5 + - - +
48A GLU* 3.1 15.4 + - - +
49A ALA* 2.9 30.8 + - - +
76A ARG* 5.7 0.2 - - - +
79A ALA* 3.0 29.4 - - - +
80A ILE* 3.2 40.2 - - - +
83A ASP* 3.8 21.0 - - - +
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Residues in contact with GLU 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ARG* 2.8 23.9 + - - +
43A HIS* 3.6 7.6 + - - +
44A GLN 3.3 0.2 - - - -
45A GLN* 1.3 72.7 - - - +
47A GLN* 1.3 57.8 + - - +
49A ALA* 4.5 3.8 - - - +
50A GLU* 2.7 67.9 + - - +
54A ALA* 4.2 3.8 - - + -
55A PRO* 3.6 18.0 - - + +
136A TYR* 2.8 31.8 + - - +
137A ARG* 3.4 35.7 + - - -
140A LEU* 3.8 0.2 - - - +
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Residues in contact with GLN 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A HIS* 3.0 45.0 + - + +
44A GLN* 3.5 22.2 - - - +
46A GLU* 1.3 77.7 - - - +
48A GLU* 1.3 58.3 + - + +
51A GLY* 2.8 31.2 + - - +
54A ALA* 3.9 18.8 - - + -
56A ALA* 6.3 0.4 - - - +
61A VAL* 4.1 13.3 - - - +
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Residues in contact with GLU 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLN* 2.8 45.0 + - + +
45A GLN* 3.1 15.9 + - - +
47A GLN* 1.3 77.2 - - + +
49A ALA* 1.3 58.3 + - - +
51A GLY* 4.6 1.6 + - - -
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Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLN 2.9 16.1 + - - +
46A GLU* 4.0 4.7 - - - +
48A GLU* 1.3 78.1 - - - +
50A GLU* 1.3 66.7 + - + +
51A GLY 3.8 0.2 - - - -
83A ASP* 5.5 7.0 - - - +
----------------------------------------------------------
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Residues in contact with GLU 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLU* 2.7 37.5 + - + +
49A ALA* 1.3 80.3 - - + +
51A GLY* 1.3 61.2 + - - +
52A VAL* 3.3 1.4 + - - +
53A ALA* 3.0 27.7 + - + +
54A ALA* 3.3 28.3 - - - +
55A PRO* 3.4 13.5 - - - +
137A ARG* 5.2 4.0 + - - -
----------------------------------------------------------
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Residues in contact with GLY 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLN* 2.8 25.3 + - - +
48A GLU 4.5 1.8 + - - -
49A ALA 3.8 0.8 - - - -
50A GLU* 1.3 69.7 - - - +
52A VAL* 1.3 58.9 + - - -
54A ALA* 2.9 27.0 + - - +
----------------------------------------------------------
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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