Contacts of the helix formed by residues 34 - 57 (chain A) in PDB entry 4TZM
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 ASP 34 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ILE* 4.0 5.0 - - - +
33A SER* 1.3 81.0 + - - +
35A PRO* 1.3 65.5 - - + +
36A ASP* 3.5 9.9 + - - +
37A ARG* 2.6 69.0 + - - +
38A SER* 2.8 32.7 + - - -
239A HIS* 3.5 1.3 - - - -
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Residues in contact with PRO 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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34A ASP* 1.3 88.4 - - + +
36A ASP* 1.3 66.9 + - - +
38A SER* 3.6 0.4 + - - -
39A SER* 3.2 23.6 + - - -
239A HIS* 3.3 39.7 - - + +
240A HIS* 3.6 7.7 - - + -
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Residues in contact with ASP 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASP* 3.4 8.5 + - - +
35A PRO* 1.3 83.1 - - - +
37A ARG* 1.3 59.9 + - + +
39A SER* 3.2 7.5 + - - -
40A ASN* 2.8 38.8 + - - +
101A LYS* 4.7 11.2 - - - +
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Residues in contact with ARG 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PRO* 3.9 15.3 - - + +
31A ILE* 3.2 58.6 - - - +
32A VAL* 4.1 4.2 - - - -
34A ASP* 2.6 42.1 + - - +
36A ASP* 1.3 76.4 - - + +
38A SER* 1.3 60.3 + - - +
39A SER 3.2 0.7 - - - -
40A ASN* 3.8 15.8 - - - +
41A PHE* 3.0 26.7 + - - +
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Residues in contact with SER 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A VAL* 3.4 20.1 + - - +
34A ASP 2.8 20.2 + - - -
35A PRO 3.7 3.4 - - - -
37A ARG* 1.3 76.5 - - - +
39A SER* 1.3 60.3 + - - +
41A PHE* 3.5 5.0 + - - +
42A MET* 3.4 23.4 + - - +
237A PRO* 3.5 12.8 - - - +
238A GLY 3.8 0.4 - - - -
239A HIS* 2.9 22.2 + - - -
240A HIS* 2.7 29.6 + - - -
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Residues in contact with SER 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PRO 3.2 17.1 + - - -
36A ASP* 3.4 6.5 - - - -
37A ARG 3.2 0.2 - - - -
38A SER* 1.3 75.5 + - - +
40A ASN* 1.3 64.5 + - - +
41A PHE 3.1 1.3 - - - -
42A MET* 3.2 12.2 + - - +
43A ILE* 3.2 21.0 + - - +
100A THR* 3.1 17.6 + - - -
101A LYS* 3.0 37.4 + - - +
240A HIS* 3.7 14.6 - - - -
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Residues in contact with ASN 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PRO* 4.4 9.6 - - + -
36A ASP* 2.8 28.9 + - - +
37A ARG* 3.8 17.9 - - + +
38A SER 3.5 0.2 - - - -
39A SER* 1.3 75.6 - - - +
41A PHE* 1.3 62.9 + - - +
43A ILE* 3.5 10.0 + - - +
44A ARG* 3.2 28.4 + - + +
101A LYS* 3.0 31.8 + - - +
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Residues in contact with PHE 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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24A TRP* 3.7 19.3 - + - -
28A PHE* 3.6 27.1 - + - -
29A PRO* 3.9 13.0 - - + +
32A VAL* 3.8 23.6 - - + -
37A ARG 3.0 17.9 + - - +
38A SER* 3.6 6.1 - - - +
39A SER 3.1 0.4 - - - -
40A ASN* 1.3 78.7 - - - +
42A MET* 1.3 67.7 + - - +
44A ARG* 3.2 2.9 + - - +
45A ALA* 2.8 24.5 + - + -
167A VAL* 3.4 24.5 - - + -
171A MET* 3.5 24.2 - - + -
235A LEU* 4.0 28.5 - - + -
237A PRO* 4.1 10.1 - - + -
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Residues in contact with MET 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 SER 3.4 13.4 + - - +
39A SER* 3.2 8.6 + - - +
41A PHE* 1.3 83.8 - - - +
43A ILE* 1.3 56.9 + - - +
45A ALA* 3.5 4.0 - - - +
46A ILE* 2.9 37.3 + - - +
100A THR* 4.3 12.3 - - + +
127A MET* 6.2 0.2 - - - +
129A PHE* 4.3 18.3 - - + -
235A LEU* 4.2 11.4 - - + +
237A PRO* 3.6 21.8 - - + -
240A HIS* 3.5 28.9 - - + -
241A ALA 3.5 35.0 - - - +
242A ALA* 3.6 17.3 - - + +
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Residues in contact with ILE 43 (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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39A SER 3.2 13.0 + - - +
40A ASN* 3.6 12.1 - - - +
42A MET* 1.3 77.6 - - - +
44A ARG* 1.3 70.7 + - + +
46A ILE* 3.5 3.7 + - - +
47A TYR* 3.2 21.9 + - + +
93A LEU 5.1 1.9 - - - +
94A ARG* 3.6 35.0 - - - +
97A GLY* 3.2 37.2 - - - +
98A ASP* 3.4 23.1 - - - +
101A LYS* 3.7 27.4 - - + +
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Residues in contact with ARG 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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26A LYS 5.0 1.4 + - - -
27A LEU* 3.0 53.3 + - - +
28A PHE* 3.7 12.3 - - + -
29A PRO* 4.2 12.6 - - + -
40A ASN* 3.2 16.4 - - + +
41A PHE 3.2 6.8 + - - +
43A ILE* 1.3 83.1 + - - +
45A ALA* 1.3 58.2 + - - +
47A TYR* 3.3 40.1 + - - +
48A VAL* 3.0 34.6 + - + +
81A PHE* 5.9 4.9 - - - -
94A ARG* 6.3 0.4 - - - +
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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
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28A PHE* 4.0 2.4 - - - -
41A PHE* 2.8 19.0 + - + +
42A MET* 3.2 10.3 + - - +
44A ARG* 1.3 74.7 - - - +
46A ILE* 1.3 66.3 + - + +
48A VAL* 4.7 0.7 - - - -
49A VAL* 2.9 32.6 + - + +
127A MET* 4.9 4.0 - - - -
171A MET* 3.6 30.1 - - + -
235A LEU* 3.6 19.3 - - + -
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Residues in contact with ILE 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 MET 2.9 22.2 + - - +
43A ILE 3.7 4.3 - - - +
45A ALA* 1.3 75.8 - - - +
47A TYR* 1.3 63.7 + - - +
50A PHE* 3.1 48.9 + - + +
93A LEU* 4.1 25.8 - - + +
96A ALA 4.4 3.1 - - - -
97A GLY* 3.7 31.6 - - - +
100A THR* 4.7 1.8 - - + -
105A LEU* 4.6 1.8 - - + -
108A ILE* 4.5 12.6 - - + -
127A MET* 4.0 20.9 - - - -
129A PHE* 3.8 21.8 - - + -
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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
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27A LEU* 4.8 3.6 - - + -
43A ILE* 3.2 11.2 + - + +
44A ARG* 3.5 38.8 - - - +
45A ALA 3.2 0.2 - - - -
46A ILE* 1.3 79.9 - - - +
48A VAL* 1.3 67.2 + - + +
51A SER* 2.6 42.2 + - - -
78A THR* 3.4 31.9 + - + -
79A LEU* 2.6 30.6 + - + -
81A PHE* 3.5 31.6 - + - -
90A ALA* 4.0 21.5 - - + -
93A LEU* 4.2 19.6 - - + +
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Residues in contact with VAL 48 (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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27A LEU* 4.6 11.9 - - + -
28A PHE* 3.6 31.0 - - + -
44A ARG* 3.0 22.9 + - + +
45A ALA* 4.0 2.5 - - - +
47A TYR* 1.3 89.8 - - + +
49A VAL* 1.3 65.8 + - + +
51A SER* 3.4 5.4 + - - -
52A ALA* 3.0 21.7 + - + +
70A ILE* 4.6 2.2 - - + -
76A CYS* 4.2 24.3 - - + -
77A MET 4.9 0.7 - - - +
78A THR* 4.5 10.2 - - + +
171A MET* 4.8 1.6 - - - -
175A VAL* 4.4 19.1 - - + -
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Residues in contact with VAL 49 (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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45A ALA* 2.9 23.3 + - + +
48A VAL* 1.3 75.9 - - - +
50A PHE* 1.3 58.3 + - - +
52A ALA* 3.1 8.0 + - - +
53A VAL* 2.9 26.7 + - + +
127A MET* 4.1 11.7 - - + -
171A MET* 4.4 17.5 - - + -
174A ILE* 3.7 35.2 - - + -
175A VAL* 4.9 4.5 - - + -
178A VAL* 4.3 9.9 - - + -
235A LEU* 5.5 0.9 - - + -
244A MET* 3.7 33.0 - - + -
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Residues in contact with PHE 50 (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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46A ILE* 3.1 37.7 + - + +
49A VAL* 1.3 74.6 - - - +
51A SER* 1.3 60.1 + - - +
53A VAL* 3.8 5.4 - - + +
54A LEU* 3.0 35.5 + - - +
93A LEU* 4.1 19.7 - - + -
108A ILE* 3.5 45.8 - - + -
110A LEU* 3.8 21.3 - - + -
125A PHE* 3.5 21.3 - - + -
127A MET* 3.6 28.9 - - + -
197A PHE* 3.9 18.2 - + + -
244A MET* 4.3 13.2 - - + -
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Residues in contact with SER 51 (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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47A TYR* 2.6 28.3 + - - -
48A VAL* 3.5 4.9 - - - -
50A PHE* 1.3 75.6 - - - +
52A ALA* 1.3 65.3 + - - +
54A LEU* 3.4 1.6 + - - -
55A ARG* 3.0 21.1 + - - +
65A PHE* 3.3 14.5 - - - -
77A MET 3.4 18.2 - - - -
78A THR* 3.7 9.5 - - - -
79A LEU* 3.2 33.8 + - - +
93A LEU* 4.9 0.6 - - - +
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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
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48A VAL* 3.0 14.1 + - + +
49A VAL* 3.1 11.9 + - - +
51A SER* 1.3 77.1 - - - +
53A VAL* 1.3 57.0 + - - +
55A ARG* 4.0 2.0 - - - +
56A GLN* 2.8 42.9 + - - +
76A CYS* 5.0 8.3 - - + -
77A MET 3.8 8.9 + - - +
175A VAL* 5.0 15.9 - - + -
178A VAL* 4.1 17.0 - - + -
179A GLN* 5.4 3.1 - - + -
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Residues in contact with VAL 53 (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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49A VAL* 2.9 25.4 + - + +
50A PHE* 3.8 8.5 - - + +
52A ALA* 1.3 76.2 - - - +
54A LEU* 1.3 64.2 + - - +
56A GLN* 4.8 1.1 - - - -
57A ARG* 3.0 28.6 + - + +
59A ILE* 5.2 0.7 - - + -
110A LEU* 3.7 17.3 - - + -
125A PHE* 3.5 54.3 - - + -
178A VAL* 4.1 17.5 - - + -
182A CYS* 4.9 1.1 - - - -
244A MET* 4.2 12.6 - - + -
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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
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50A PHE* 3.0 22.4 + - + +
51A SER 3.7 4.0 - - - +
53A VAL* 1.3 77.8 - - - +
55A ARG* 1.3 61.0 + - - +
58A ASN 3.4 0.2 + - - -
59A ILE* 2.9 55.1 + - + -
60A LEU* 3.3 16.8 + - + -
65A PHE* 3.8 10.1 - - + -
79A LEU* 4.1 26.9 - - + -
89A ILE* 4.1 15.0 - - + -
93A LEU* 5.5 0.2 - - + -
110A LEU* 3.7 29.4 - - + -
197A PHE* 4.3 11.0 - - + -
496C ILE* 4.3 11.7 - - + -
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Residues in contact with ARG 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 SER 3.0 16.6 + - - +
52A ALA* 4.0 2.2 - - - +
54A LEU* 1.3 75.4 - - - +
56A GLN* 1.3 66.9 + - - +
58A ASN* 2.8 46.8 + - - +
60A LEU 3.0 19.4 + - - -
61A GLU* 4.1 0.2 - - - +
62A LYS* 3.9 30.6 - - - +
65A PHE* 3.5 34.7 - - + -
77A MET* 3.7 32.3 - - + +
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Residues in contact with GLN 56 (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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52A ALA* 2.8 26.6 + - - +
55A ARG* 1.3 83.2 - - - +
57A ARG* 1.3 58.4 + - - +
58A ASN* 3.1 2.3 + - - +
77A MET* 5.4 5.5 + - - +
178A VAL* 4.8 1.6 - - + -
179A GLN* 3.9 40.3 + - + +
182A CYS* 3.6 39.4 - - + +
183A THR* 3.7 18.1 + - - +
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Residues in contact with ARG 57 (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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53A VAL* 3.0 19.8 + - + +
56A GLN* 1.3 74.6 - - - +
58A ASN* 1.3 70.3 + - - +
59A ILE* 3.1 20.0 + - + +
123A GLU* 2.9 40.2 + - - +
125A PHE* 4.2 9.2 - - + -
182A CYS* 3.5 41.3 + - - -
186A LEU* 3.5 20.2 + - - +
187A GLU 2.7 33.3 + - - -
188A PRO* 4.0 6.1 - - - +
189A LEU* 3.4 41.9 + - + +
250A SER* 3.4 6.5 + - - -
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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