Contacts of the helix formed by residues 30 - 53 (chain C) in PDB entry 2J3T
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 30 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ILE* 1.3 91.6 - - + +
31C LYS* 1.3 60.5 + - - +
32C GLU* 4.3 17.0 - - + +
33C GLU* 2.8 38.7 + - + +
34C GLU 3.0 9.0 + - - -
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Residues in contact with LYS 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C TYR* 3.8 18.2 - - + -
20C GLU* 3.8 25.5 + - - +
23C ARG* 5.5 0.2 - - - +
26C GLN* 4.2 17.2 + - - +
29C ILE 3.6 3.5 + - - +
30C PRO* 1.3 71.4 - - - +
32C GLU* 1.3 70.1 + - - +
34C GLU* 4.0 17.7 - - - +
35C TYR* 3.0 58.3 + - + +
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Residues in contact with GLU 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C PRO* 4.3 14.6 - - + +
31C LYS* 1.3 82.8 + - - +
33C GLU* 1.3 58.8 + - + +
35C TYR* 3.9 18.3 - - - +
36C LYS* 3.7 24.7 + - - +
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Residues in contact with GLU 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ILE* 3.4 28.1 - - + +
30C PRO* 2.8 31.3 + - + +
32C GLU* 1.3 79.0 - - + +
34C GLU* 1.3 64.7 + - - +
35C TYR 3.1 1.8 - - - -
36C LYS* 3.1 10.4 + - + +
37C LEU* 2.9 25.8 + - + +
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Residues in contact with GLU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C TYR* 2.5 34.3 + - + +
18C TYR* 4.5 2.9 - - - -
23C ARG* 2.7 41.6 + - - -
26C GLN* 5.0 1.4 - - - +
27C ALA* 3.4 10.3 + - + +
29C ILE* 3.9 16.9 - - + +
30C PRO 3.0 8.0 + - - +
31C LYS* 3.1 25.3 + - - +
33C GLU* 1.3 75.5 - - - +
35C TYR* 1.3 57.8 + - + +
37C LEU* 3.5 3.2 - - - +
38C MET* 2.7 37.1 + - - +
125D LEU* 3.6 19.7 - - + -
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Residues in contact with TYR 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C TYR* 4.2 10.5 - + - -
9C PHE* 3.7 7.5 - - + -
13C GLY 5.8 1.3 - - - +
15C CYS* 3.7 37.5 - - + -
18C TYR* 3.2 51.5 - + + +
31C LYS* 3.0 42.5 + - + +
32C GLU* 3.9 17.7 - - - +
33C GLU 3.1 0.2 - - - -
34C GLU* 1.3 81.5 - - + +
36C LYS* 1.3 58.7 + - + +
38C MET* 3.8 3.5 - - - +
39C TYR* 3.0 30.7 + - - +
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Residues in contact with LYS 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C GLU 3.7 14.3 + - - +
33C GLU* 3.1 14.1 + - + +
35C TYR* 1.3 75.8 - - + +
37C LEU* 1.3 60.1 + - - +
39C TYR* 3.9 4.1 - - - +
40C GLY* 2.9 27.0 + - - -
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Residues in contact with LEU 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ILE* 4.4 9.2 - - + -
33C GLU* 2.9 16.6 + - + +
34C GLU* 3.5 9.4 - - - +
36C LYS* 1.3 74.4 - - - +
38C MET* 1.3 65.6 - - - +
40C GLY* 3.3 1.1 + - - -
41C MET* 2.9 25.6 + - - +
121D ILE* 3.7 27.8 - - + -
124D GLN* 3.8 33.9 - - - +
125D LEU* 4.0 24.7 - - + -
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Residues in contact with MET 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C TYR* 3.9 35.0 - - + +
9C PHE* 3.7 24.2 - - + -
34C GLU 2.7 20.4 + - - +
35C TYR 3.8 4.0 - - - +
37C LEU* 1.3 74.3 - - - +
39C TYR* 1.3 58.5 + - - +
41C MET* 3.3 14.6 + - - +
42C LEU* 2.9 61.8 + - + +
71C LEU* 4.0 20.6 - - + -
83C VAL* 4.9 1.6 - - - -
85C ASN* 5.8 1.3 - - - -
125D LEU* 3.6 23.7 - - + +
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Residues in contact with TYR 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A ASN 6.2 2.2 - - - -
9C PHE* 3.5 29.4 - + + -
10C ASP 3.8 0.3 + - - -
11C ARG 3.9 8.0 + - - -
12C ASN 4.1 2.6 - - - -
13C GLY* 3.2 43.9 + - - +
35C TYR 3.0 19.2 + - - +
36C LYS* 3.9 4.9 - - - +
38C MET* 1.3 75.7 - - - +
40C GLY* 1.3 56.4 + - - +
42C LEU* 3.1 7.4 + - + +
43C PHE* 2.6 70.5 + + + +
81C LYS* 3.1 43.1 + - + -
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Residues in contact with GLY 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C LYS 2.9 17.8 + - - -
37C LEU* 3.7 1.6 - - - -
39C TYR* 1.3 78.4 - - - +
41C MET* 1.3 56.7 - - - +
43C PHE* 3.3 6.2 + - - +
44C SER* 2.9 33.9 + - - -
121D ILE* 5.6 0.4 - - - -
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Residues in contact with MET 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C LEU* 2.9 12.9 + - - +
38C MET* 3.5 26.5 - - - +
40C GLY* 1.3 76.4 - - - +
42C LEU* 1.3 62.4 + - - +
44C SER* 3.1 7.1 + - - -
45C ILE* 3.0 33.8 + - + +
64C PHE* 3.5 30.1 - - + -
71C LEU* 5.4 0.2 - - - -
118D LEU* 3.2 34.7 - - + +
121D ILE* 3.6 35.7 - - + +
122D GLY* 3.3 22.9 - - - +
125D LEU* 4.8 2.0 - - - -
134D ILE* 3.9 7.0 - - + -
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Residues in contact with LEU 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C PHE* 3.9 22.0 - - + -
38C MET* 2.9 40.6 + - + +
39C TYR* 3.4 13.9 - - + +
41C MET* 1.3 76.0 - - - +
43C PHE* 1.3 62.6 + - - +
45C ILE* 3.4 21.3 + - + +
46C ARG* 3.2 27.4 + - - +
61C PHE* 4.5 4.9 - - + -
71C LEU* 4.4 12.3 - - + -
73C TYR* 3.7 28.9 - - + -
81C LYS* 5.2 2.7 - - + -
83C VAL* 3.5 26.9 - - + -
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Residues in contact with PHE 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ASP* 4.4 18.4 - - + -
174A ASN 4.5 7.9 - - - -
175A LEU 4.2 17.3 - - - -
11C ARG 5.8 0.9 - - - -
39C TYR* 2.6 51.7 + + + +
40C GLY* 3.7 6.3 - - - +
42C LEU* 1.3 75.5 - - - +
44C SER* 1.3 61.9 + - - +
46C ARG* 3.2 42.2 + - - +
47C SER* 3.2 24.3 + - - -
81C LYS* 5.7 0.4 - - - -
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Residues in contact with SER 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C GLY 2.9 19.7 + - - -
41C MET 3.1 0.9 + - - -
43C PHE* 1.3 73.4 - - - +
45C ILE* 1.3 56.1 + - - +
47C SER* 3.2 4.0 + - - -
48C PHE* 2.7 37.9 + - - +
114D MET* 3.3 20.0 - - - +
118D LEU* 3.4 27.9 - - - +
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Residues in contact with ILE 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C MET* 3.0 24.4 + - + +
42C LEU* 3.5 15.9 - - + +
43C PHE 3.2 0.2 - - - -
44C SER* 1.3 77.4 - - - +
46C ARG* 1.3 56.6 + - - +
48C PHE* 4.1 5.6 - - - -
49C VAL* 2.9 36.8 + - + +
61C PHE* 3.6 46.9 - - + -
64C PHE* 3.9 30.7 - - + -
118D LEU* 4.1 17.3 - - + -
134D ILE* 5.2 1.1 - - + -
137D LEU* 4.0 16.4 - - + -
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Residues in contact with ARG 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ARG* 4.2 14.6 - - - +
173A ASP* 3.7 22.2 + - - -
42C LEU 3.2 16.4 + - - +
43C PHE* 3.2 42.9 + - - +
45C ILE* 1.3 78.0 - - + +
47C SER* 1.3 60.2 + - - +
49C VAL* 4.1 6.5 - - - +
50C SER* 3.3 22.5 + - - -
61C PHE* 5.3 7.9 - - + -
73C TYR* 3.3 24.9 - - + +
75C GLU* 2.7 37.7 + - - +
81C LYS* 4.1 12.7 - - - +
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Residues in contact with SER 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C PHE* 3.2 15.3 + - - -
44C SER* 3.2 8.7 + - - -
46C ARG* 1.3 78.8 - - - +
48C PHE* 1.3 64.7 + - - +
50C SER* 3.2 14.9 + - - -
51C LYS* 3.3 38.0 + - - +
114D MET* 4.5 10.3 - - - +
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Residues in contact with PHE 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C SER 2.7 22.3 + - - +
45C ILE* 3.6 5.8 - - - +
47C SER* 1.3 72.2 - - - +
49C VAL* 1.3 68.3 + - + +
51C LYS* 3.1 4.2 + - - +
52C MET* 2.9 61.0 + - + +
111D LEU* 3.2 44.8 - - + +
114D MET* 3.7 17.9 - - + +
115D PHE* 3.9 20.0 - + + -
118D LEU* 4.3 10.8 - - + -
137D LEU* 4.9 10.3 - - + -
142D PHE* 5.1 3.1 - + - -
144D LEU* 3.6 32.1 - - + -
156D VAL* 6.1 0.2 - - + -
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Residues in contact with VAL 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C ILE* 2.9 29.2 + - + +
46C ARG* 4.2 5.4 - - - +
48C PHE* 1.3 79.5 - - + +
50C SER* 1.3 64.7 + - - +
53C SER* 3.2 27.0 + - - -
57C MET* 3.3 28.2 - - + +
60C GLY* 4.4 1.6 - - - -
61C PHE* 4.0 16.4 - - + +
137D LEU* 3.7 26.9 - - + -
139D THR* 3.6 14.6 - - - +
142D PHE* 3.7 13.0 - - + -
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Residues in contact with SER 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C ARG 3.3 12.4 + - - -
47C SER* 3.2 12.7 + - - -
48C PHE 3.1 0.6 - - - -
49C VAL* 1.3 85.1 - - - +
51C LYS* 1.3 60.2 + - - +
53C SER* 4.4 1.4 + - - -
57C MET* 4.4 7.5 - - - +
100D ARG* 3.2 23.7 + - - -
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Residues in contact with LYS 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C SER* 3.3 27.5 + - - +
48C PHE 3.1 6.0 + - - +
50C SER* 1.3 80.6 - - - +
52C MET* 1.3 65.4 + - - +
53C SER 3.5 5.6 + - - +
43D HIS* 5.8 6.1 - - - -
44D ASP* 5.3 6.4 + - - -
100D ARG* 4.6 2.8 + - - +
103D LEU* 3.5 35.5 - - + +
107D GLU* 5.4 8.5 + - + +
110D MET* 3.8 32.3 - - + +
111D LEU* 4.2 11.2 - - + -
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Residues in contact with MET 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C PHE* 2.9 51.3 + - + +
51C LYS* 1.3 78.3 - - - +
53C SER* 1.3 65.8 + - - +
54C PRO* 3.3 7.8 - - - +
7D TYR* 2.8 42.4 - - + +
22D TYR* 4.7 5.0 + - - -
103D LEU* 3.3 27.1 - - + +
111D LEU* 3.8 17.9 - - + -
142D PHE* 4.2 12.6 - - + -
158D LEU* 3.3 36.3 - - + +
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Residues in contact with SER 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C VAL 3.2 18.6 + - - -
51C LYS 3.5 2.8 - - - +
52C MET* 1.3 78.9 - - - +
54C PRO* 1.3 61.7 - - - +
55C LEU 2.6 29.7 + - - -
57C MET* 3.5 11.5 - - - +
100D ARG* 2.8 31.7 + - - -
141D THR* 2.8 16.8 + - - -
142D PHE* 3.5 17.2 - - - -
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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
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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) + - + + + + + -
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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