Contacts of the helix formed by residues 45 - 70 (chain B) in PDB entry 5UNH
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 45 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B LEU* 1.3 70.7 - - - +
46B ALA* 1.3 64.8 + - - +
47B ILE 3.3 0.2 - - - -
48B PRO* 3.1 19.8 - - - +
49B ILE* 3.5 24.5 + - + +
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Residues in contact with ALA 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU* 3.3 13.0 - - + +
45B ASP* 1.3 77.9 - - - +
47B ILE* 1.4 63.1 + - + +
49B ILE* 3.5 6.8 + - - +
50B LEU* 3.1 39.5 + - + +
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Residues in contact with ILE 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 3.7 30.3 + - + -
46B ALA* 1.4 75.4 - - + +
48B PRO* 1.4 70.0 - - + +
50B LEU* 3.1 10.6 + - + +
51B TYR* 3.1 51.5 + - + -
101B ALA* 6.4 0.4 - - - -
104B TYR* 3.4 49.8 - - + +
298B LEU 5.5 3.4 - - - +
301B PRO* 4.4 23.8 - - + -
302B PHE* 5.4 4.9 - - + +
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Residues in contact with PRO 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU 3.3 14.4 - - - +
45B ASP* 3.1 26.0 - - - +
47B ILE* 1.4 85.8 - - + +
49B ILE* 1.4 62.5 + - + +
51B TYR* 3.2 10.1 + - + +
52B TYR* 3.1 22.0 + - - +
101B ALA* 4.1 22.9 - - + +
104B TYR* 4.0 11.7 - - + -
105B SER* 3.7 24.9 - - - +
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Residues in contact with ILE 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ASP* 3.5 20.9 - - + +
46B ALA* 3.5 10.0 + - - +
47B ILE 3.3 0.4 - - - -
48B PRO* 1.4 77.6 - - + +
50B LEU* 1.3 65.1 + - + +
52B TYR* 3.3 6.4 + - + +
53B ILE* 2.9 43.9 + - + +
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Residues in contact with LEU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ALA* 3.1 31.3 + - + +
47B ILE* 3.5 9.9 - - + +
49B ILE* 1.3 81.7 - - + +
51B TYR* 1.3 62.3 + - + +
53B ILE* 3.4 19.4 - - + +
54B ILE* 3.4 28.1 - - + +
305B LEU* 3.6 27.3 - - + +
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Residues in contact with TYR 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ILE* 3.1 42.9 + - + +
48B PRO* 3.2 9.6 + - + +
50B LEU* 1.3 74.9 - - - +
52B TYR* 1.3 61.2 + - - +
54B ILE* 3.7 4.7 - - - +
55B PHE* 3.3 21.7 + - - +
97B LEU* 3.6 33.8 - - + +
100B TRP* 4.3 9.4 - + + -
101B ALA* 4.1 28.7 - - + -
301B PRO* 2.7 38.2 + - - +
304B ILE* 3.5 21.5 - - + +
305B LEU* 3.6 26.2 - - + -
1501B 8EM 3.8 23.2 - + - -
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Residues in contact with TYR 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B PRO 3.1 12.4 + - - +
49B ILE* 3.8 7.9 - - - +
51B TYR* 1.3 73.6 - - - +
53B ILE* 1.3 65.3 - - + +
54B ILE 3.2 2.0 - - - -
55B PHE* 2.9 23.1 + - + +
56B VAL* 3.3 17.1 + - + +
97B LEU 6.4 0.2 - - - -
98B PRO* 6.6 0.2 - - - -
101B ALA* 5.3 3.8 - - + +
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Residues in contact with ILE 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ILE* 2.9 39.0 + - + +
50B LEU* 3.4 25.1 - - + +
52B TYR* 1.3 72.1 - - + +
54B ILE* 1.4 75.1 + - + +
56B VAL* 3.4 13.2 - - + +
57B ILE* 3.2 25.7 - - + +
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Residues in contact with ILE 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B LEU* 3.4 19.3 + - + +
51B TYR 3.7 4.9 - - - +
52B TYR 3.2 0.6 - - - -
53B ILE* 1.4 89.0 - - + +
55B PHE* 1.3 65.6 + - - +
57B ILE* 4.1 7.0 - - + -
58B GLY* 3.2 16.8 + - - -
94B LEU* 4.2 3.4 - - + +
97B LEU* 3.9 9.9 - - + -
305B LEU* 3.6 21.8 - - + -
308B PHE* 3.6 43.1 - - + +
309B THR* 4.1 15.3 - - + +
312B CYS* 3.6 14.6 - - - -
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Residues in contact with PHE 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B TYR 3.3 15.9 + - - +
52B TYR* 2.9 16.7 + - + +
54B ILE* 1.3 79.1 - - - +
56B VAL* 1.3 84.0 + - + +
58B GLY* 3.7 0.5 - - - -
59B PHE* 2.9 56.9 + + + +
94B LEU* 3.1 29.9 - - - +
95B ALA* 4.0 10.5 - - - -
97B LEU* 3.8 15.9 - - + -
98B PRO* 4.2 24.9 - - + -
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Residues in contact with VAL 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B TYR* 3.5 8.7 - - + +
53B ILE* 3.4 18.4 - - - +
55B PHE* 1.3 98.2 - - + +
57B ILE* 1.3 63.8 + - + +
59B PHE* 3.4 6.0 + - - +
60B LEU* 2.9 42.0 + - + +
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Residues in contact with ILE 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B ILE* 3.2 21.5 + - + +
54B ILE* 4.2 4.9 - - - +
55B PHE 3.3 0.2 - - - -
56B VAL* 1.3 80.6 - - + +
58B GLY* 1.3 55.3 + - - +
60B LEU* 3.1 15.8 + - + +
61B VAL* 2.9 44.6 + - + +
312B CYS* 4.5 16.6 - - + -
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Residues in contact with GLY 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ILE 3.2 8.2 + - - -
55B PHE 3.7 1.8 - - - -
57B ILE* 1.3 78.7 - - - +
59B PHE* 1.3 56.1 + - - +
61B VAL* 3.8 7.0 - - - -
62B ASN* 2.8 37.2 + - - +
94B LEU* 3.4 16.2 - - - +
312B CYS* 3.6 23.6 - - - -
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Residues in contact with PHE 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B PHE* 2.9 37.5 + + + +
56B VAL* 3.7 8.1 - - - +
58B GLY* 1.3 73.6 - - - +
60B LEU* 1.3 60.6 + - - +
63B ILE* 2.9 44.7 + - + +
91B LEU* 3.2 56.5 - - + +
94B LEU* 3.9 8.9 - - + +
95B ALA* 3.8 19.5 - - + -
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B VAL* 2.9 26.4 + - + +
57B ILE* 3.4 15.7 - - + +
59B PHE* 1.3 76.0 - - - +
61B VAL* 1.4 64.3 + - + +
63B ILE* 3.3 16.6 - - + +
64B VAL* 3.1 29.2 + - + +
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Residues in contact with VAL 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B ILE* 2.9 31.8 + - + +
58B GLY* 3.6 14.8 - - - +
60B LEU* 1.4 73.2 - - + +
62B ASN* 1.4 58.9 + - - +
64B VAL* 3.4 10.9 - - - +
65B VAL* 3.3 27.4 + - - +
312B CYS* 3.8 17.5 - - + +
315B PRO* 3.7 25.5 - - + +
316B PHE* 3.7 27.4 - - + -
320B PHE* 4.1 5.6 - - + -
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Residues in contact with ASN 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B GLY 2.8 28.4 + - - +
61B VAL* 1.4 72.6 - - - +
63B ILE* 1.4 62.2 + - - +
64B VAL 3.2 1.8 - - - -
65B VAL* 3.4 5.7 + - - +
66B VAL* 3.3 28.4 + - - +
87B ALA* 3.6 27.4 - - - +
90B ASP* 3.6 18.2 - - - +
91B LEU* 3.7 18.8 - - + -
94B LEU* 3.9 7.1 - - - +
311B SER 2.8 28.3 + - - -
314B ASN* 5.3 0.2 - - - +
315B PRO* 3.8 13.6 - - - +
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Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B PHE* 2.9 30.1 + - + +
60B LEU* 3.3 28.0 - - + +
62B ASN* 1.4 75.3 - - - +
64B VAL* 1.4 54.6 + - + +
66B VAL* 3.7 9.4 + - + +
67B THR* 2.7 49.6 + - + +
91B LEU* 4.0 22.6 - - + +
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Residues in contact with VAL 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B LEU* 3.1 18.8 + - + +
61B VAL* 3.4 11.0 - - - +
62B ASN 3.2 0.2 - - - -
63B ILE* 1.4 77.8 - - + +
65B VAL* 1.4 54.2 + - - +
67B THR* 2.8 6.9 + - - +
68B LEU* 2.8 40.8 + - + +
320B PHE* 3.7 29.6 - - + -
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Residues in contact with VAL 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B VAL 3.3 15.1 + - - +
62B ASN* 3.7 8.3 - - - +
63B ILE 3.4 0.4 - - - -
64B VAL* 1.4 71.7 - - - +
66B VAL* 1.4 59.2 + - - +
68B LEU* 3.3 8.9 + - - +
69B PHE* 2.9 37.1 + - + +
83B ILE* 3.8 30.3 - - + +
84B PHE* 5.4 1.1 - - - +
87B ALA* 3.8 17.9 - - + -
315B PRO* 3.5 28.0 - - + -
319B CYS* 3.8 20.2 - - + -
320B PHE* 4.2 5.4 - - + -
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Residues in contact with VAL 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ASN 3.3 16.6 + - - +
63B ILE* 4.1 12.1 - - + +
65B VAL* 1.4 75.4 - - - +
67B THR* 1.3 59.9 + - + +
69B PHE* 3.9 5.5 - - - +
70B CYS* 3.2 32.6 + - - +
84B PHE* 3.9 30.8 - - + -
87B ALA* 4.0 20.6 - - + -
88B VAL* 4.7 5.6 - - + -
91B LEU* 4.2 17.5 - - + -
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Residues in contact with THR 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ILE* 2.7 35.5 + - + +
64B VAL* 2.8 17.8 + - - +
66B VAL* 1.3 78.2 - - + +
68B LEU* 1.3 64.2 + - - +
70B CYS* 3.1 23.3 + - + +
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Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B VAL* 2.8 32.7 + - + +
65B VAL 3.6 4.5 - - - +
67B THR* 1.3 72.8 + - - +
69B PHE* 1.4 67.0 + - - +
70B CYS 3.3 5.4 + - - -
319B CYS* 3.5 33.7 - - - +
320B PHE* 3.7 24.5 - - + -
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Residues in contact with PHE 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B VAL* 2.9 22.6 + - + +
66B VAL* 3.9 6.7 - - - +
68B LEU* 1.4 80.3 - - + +
70B CYS* 1.3 60.5 + - - +
80B SER* 5.6 7.0 - - - +
83B ILE* 6.3 2.5 - - + -
84B PHE* 5.3 16.6 - - + +
319B CYS* 5.8 1.8 - - - -
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Residues in contact with CYS 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B VAL* 3.2 22.0 + - - +
67B THR* 3.1 20.9 + - - +
68B LEU 4.0 4.9 - - - -
69B PHE* 1.3 82.0 - - - +
84B PHE* 5.9 4.9 - - - -
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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
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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