Contacts of the helix formed by residues 48 - 70 (chain L) in PDB entry 3D29
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 PHE 48 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-6L PRO 3.6 11.7 - - - -
-5L TYR* 4.1 6.7 - + - -
-4L GLY* 3.3 42.1 + - - +
-2L ASN* 3.9 5.2 - - - -
47L GLY* 1.3 70.3 - - - -
49L ALA* 1.3 62.0 + - - +
50L ALA* 3.5 20.4 - - + -
51L ASP* 3.0 33.5 + - + +
52L GLY 2.9 22.3 + - - -
96L TYR* 2.9 26.1 + - + +
97L VAL* 3.7 1.8 - - - +
91M ARG* 3.4 24.9 - - - -
116M LEU* 3.6 21.5 - - + -
118M VAL* 3.3 23.3 - - + -
4b HXD 5.6 0.2 - - - +
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Residues in contact with ALA 49 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-2L ASN* 2.7 33.1 + - + +
20L ASN* 4.2 14.8 - - - +
47L GLY 3.2 6.0 + - - +
48L PHE* 1.3 71.0 - - - +
50L ALA* 1.3 55.5 + - - +
52L GLY* 3.6 2.9 - - - +
53L ASP* 2.8 40.9 + - - +
118M VAL* 4.5 8.1 - - + -
119M THR 5.3 4.0 - - - +
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Residues in contact with ALA 50 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48L PHE* 3.2 28.6 - - + -
49L ALA* 1.3 77.4 - - - +
51L ASP* 1.3 61.9 + - - +
53L ASP* 3.6 4.9 + - - +
54L ALA* 3.2 22.0 + - - +
88M TYR* 3.6 22.6 - - + -
116M LEU 3.7 8.5 - - - +
117M GLY 3.7 20.6 - - - +
118M VAL* 3.9 5.9 - - - +
119M THR 5.7 0.4 - - - +
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Residues in contact with ASP 51 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-5L TYR* 3.5 12.8 - - - -
48L PHE* 3.0 27.6 + - + +
50L ALA* 1.3 78.0 - - - +
52L GLY* 1.3 64.1 + - - +
54L ALA* 3.2 3.5 + - - +
55L LEU* 3.0 23.6 + - - +
90L LYS* 5.6 0.2 - - - -
94L PRO 3.5 1.1 - - - +
95L TYR* 3.2 24.5 - - + -
96L TYR 2.9 30.5 + - - +
97L VAL* 4.1 3.8 - - + -
88M TYR* 2.6 30.4 + - - -
91M ARG* 3.4 12.0 + - - -
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Residues in contact with GLY 52 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45L ALA* 3.4 29.7 - - - +
48L PHE 2.9 12.2 + - - -
49L ALA* 3.1 4.4 + - - -
51L ASP* 1.3 75.9 - - - +
53L ASP* 1.3 63.2 + - - +
55L LEU* 3.3 3.8 + - - +
56L VAL* 3.1 27.9 + - - +
97L VAL* 3.5 9.8 - - - +
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Residues in contact with ASP 53 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35L PHE* 4.8 17.1 - - - -
49L ALA* 2.8 25.6 + - - +
50L ALA* 4.0 5.3 - - - +
52L GLY* 1.3 74.2 - - - +
54L ALA* 1.3 66.4 + - - +
56L VAL* 3.4 5.6 + - - +
57L LYS* 2.9 31.0 + - + +
111M ARG* 4.9 4.9 + - - -
119M THR* 4.1 18.0 + - - +
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Residues in contact with ALA 54 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50L ALA 3.2 12.0 + - - +
51L ASP 3.2 9.5 + - - +
53L ASP* 1.3 78.7 - - - +
55L LEU* 1.3 58.2 + - - +
57L LYS* 3.6 6.9 - - - +
58L ARG* 2.9 37.0 + - - +
95L TYR* 4.0 12.3 - - + +
88M TYR* 3.9 27.1 - - + +
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Residues in contact with LEU 55 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43L MET* 3.9 14.8 - - + -
45L ALA* 3.8 11.9 - - + -
51L ASP 3.0 12.7 + - - +
52L GLY 3.6 7.9 - - - +
53L ASP 3.2 0.2 - - - -
54L ALA* 1.3 74.9 - - - +
56L VAL* 1.3 67.3 + - - +
58L ARG* 3.0 7.0 + - + +
59L PHE* 2.8 24.3 + - - +
83L ILE* 4.7 3.6 - - + -
86L LEU* 4.1 22.2 - - + +
87L LEU* 3.7 20.2 - - + -
95L TYR* 3.6 33.4 - - + -
97L VAL* 4.0 4.3 - - + -
99L THR* 3.6 31.0 - - + -
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Residues in contact with VAL 56 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35L PHE* 3.9 37.7 - - + -
37L CYS* 4.5 7.9 - - - -
43L MET* 4.1 27.1 - - + +
45L ALA* 4.4 13.9 - - + +
52L GLY 3.1 16.6 + - - +
53L ASP* 4.0 4.7 - - - +
55L LEU* 1.3 75.1 - - - +
57L LYS* 1.3 56.3 + - - +
59L PHE* 3.3 1.6 + - - +
60L LYS* 2.9 52.9 + - + +
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Residues in contact with LYS 57 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E SER 5.0 0.6 + - - -
101E LEU* 3.1 58.5 + - + +
53L ASP* 2.9 21.5 + - + +
54L ALA* 3.6 7.4 - - - +
56L VAL* 1.3 79.4 - - - +
58L ARG* 1.3 60.6 + - - +
60L LYS* 3.5 8.0 + - - +
61L ASN* 3.1 23.9 + - - +
81M GLU* 3.1 22.4 + - - +
85M THR* 5.4 1.6 + - - -
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Residues in contact with ARG 58 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54L ALA* 2.9 20.8 + - - +
55L LEU* 3.6 5.1 - - + +
57L LYS* 1.3 75.9 - - - +
59L PHE* 1.3 62.1 + - - +
61L ASN* 3.5 7.8 + - + +
62L SER* 3.1 19.8 + - - -
86L LEU* 3.6 54.4 + - + +
89L GLY* 5.9 2.0 - - - -
90L LYS* 5.0 5.9 - - - +
95L TYR* 2.7 29.1 + - - -
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Residues in contact with PHE 59 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37L CYS* 3.8 32.3 - - + -
41L ILE* 4.2 15.0 - - + -
43L MET* 3.5 30.5 - - + -
55L LEU 2.8 15.2 + - - +
56L VAL 3.7 2.2 - - - +
58L ARG* 1.3 73.8 - - - +
60L LYS* 1.3 60.0 + - - +
61L ASN 3.1 1.3 - - - -
62L SER* 2.8 21.0 + - - -
63L VAL* 2.9 24.3 + - + +
74L LEU* 4.2 10.3 - - + -
79L ALA* 3.5 37.0 - - + -
82L ASN* 4.3 13.7 - - - -
83L ILE* 3.7 23.1 - - + -
86L LEU* 3.8 13.2 - - + +
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Residues in contact with LYS 60 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35L PHE* 4.4 18.4 - - - +
36L ASP 3.8 21.6 + - - -
37L CYS* 4.0 24.5 - - + +
56L VAL* 2.9 35.9 + - + +
57L LYS* 3.9 6.7 - - - +
59L PHE* 1.3 77.2 - - - +
61L ASN* 1.3 63.1 + - - +
63L VAL* 3.1 12.9 + - - +
64L LYS* 3.0 21.8 + - - +
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Residues in contact with ASN 61 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E ASN* 2.6 41.1 + - - +
101E LEU* 3.9 18.6 - - + +
57L LYS 3.1 18.2 + - - +
58L ARG* 3.6 9.3 - - + +
59L PHE 3.1 0.2 - - - -
60L LYS* 1.3 78.1 - - - +
62L SER* 1.3 61.9 + - - +
64L LYS* 3.4 6.9 + - - +
65L TRP* 3.1 46.6 + - - +
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Residues in contact with SER 62 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D TYR* 4.2 12.8 + - - -
58L ARG 3.1 13.3 + - - -
59L PHE* 2.8 16.5 + - - -
61L ASN* 1.3 76.8 - - - +
63L VAL* 1.3 58.0 + - - +
65L TRP* 3.3 5.3 + - - +
66L TYR* 2.8 29.2 + - - +
74L LEU* 5.7 1.5 - - - +
82L ASN* 2.5 32.4 + - - -
86L LEU* 5.3 3.6 - - - -
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Residues in contact with VAL 63 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37L CYS* 4.0 22.4 - - + +
38L GLY* 5.3 1.6 - - - +
39L ASP* 4.6 10.3 - - + +
41L ILE* 5.7 3.1 - - + -
59L PHE* 2.9 43.9 + - + +
60L LYS* 3.1 9.4 + - - +
62L SER* 1.3 76.5 - - - +
64L LYS* 1.3 61.6 - - - +
66L TYR* 3.1 9.2 + - - +
67L HIS* 3.0 47.4 + - + +
74L LEU* 4.0 15.0 - - + -
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Residues in contact with LYS 64 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E CYS 5.3 0.4 + - - -
71E ASP* 3.5 32.2 + - - -
72E GLU* 5.9 3.8 - - - +
93E ARG 5.2 1.8 + - - -
96E CYS* 5.2 0.2 - - - +
97E ASN* 3.0 41.3 - - - +
100E SER* 5.1 4.8 + - - -
60L LYS 3.0 12.4 + - - +
61L ASN* 3.5 13.5 - - - +
63L VAL* 1.3 79.3 - - - +
65L TRP* 1.3 63.7 + - + +
67L HIS* 3.3 12.0 + - - +
68L PHE* 3.2 50.2 + - + -
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Residues in contact with TRP 65 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E ASN* 3.7 31.4 - - - -
93E ARG* 3.7 38.8 - - + -
94E GLN* 4.3 18.2 - - + -
97E ASN* 3.6 22.9 + - - +
61L ASN* 3.1 39.5 + - - +
62L SER* 3.9 4.7 - - - +
64L LYS* 1.3 79.5 - - + +
66L TYR* 1.3 62.7 + - - +
68L PHE* 3.1 30.1 + + + -
69L ASP* 2.7 54.7 + - - +
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Residues in contact with TYR 66 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D HIS* 4.5 0.9 - + - -
103D TYR* 3.8 29.4 - + + +
105D GLU* 2.5 35.9 + - - -
62L SER 2.8 14.2 + - - +
63L VAL* 3.1 14.1 + - - +
65L TRP* 1.3 77.8 - - - +
67L HIS* 1.3 57.9 + - - +
69L ASP* 4.8 0.9 - - - -
70L HIS* 2.8 59.3 + + + +
72L LYS* 3.2 49.7 - - + +
73L LYS 3.6 12.7 + - - -
74L LEU* 3.7 33.0 - - + +
75L SER 5.4 0.5 + - - -
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Residues in contact with HIS 67 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38L GLY* 6.0 0.4 - - - -
39L ASP* 3.0 41.8 + - - -
63L VAL* 3.0 32.0 + - + +
64L LYS* 3.5 10.8 - - - +
65L TRP 3.2 0.2 - - - -
66L TYR* 1.3 76.9 - + - +
68L PHE* 1.3 69.5 + - + +
70L ASN* 3.4 1.2 + - - -
71L ASP* 2.6 61.1 + - - +
72L LYS 3.2 18.1 + - - -
74L LEU 4.6 0.2 - - - -
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Residues in contact with PHE 68 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E LYS* 3.9 29.2 - - + -
70E CYS 3.6 22.4 - - - -
71E ASP* 4.5 2.0 - - - -
72E GLU* 5.9 0.4 - - - -
93E ARG* 3.6 55.6 + - + +
97E ASN* 6.5 0.2 - - - -
64L LYS* 3.2 46.1 + - + -
65L TRP* 3.1 38.6 + + + +
67L HIS* 1.3 82.4 - - + +
69L ASP* 1.3 63.4 + - - +
70L HIS* 3.3 6.4 + - - -
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Residues in contact with ASP 69 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D GLU* 4.9 6.2 - - - +
111D SER* 3.8 11.6 + - - -
86E ARG* 5.1 9.9 + - - -
90E ASN* 5.3 3.3 + - - -
93E ARG* 5.2 2.9 + - - -
65L TRP* 2.7 46.9 + - - +
66L TYR* 4.8 0.6 - - - -
68L PHE* 1.3 76.2 - - - +
70L HIS* 1.3 82.3 + - + +
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Residues in contact with HIS 70 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D HIS* 3.4 34.3 + + - -
103D TYR* 5.9 2.0 - + - -
105D GLU* 5.3 0.4 - - - -
107D ILE* 5.2 1.2 - - - +
108D ASN* 4.6 20.9 - - + +
111D SER* 3.3 28.0 + - - -
66L TYR* 2.8 44.1 + + + +
67L HIS 3.9 0.2 - - - -
69L ASP* 1.3 93.0 - - + +
70L ASN* 1.3 70.6 + - - +
71L ASP 3.3 2.0 - - - -
72L LYS* 3.0 32.2 + - + +
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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