Contacts of the helix formed by residues 48 - 71 (chain Y) 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 GLY 48 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46Y ALA 4.1 0.2 + - - -
47Y GLY* 1.3 69.6 - - - -
49Y ALA* 1.3 65.1 + - - -
50Y ALA 3.5 1.8 - - - -
51Y ASP* 3.2 11.0 + - - +
52Y CYS* 2.9 26.5 + - - -
96Y SER* 2.8 26.8 + - - -
1e ASN 3.8 1.1 - - - -
2e GLN* 3.8 16.6 - - - -
3e LEU* 4.8 0.2 - - - -
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Residues in contact with ALA 49 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20Y ALA* 5.9 0.2 - - + -
47Y GLY 3.4 3.6 + - - -
48Y GLY* 1.3 70.7 - - - +
50Y ALA* 1.3 65.6 + - - +
52Y CYS* 3.9 0.7 - - - +
53Y GLN* 3.0 31.2 + - - +
114Z ASP* 4.4 0.2 - - - +
118Z SER* 3.3 21.8 - - - +
1e ASN* 3.0 29.5 + - + +
3e LEU* 3.7 34.3 - - + +
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Residues in contact with ALA 50 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48Y GLY 3.5 0.4 - - - -
49Y ALA* 1.3 78.5 - - - +
51Y ASP* 1.3 57.5 + - - +
53Y GLN* 4.5 2.5 - - - -
54Y PHE* 2.8 35.7 + - - +
84Z GLN* 5.8 0.9 - - - +
88Z TYR* 3.9 8.7 - - + -
114Z ASP* 4.2 1.2 + - - -
116Z VAL* 3.4 47.6 - - + +
117Z GLY 4.4 1.1 - - - -
118Z SER* 3.6 21.7 - - - +
1e ASN 4.8 0.2 + - - -
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Residues in contact with ASP 51 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48Y GLY* 3.2 13.3 + - - +
50Y ALA* 1.3 77.6 - - - +
52Y CYS* 1.3 63.0 + - - +
55Y TRP* 3.1 30.5 + - - +
95Y LEU* 3.5 8.4 - - - +
96Y SER* 2.9 36.6 + - - +
97Y MET* 3.7 11.1 - - - +
88Z TYR* 2.6 32.0 + - - +
91Z ARG* 2.8 30.9 + - - -
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Residues in contact with CYS 52 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45Y MET* 3.6 26.5 - - + -
46Y ALA 3.1 41.1 - - - -
48Y GLY 2.9 20.8 + - - +
49Y ALA 3.9 1.3 - - - +
51Y ASP* 1.3 73.0 - - - +
53Y GLN* 1.3 57.4 + - - +
56Y GLU* 2.7 45.9 + - - +
97Y MET* 3.5 25.6 - - - -
98Y GLY 4.7 2.5 - - - -
99Y THR* 5.3 0.9 - - - -
3e LEU* 4.7 2.0 - - + -
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Residues in contact with GLN 53 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31Y VAL* 5.1 12.3 - - - +
35Y ILE* 5.3 0.7 - - - +
45Y MET* 3.4 25.0 - - + +
49Y ALA* 3.0 17.7 + - - +
50Y ALA* 4.1 0.7 - - - +
52Y CYS* 1.3 81.3 - - - +
54Y PHE* 1.3 55.9 + - - +
56Y GLU* 4.9 0.4 - - - -
57Y THR* 2.7 33.8 + - - +
84Z GLN* 3.4 21.0 + - - +
118Z SER* 2.8 26.0 + - - -
119Z TYR* 3.2 34.8 + - - +
120Z GLU* 5.6 1.4 + - - -
3e LEU* 5.4 1.2 - - - +
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Residues in contact with PHE 54 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101R LEU* 5.3 3.3 - - + +
50Y ALA* 2.8 24.2 + - - +
51Y ASP 4.3 0.4 - - - +
53Y GLN* 1.3 75.0 - - - +
55Y TRP* 1.3 90.8 + + - +
57Y THR* 3.2 6.1 + - - -
58Y TRP* 3.0 30.5 + + + +
84Z GLN* 4.1 25.8 - - + +
85Z HIS* 3.7 37.2 - + - -
88Z TYR* 3.5 55.6 - + + -
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Residues in contact with TRP 55 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51Y ASP 3.1 24.6 + - - +
54Y PHE* 1.3 102.7 - + - +
56Y GLU* 1.3 58.0 + - - +
58Y TRP* 3.5 42.6 - + + +
59Y LEU* 2.9 22.3 + - - +
83Y LEU* 4.0 8.4 - - + +
86Y LEU* 3.5 42.4 - - + -
90Y TYR* 3.7 33.4 - + - -
95Y LEU* 3.9 13.6 - - + +
97Y MET* 3.9 25.1 - - + -
88Z TYR* 3.0 31.6 + + - -
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Residues in contact with GLU 56 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35Y ILE* 3.0 40.7 - - + +
37Y ILE* 5.0 2.9 - - + +
43Y GLY* 3.5 14.1 - - - -
44Y THR 2.9 9.0 - - - +
45Y MET* 3.4 17.8 - - - +
52Y CYS* 2.7 28.1 + - - +
53Y GLN* 4.6 2.2 - - - +
55Y TRP* 1.3 72.1 - - - +
57Y THR* 1.3 66.1 + - - +
59Y LEU* 3.0 13.8 + - + +
60Y GLY* 3.0 18.0 + - - -
83Y LEU* 4.4 19.1 - - + -
97Y MET* 5.2 1.7 - - + +
99Y THR* 2.5 29.1 + - - -
101Y ILE* 5.0 1.8 - - - -
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Residues in contact with THR 57 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101R LEU* 3.3 22.2 - - + -
35Y ILE* 3.9 17.6 - - + +
53Y GLN* 2.7 24.9 + - - +
54Y PHE* 3.2 6.6 + - - -
56Y GLU* 1.3 77.0 - - - +
58Y TRP* 1.3 64.3 + - - +
60Y GLY* 3.0 11.4 + - - -
61Y SER* 3.2 12.5 + - - -
81Z ARG* 4.0 29.0 + - - +
84Z GLN* 5.3 4.5 + - - +
85Z HIS* 6.1 0.2 - - + -
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Residues in contact with TRP 58 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101R LEU* 4.0 26.2 - - + +
54Y PHE* 3.0 20.2 + + + +
55Y TRP* 3.5 42.0 - + + +
57Y THR* 1.3 77.6 - - - +
59Y LEU* 1.3 76.0 + - + +
61Y SER* 2.9 6.8 + - - -
62Y GLN* 2.9 51.3 + - + +
82Y ILE* 3.8 32.3 - - + -
83Y LEU* 4.8 5.6 - - + -
86Y LEU* 3.6 38.8 - - + -
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Residues in contact with LEU 59 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Y ILE* 3.6 26.2 - - + -
55Y TRP 2.9 15.3 + - - +
56Y GLU* 3.0 13.7 + - + +
58Y TRP* 1.3 82.8 - - + +
60Y GLY* 1.3 56.4 + - - +
62Y GLN* 3.0 3.5 + - + +
63Y CYS* 2.8 38.9 + - - -
79Y ALA* 3.5 28.5 - - + +
82Y ILE* 3.7 25.8 - - + -
83Y LEU* 4.2 18.2 - - + +
101Y ILE* 4.0 19.7 - - + -
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Residues in contact with GLY 60 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35Y ILE* 5.9 1.8 - - - -
37Y ILE* 4.1 29.3 - - - +
56Y GLU 3.0 12.4 + - - -
57Y THR* 3.0 5.5 + - - -
59Y LEU* 1.3 76.0 - - - +
61Y SER* 1.3 56.8 + - - +
63Y CYS* 3.3 2.1 + - - +
64Y ARG* 3.0 30.0 + - - +
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Residues in contact with SER 61 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97R VAL* 3.7 27.8 + - - +
101R LEU* 3.4 44.2 - - - +
57Y THR* 3.2 4.3 + - - +
58Y TRP 2.9 10.4 + - - -
60Y GLY* 1.3 76.3 - - - +
62Y GLN* 1.3 69.3 + - - +
64Y ARG* 3.4 2.8 + - - +
65Y LEU* 3.1 23.7 + - - +
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Residues in contact with GLN 62 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101R LEU* 5.7 0.4 - - - +
58Y TRP* 2.9 67.0 + - + +
59Y LEU* 3.5 7.0 - - + +
61Y SER* 1.3 83.1 - - - +
63Y CYS* 1.3 62.9 + - - +
65Y LEU* 3.4 20.0 + - - +
66Y HIS* 3.1 21.8 + - - +
69Y ARG* 5.0 8.0 + - - -
82Y ILE* 4.3 24.3 - - + +
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Residues in contact with CYS 63 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37Y ILE* 4.0 23.3 - - + -
38Y ASN* 5.5 2.0 - - - +
41Y LEU* 4.3 0.2 - - - -
59Y LEU* 2.8 29.6 + - - +
60Y GLY 3.5 6.1 - - - +
61Y SER 3.2 0.2 - - - -
62Y GLN* 1.3 76.9 - - - +
64Y ARG* 1.3 62.4 + - - +
66Y HIS* 3.0 22.9 + - - +
67Y GLU* 3.2 12.5 + - - +
74Y ILE* 3.9 29.6 - - + +
79Y ALA* 3.9 22.4 - - - -
82Y ILE* 6.1 1.8 - - - -
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Residues in contact with ARG 64 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69R GLU* 3.0 26.9 + - - -
71R ASP* 3.2 25.9 + - - -
72R ARG* 3.4 12.2 - - - +
97R VAL* 4.0 18.8 - - + -
60Y GLY 3.0 17.0 + - - +
61Y SER* 3.7 7.0 - - - +
62Y GLN 3.4 0.2 - - - -
63Y CYS* 1.3 74.6 - - - +
65Y LEU* 1.3 63.7 + - - +
67Y GLU* 3.2 22.5 + - - +
68Y LEU* 3.0 45.6 + - + +
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Residues in contact with LEU 65 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93R ARG* 3.9 20.9 - - + +
94R THR* 4.4 15.3 - - + +
97R VAL* 3.4 37.7 - - + -
98R THR* 6.1 0.7 - - - +
61Y SER 3.1 16.5 + - - +
62Y GLN* 3.5 28.7 - - - +
64Y ARG* 1.3 76.7 - - - +
66Y HIS* 1.3 62.0 + - - +
68Y LEU* 3.3 11.2 + - + +
69Y ARG* 3.0 55.5 + - - +
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Residues in contact with HIS 66 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103Q LEU* 4.1 26.0 - - + +
62Y GLN 3.1 11.5 + - - +
63Y CYS* 3.0 11.7 + - - +
65Y LEU* 1.3 76.1 - - - +
67Y GLU* 1.3 52.3 + - - +
69Y ARG* 3.2 11.0 + - - +
70Y GLU* 2.7 60.6 + - + +
72Y GLU* 3.7 13.2 + - - +
73Y ARG 4.4 2.2 + - - -
74Y ILE* 3.4 47.4 - - + +
75Y SER 5.0 0.8 + - - -
82Y ILE* 6.1 2.7 - - + -
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Residues in contact with GLU 67 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38Y ASN* 4.2 9.0 + - - -
63Y CYS 3.7 12.6 - - - +
64Y ARG* 3.2 22.4 + - - +
66Y HIS* 1.3 72.8 - - - +
68Y LEU* 1.3 58.5 + - - +
71Y LYS* 2.7 33.3 + - - -
72Y GLU 3.1 21.4 + - - +
73Y ARG* 2.6 43.8 + - - +
74Y ILE* 3.1 13.1 + - + +
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Residues in contact with LEU 68 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69R GLU* 3.6 46.0 - - + +
70R ILE 3.3 22.2 - - - +
71R ASP* 4.8 0.9 - - - +
93R ARG* 3.3 42.4 + - + +
97R VAL* 4.2 19.5 - - + -
64Y ARG* 3.0 44.7 + - - +
65Y LEU* 3.7 9.0 - - + +
67Y GLU* 1.3 76.9 - - - +
69Y ARG* 1.3 61.8 + - - +
71Y LYS* 4.2 9.2 + - - +
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Residues in contact with ARG 69 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114Q ARG* 4.1 17.1 + - - +
90R GLU* 2.8 48.3 + - - -
93R ARG* 4.0 16.2 + - - +
94R THR* 4.7 0.2 + - - -
62Y GLN* 5.0 8.3 + - - -
65Y LEU* 3.0 47.5 + - - +
66Y HIS* 3.5 8.4 - - - +
68Y LEU* 1.3 80.3 - - - +
70Y GLU* 1.3 77.8 + - + +
71Y LYS* 3.5 5.8 + - - +
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Residues in contact with GLU 70 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99Q HIS* 6.3 0.2 - - - -
108Q THR* 5.4 0.7 + - - -
111Q TYR* 3.4 22.5 - - - +
114Q ARG* 3.0 40.9 + - - +
66Y HIS* 2.7 51.1 + - + +
69Y ARG* 1.3 88.5 - - + +
71Y LYS* 1.3 72.5 + - - +
72Y GLU* 3.0 13.3 + - + +
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Residues in contact with LYS 71 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110Q GLU* 5.6 4.9 + - - -
65R GLU* 3.3 36.3 + - - +
93R ARG* 5.9 2.2 - - - +
67Y GLU 2.7 20.6 + - - +
68Y LEU 4.7 7.9 - - - +
69Y ARG 3.5 6.2 - - - +
70Y GLU* 1.3 74.7 - - - +
72Y GLU* 1.3 56.7 + - - +
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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) + - + + + + + -
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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