Contacts of the helix formed by residues 48 - 71 (chain K) in PDB entry 3SDI
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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47K GLY* 1.3 68.3 - - - -
49K ALA* 1.3 67.5 + - - -
50K ALA 3.4 2.5 - - - -
51K ASP* 3.6 10.8 + - - +
52K CYS* 3.0 27.9 + - - +
96K SER 2.8 17.4 + - - -
302K 3SD 3.6 26.5 - - - -
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Residues in contact with ALA 49 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47K GLY 3.3 2.2 + - - -
48K GLY* 1.3 70.0 - - - +
50K ALA* 1.3 55.2 + - - +
52K CYS* 3.1 3.3 + - - +
53K GLN* 2.7 36.5 + - - +
302K 3SD 2.9 68.5 + - + +
118L SER* 3.5 24.0 - - - +
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Residues in contact with ALA 50 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48K GLY 3.4 0.2 - - - -
49K ALA* 1.3 77.3 - - - +
51K ASP* 1.3 57.1 + - - +
52K CYS 3.1 0.2 + - - -
53K GLN* 4.5 1.6 - - - -
54K PHE* 2.8 37.6 + - - +
302K 3SD 4.8 0.2 + - - -
84L GLN* 5.5 0.4 - - - +
88L TYR* 4.0 9.9 - - + -
114L ASP* 4.4 1.4 + - - +
116L VAL* 3.4 45.1 - - + +
117L GLY 4.3 1.1 - - - -
118L SER* 3.3 24.2 - - - +
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Residues in contact with ASP 51 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48K GLY* 3.6 12.6 + - - +
50K ALA* 1.3 76.5 - - - +
52K CYS* 1.3 62.0 + - - +
55K TRP* 3.2 31.0 + - - +
95K LEU* 3.3 12.1 - - - +
96K SER* 2.8 37.7 + - - +
97K MET* 3.8 14.1 - - - +
88L TYR* 2.9 18.3 + - - +
91L ARG* 2.7 39.5 + - - -
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Residues in contact with CYS 52 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45K MET* 3.6 25.4 - - + -
46K ALA 3.2 41.7 - - - -
48K GLY 3.0 21.8 + - - +
49K ALA* 3.5 4.5 - - - +
51K ASP* 1.3 74.3 - - - +
53K GLN* 1.3 67.4 + - - +
54K PHE 3.2 0.2 + - - -
55K TRP* 4.4 0.2 - - - +
56K GLU* 2.9 33.7 + - - +
97K MET* 3.5 22.4 - - - -
98K GLY 4.5 1.6 - - - -
99K THR* 4.7 0.4 - - - -
302K 3SD 4.6 1.1 - - + -
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Residues in contact with GLN 53 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32K LYS 5.6 1.0 + - - -
45K MET* 3.8 19.6 - - + +
49K ALA 2.7 20.2 + - - +
50K ALA* 3.8 2.5 - - - +
52K CYS* 1.3 70.8 - - - +
54K PHE* 1.3 56.0 + - - +
56K GLU* 3.9 0.5 - - - +
57K THR* 2.8 43.2 + - - +
302K 3SD 4.0 18.3 - - + +
84L GLN* 2.8 30.2 + - - +
118L SER* 3.3 5.0 + - - +
119L TYR* 2.8 47.2 + - + +
120L GLU* 3.4 11.5 + - - -
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Residues in contact with PHE 54 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D LEU* 5.4 3.5 - - + +
50K ALA 2.8 24.8 + - - +
51K ASP 4.2 1.3 - - - +
53K GLN* 1.3 75.1 - - - +
55K TRP* 1.3 89.6 + + - +
57K THR* 3.8 3.2 - - - -
58K TRP* 3.1 28.3 + + + +
84L GLN* 4.2 23.6 - - + +
85L HIS* 3.5 41.1 - + - -
88L TYR* 3.6 56.8 - + + -
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Residues in contact with TRP 55 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51K ASP* 3.2 26.9 + - - +
54K PHE* 1.3 102.3 - + - +
56K GLU* 1.3 63.3 + - - +
58K TRP* 3.6 41.7 - + + +
59K LEU* 2.9 25.1 + - - +
83K LEU* 4.1 9.9 - - + +
86K LEU* 3.5 35.2 - - + -
90K TYR* 3.8 33.4 - + - -
95K LEU* 3.9 15.7 - - + +
97K MET* 3.9 19.5 - - + -
88L TYR* 2.9 31.8 + + - -
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Residues in contact with GLU 56 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35K ILE* 3.2 38.2 - - + +
37K ILE* 4.6 4.2 - - + +
43K GLY* 3.2 19.2 - - - -
44K THR 2.7 22.8 - - - +
45K MET* 3.4 18.8 - - + +
52K CYS* 2.9 21.4 + - - +
53K GLN 4.2 0.9 - - - +
55K TRP* 1.3 78.9 - - - +
57K THR* 1.3 63.3 + - - +
59K LEU* 3.3 9.1 + - + +
60K GLY* 3.2 16.8 + - - -
83K LEU* 4.3 17.0 - - + -
97K MET* 5.0 2.0 - - + -
99K THR* 2.9 20.2 + - - +
101K ILE* 4.2 3.9 - - + +
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Residues in contact with THR 57 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D LEU* 3.5 19.5 - - + -
35K ILE* 4.3 19.2 - - + +
45K MET* 5.9 0.3 - - - +
53K GLN* 2.8 29.3 + - - +
54K PHE* 3.8 5.6 - - - -
56K GLU* 1.3 75.9 - - - +
58K TRP* 1.3 62.1 + - - +
60K GLY* 3.0 13.8 + - - -
61K SER* 3.3 11.6 + - - -
81L ARG* 3.6 31.3 + - - +
84L GLN* 4.9 5.4 + - - +
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Residues in contact with TRP 58 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D LEU* 3.9 30.6 - - + +
54K PHE* 3.1 24.0 + + + +
55K TRP* 3.6 39.0 - + + +
57K THR* 1.3 73.6 - - - +
59K LEU* 1.3 82.2 + - + +
61K SER* 3.0 13.7 + - - -
62K GLN* 3.0 40.3 + - + +
82K ILE* 3.6 35.2 - - + -
83K LEU* 4.7 4.3 - - + -
86K LEU* 3.8 37.2 - - + -
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Residues in contact with LEU 59 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37K ILE* 3.9 24.5 - - + -
55K TRP 2.9 19.2 + - - +
56K GLU* 3.5 9.9 - - + +
57K THR 3.2 0.4 - - - -
58K TRP* 1.3 82.4 - - + +
60K GLY* 1.3 56.5 + - - +
62K GLN* 3.2 4.3 + - - +
63K CYS* 2.8 37.8 + - - -
79K ALA* 3.1 34.3 - - + +
82K ILE* 3.7 22.9 - - + -
83K LEU* 3.9 18.6 - - + +
101K ILE* 4.0 22.0 - - + -
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Residues in contact with GLY 60 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35K ILE* 6.4 0.4 - - - -
37K ILE* 3.9 29.3 - - - +
56K GLU 3.2 6.5 + - - -
57K THR 3.0 10.0 + - - -
59K LEU* 1.3 77.2 - - - +
61K SER* 1.3 57.5 + - - +
63K CYS* 3.3 2.6 + - - +
64K ARG* 3.0 28.6 + - - +
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Residues in contact with SER 61 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D VAL* 3.5 25.7 + - - +
100D ASN* 5.3 3.1 + - - -
101D LEU* 3.5 41.9 + - - +
57K THR 3.3 3.3 + - - -
58K TRP 3.0 10.2 + - - -
60K GLY* 1.3 74.9 - - - +
62K GLN* 1.3 69.9 + - - +
64K ARG* 3.3 4.2 + - - +
65K LEU* 3.0 27.9 + - - +
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Residues in contact with GLN 62 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D LEU* 6.1 0.2 - - - +
58K TRP* 3.0 64.9 + - + +
59K LEU 3.2 7.2 + - - +
61K SER* 1.3 79.4 - - - +
63K CYS* 1.3 61.4 + - - +
65K LEU* 3.5 22.6 + - - +
66K HIS* 3.2 19.9 + - - +
69K ARG* 5.3 6.8 + - - -
82K ILE* 4.1 25.3 - - + +
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Residues in contact with CYS 63 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37K ILE* 4.0 23.8 - - + -
38K ASN* 5.2 3.6 - - + +
41K LEU* 4.2 0.2 - - - -
59K LEU* 2.8 28.3 + - - +
60K GLY 3.6 5.2 - - - +
61K SER 3.2 0.2 - - - -
62K GLN* 1.3 75.5 - - - +
64K ARG* 1.3 64.8 + - - +
66K HIS* 3.1 16.3 + - - +
67K GLU* 3.3 14.9 + - - +
74K ILE* 3.5 39.8 - - + +
79K ALA* 3.7 20.4 - - - -
82K ILE* 5.2 0.7 - - - -
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Residues in contact with ARG 64 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D GLU* 3.1 26.9 + - - -
71D ASP* 3.3 24.6 + - - +
72D ARG* 3.5 13.2 - - - +
97D VAL* 4.0 18.8 - - + -
60K GLY 3.0 17.6 + - - +
61K SER* 3.3 8.0 + - - +
63K CYS* 1.3 75.7 - - - +
65K LEU* 1.3 61.4 + - - +
67K GLU* 2.8 57.9 + - - +
68K LEU* 3.2 33.8 + - + +
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Residues in contact with LEU 65 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D ARG* 4.1 19.1 - - + +
94D THR* 4.5 12.8 - - + +
97D VAL* 3.3 39.9 - - + -
98D THR* 6.1 0.2 - - - +
61K SER 3.0 18.6 + - - +
62K GLN* 3.6 29.2 - - - +
64K ARG* 1.3 74.3 - - - +
66K HIS* 1.3 64.8 + - - +
68K LEU* 3.5 11.9 + - + +
69K ARG* 3.1 58.9 + - - +
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Residues in contact with HIS 66 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C LEU* 3.7 28.5 - - + +
62K GLN 3.2 12.5 + - - +
63K CYS 3.1 11.2 + - - +
65K LEU* 1.3 75.7 - - - +
67K GLU* 1.3 53.9 + - - +
69K ARG* 3.2 8.3 + - - +
70K GLU* 2.9 55.4 + - + +
72K GLU* 3.5 21.5 + - - +
73K ARG 4.3 2.8 + - - -
74K ILE* 3.6 42.5 - - + +
75K SER 5.1 0.8 + - - -
78K ALA* 5.5 0.2 - - + -
82K ILE* 5.8 1.1 - - + +
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Residues in contact with GLU 67 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38K ASN* 4.3 17.7 + - - +
39K PRO* 5.8 0.5 - - - +
63K CYS 3.3 9.5 + - - +
64K ARG* 2.8 41.8 + - - +
66K HIS* 1.3 75.8 - - - +
68K LEU* 1.3 60.4 + - - +
71K LYS* 2.9 29.3 + - - +
72K GLU 3.4 22.1 + - - +
73K ARG* 3.9 28.1 - - + +
74K ILE 4.9 0.8 + - - +
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Residues in contact with LEU 68 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D GLU* 3.8 34.3 - - + +
70D ILE 3.4 29.2 - - - +
71D ASP* 4.8 0.9 - - - +
93D ARG* 3.1 42.6 + - + +
97D VAL* 4.3 11.4 - - + -
64K ARG* 3.2 42.4 + - - +
65K LEU* 3.9 21.5 - - + +
66K HIS 3.4 0.2 - - - -
67K GLU* 1.3 79.1 - - - +
69K ARG* 1.3 62.3 + - - +
71K LYS* 4.3 10.6 - - - +
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Residues in contact with ARG 69 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C ARG* 4.0 20.9 + - - +
90D GLU* 2.6 49.8 + - - +
93D ARG* 3.9 17.3 + - - +
94D THR* 4.4 1.2 + - - -
62K GLN* 5.3 6.7 + - - -
65K LEU* 3.1 51.0 + - - +
66K HIS* 3.2 6.9 + - - +
68K LEU* 1.3 79.6 - - - +
70K GLU* 1.3 78.9 + - + +
71K LYS* 4.9 5.1 - - - +
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Residues in contact with GLU 70 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C HIS* 5.7 1.5 + - - -
108C THR* 5.1 1.9 + - - -
110C GLU* 4.8 0.7 - - - +
111C TYR* 3.5 24.6 - - - +
114C ARG* 3.2 39.7 + - - +
66K HIS* 2.9 46.2 + - + +
69K ARG* 1.3 89.6 - - + +
71K LYS* 1.3 70.9 + - - +
72K GLU* 3.3 11.3 + - + +
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Residues in contact with LYS 71 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D GLU* 3.1 41.4 + - - +
67D ILE 5.4 0.6 + - - -
68D VAL* 6.2 0.4 - - - +
93D ARG* 6.0 2.0 - - - +
223D ILE* 5.0 15.6 - - - +
67K GLU 2.9 17.4 + - - +
68K LEU* 4.4 11.4 - - - +
69K ARG 5.0 3.8 - - - +
70K GLU* 1.3 80.6 - - - +
72K GLU* 1.3 58.7 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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