Contacts of the helix formed by residues 48 - 71 (chain I) 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 LEU 48 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-6I PRO* 3.6 35.5 + - + +
-3I ILE* 4.2 16.6 - - + -
-2I ASN* 3.5 15.0 - - - +
47I GLY* 1.3 69.1 - - - -
49I ALA* 1.3 58.8 + - - +
50I THR* 3.2 24.5 - - + -
51I ASP* 3.0 29.7 + - + +
52I VAL* 3.0 13.0 + - - +
96I PHE* 2.9 31.9 + - + +
97I VAL* 4.4 0.2 - - - +
90J ARG* 5.1 3.6 - - + +
116J LEU* 4.0 27.1 - - + -
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Residues in contact with ALA 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-2I ASN* 2.7 21.7 + - + +
20I LEU* 3.5 28.7 - - + -
31I PHE* 3.9 14.2 - - + -
47I GLY 3.2 2.9 + - - +
48I LEU* 1.3 68.7 - - - +
50I THR* 1.3 64.0 + - - +
52I VAL* 3.3 12.3 + - - +
53I THR* 2.9 30.0 + - - -
118J THR* 3.7 13.9 - - + -
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Residues in contact with THR 50 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I LEU* 3.7 24.9 - - + +
49I ALA* 1.3 77.9 - - - +
51I ASP* 1.3 71.6 + - - +
53I THR* 3.4 1.0 + - - -
54I THR* 2.9 29.5 + - - -
84J ARG* 3.3 9.9 + - - +
88J ALA* 4.1 6.6 - - - +
90J ILE* 5.2 5.8 - - + +
116J LEU* 2.5 38.3 + - + +
117J GLY* 3.2 24.3 + - - -
118J THR* 4.1 7.0 + - - +
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Residues in contact with ASP 51 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I LEU* 3.0 16.4 + - + +
50I THR* 1.3 88.5 + - - +
52I VAL* 1.3 60.4 + - - +
54I THR* 3.8 6.8 + - - -
55I LEU* 3.0 34.3 + - - +
95I TYR* 3.2 15.4 - - + -
96I PHE* 2.9 27.8 + - - +
97I VAL* 3.6 18.4 - - + -
90J ARG* 2.6 36.3 - - - -
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Residues in contact with VAL 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31I PHE* 4.1 22.9 - - + -
33I LYS* 5.0 2.9 - - + -
35I PHE* 4.1 22.9 - - + -
45I ILE* 3.6 50.4 - - + +
46I THR 4.0 13.7 - - - +
47I GLY 4.1 2.2 - - - +
48I LEU 3.0 17.6 + - - +
49I ALA* 3.4 13.5 - - - +
51I ASP* 1.3 78.2 - - - +
53I THR* 1.3 64.4 + - - +
56I ASN* 3.1 20.4 + - - +
97I VAL* 4.5 1.1 - - + -
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Residues in contact with THR 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31I PHE* 4.1 15.4 - - - -
35I PHE* 5.5 2.7 - - - -
49I ALA 2.9 14.6 + - - -
50I THR* 3.6 7.5 - - - -
52I VAL* 1.3 77.8 - - - +
54I THR* 1.3 63.4 + - - +
56I ASN* 3.1 11.2 + - + +
57I GLU* 3.1 33.6 + - + +
84J ARG* 3.3 36.9 - - - +
117J GLY 5.1 0.7 + - - -
119J LYS* 5.1 7.8 + - + -
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Residues in contact with THR 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I THR* 2.9 18.1 + - - -
51I ASP* 4.0 8.8 + - - -
53I THR* 1.3 75.6 - - - +
55I LEU* 1.3 59.0 + - - +
57I GLU* 3.1 7.8 + - - +
58I MET* 2.8 32.4 + - + +
95I TYR* 4.3 27.6 - - + +
84J ARG* 3.0 25.8 + - - +
88J ALA* 4.2 11.3 - - - +
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Residues in contact with LEU 55 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45I ILE* 4.0 16.4 - - + -
51I ASP 3.0 21.4 + - - +
54I THR* 1.3 77.1 - - - +
56I ASN* 1.3 58.2 + - - +
58I MET* 3.8 20.8 - - + +
59I PHE* 2.9 55.8 + - + -
86I SER* 6.0 0.9 - - - +
87I LEU* 4.1 10.3 - - + -
95I TYR* 3.6 40.6 - - + -
97I VAL* 3.5 35.4 - - + -
99I PRO* 5.1 2.7 - - + -
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Residues in contact with ASN 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I PHE* 3.2 49.6 - - + +
38I TYR* 2.9 27.5 + - - -
45I ILE* 4.1 3.4 - - - +
52I VAL 3.1 13.3 + - - +
53I THR* 3.4 11.3 + - - +
55I LEU* 1.3 77.5 - - - +
57I GLU* 1.3 63.5 + - - +
59I PHE 3.3 0.2 + - - -
60I ARG* 2.9 37.6 + - - +
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Residues in contact with GLU 57 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LYS* 4.2 33.8 - - + +
104B ASN* 3.1 22.6 + - - +
53I THR* 3.1 25.1 + - - +
54I THR* 3.5 6.1 - - - +
56I ASN* 1.3 82.0 - - - +
58I MET* 1.3 62.9 + - - +
60I ARG* 3.4 29.9 + - - +
61I TYR* 3.1 23.1 + - - +
81J SER* 5.4 1.4 + - - -
84J ARG* 2.9 33.2 + - - -
85J GLN* 5.4 2.9 + - - +
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Residues in contact with MET 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LYS* 4.9 8.2 - - + +
54I THR* 2.8 21.4 + - + +
55I LEU* 3.8 21.5 - - + +
57I GLU* 1.3 76.8 - - - +
59I PHE* 1.3 68.7 + - + +
61I TYR* 3.2 8.5 - - + +
62I LYS* 2.9 58.7 + - + +
86I SER* 4.6 8.1 - - - +
95I TYR* 3.4 33.7 - - + +
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Residues in contact with PHE 59 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I TYR* 3.7 17.5 - - + +
43I LEU* 3.6 25.8 - - + -
45I ILE* 5.4 0.2 - - + -
55I LEU* 2.9 53.1 + - + +
58I MET* 1.3 81.7 - - + +
60I ARG* 1.3 55.1 + - - +
62I LYS* 4.3 4.0 - - + +
63I THR* 2.5 40.0 + - - +
79I PHE* 3.9 20.4 - + + -
82I LEU* 4.3 10.5 - - + -
83I VAL* 3.8 38.6 - - + -
86I SER* 3.8 29.2 - - - -
87I LEU* 5.5 2.5 - - + -
99I PRO* 6.0 1.3 - - + -
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Residues in contact with ARG 60 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B GLN* 5.8 0.2 - - - +
100B LEU* 3.5 52.2 + - - +
101B LYS* 4.3 2.6 - - - +
104B ASN* 3.4 23.0 + - - +
38I TYR* 3.6 16.2 - - + -
56I ASN* 2.9 23.7 + - - +
57I GLU* 3.6 32.5 + - - +
59I PHE* 1.3 75.9 - - - +
61I TYR* 1.3 56.5 + - - +
63I THR* 3.1 5.9 + - - +
64I ASN* 2.8 50.8 + - - +
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Residues in contact with TYR 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ILE* 3.4 21.5 - - + +
97B GLN* 3.5 45.6 - - + +
98B ASN* 3.1 30.5 + - - -
101B LYS* 4.2 21.5 - - + -
57I GLU 3.1 13.5 + - - +
58I MET* 3.2 12.6 - - + +
60I ARG* 1.3 77.2 - - - +
62I LYS* 1.3 76.5 + - + +
64I ASN* 3.7 2.1 - - - +
65I LEU* 3.2 43.7 + - + +
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Residues in contact with LYS 62 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TYR* 5.0 3.8 + - - +
58I MET* 2.9 46.3 + - + +
59I PHE* 4.3 4.9 - - + +
60I ARG 3.3 0.2 - - - -
61I TYR* 1.3 86.8 - - + +
63I THR* 1.3 58.4 + - - +
65I LEU* 3.7 5.6 + - - +
66I TYR* 3.0 26.2 + - - +
82I LEU* 4.0 37.0 - - + +
86I SER* 3.4 25.1 + - - +
89I GLU* 4.6 11.9 + - - -
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Residues in contact with THR 63 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I TYR* 3.7 20.9 - - + +
59I PHE 2.5 25.5 + - - +
60I ARG* 3.1 10.7 + - - +
62I LYS* 1.3 76.6 - - - +
64I ASN* 1.3 62.2 + - - +
66I TYR* 3.5 8.0 - - - +
67I LYS* 3.0 29.6 + - - +
74I ILE* 3.8 29.0 + - + +
79I PHE* 3.8 28.0 - - + -
82I LEU* 4.6 2.7 - - + -
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Residues in contact with ASN 64 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ASP* 5.5 2.8 - - - +
97B GLN* 2.9 41.7 + - - +
100B LEU* 3.8 15.8 - - - +
60I ARG* 2.8 30.9 + - - +
61I TYR 3.7 0.4 - - - +
63I THR* 1.3 77.0 + - - +
65I LEU* 1.3 62.9 + - - +
67I LYS* 3.2 10.2 + - - +
68I LEU* 3.1 27.8 + - + +
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Residues in contact with LEU 65 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ARG* 3.8 42.0 - - + +
94B ILE* 4.2 17.5 - - + +
97B GLN* 3.8 10.5 - - + -
61I TYR* 3.2 38.8 + - + +
62I LYS* 4.0 5.2 - - - +
64I ASN* 1.3 74.2 - - - +
66I TYR* 1.3 67.3 + - - +
68I LEU* 3.1 9.8 + - + +
69I LYS* 3.0 44.1 + - - +
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Residues in contact with TYR 66 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A TYR* 4.0 6.3 + - - -
103A TYR* 3.5 41.7 + + + +
105A GLU* 4.9 1.0 + - - -
62I LYS 3.0 19.6 + - - +
63I THR* 3.5 8.7 - - - +
64I ASN 3.3 0.4 - - - -
65I LEU* 1.3 74.9 - - - +
67I LYS* 1.3 59.0 + - - +
69I LYS* 3.8 4.8 - - - +
70I GLU* 2.9 67.6 + - + +
72I ARG* 3.3 39.4 + - - -
73I ALA 4.4 1.3 - - - -
74I ILE* 3.5 47.2 - - + +
78I THR* 3.8 15.9 + - + +
82I LEU* 6.2 0.2 - - + -
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Residues in contact with LYS 67 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ASP* 5.6 7.0 + - - +
223H ASP* 3.1 35.2 + - - -
63I THR 3.0 14.2 + - - +
64I ASN* 3.5 12.1 - - - +
66I TYR* 1.3 76.4 - - + +
68I LEU* 1.3 59.3 + - + +
71I GLU* 2.8 30.9 + - - +
72I ARG* 3.5 26.2 - - - +
73I ALA* 4.3 20.6 - - + +
74I ILE 5.8 0.2 - - - +
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Residues in contact with LEU 68 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LYS* 3.9 42.1 - - + +
70B LEU 3.7 22.9 - - - +
71B ASN* 4.3 11.9 - - - +
72B ASP* 5.3 3.4 - - - +
93B ARG* 3.9 41.6 + - + +
97B GLN* 5.2 6.5 - - - +
64I ASN* 3.1 17.3 + - + +
65I LEU* 3.1 13.5 + - + +
67I LYS* 1.3 82.4 - - + +
69I LYS* 1.3 62.1 + - + +
71I GLU* 3.6 14.0 - - - +
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Residues in contact with LYS 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LYS* 4.2 8.3 + - - +
111A LEU* 3.6 39.5 - - + +
115A GLU* 4.9 10.1 + - - -
90B ASN* 4.2 23.6 + - - +
93B ARG* 4.6 15.3 - - - +
65I LEU* 3.0 35.7 + - - +
66I TYR* 3.9 4.3 - - - +
68I LEU* 1.3 78.5 - - + +
70I GLU* 1.3 63.1 + - + +
71I GLU* 3.8 4.2 + - - +
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Residues in contact with GLU 70 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A TYR* 2.5 42.0 + - - -
103A TYR* 4.8 0.2 - - - -
108A PRO* 3.6 15.4 - - - +
110A LYS* 2.9 25.3 + - - +
111A LEU* 3.3 17.0 - - + +
145A ASN* 4.9 1.9 + - - +
66I TYR* 2.9 53.3 + - + +
69I LYS* 1.3 77.2 - - + +
71I GLU* 1.3 67.1 + - - +
72I ARG* 3.4 33.0 + - + +
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Residues in contact with GLU 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LYS* 3.4 19.8 + - - +
64B THR* 4.4 19.8 + - - +
223B ILE* 6.0 1.7 - - - +
67I LYS* 2.8 17.3 + - - +
68I LEU 3.6 15.9 - - - +
69I LYS 4.2 4.2 - - - +
70I GLU* 1.3 81.2 - - - +
72I ARG* 1.3 59.8 + - - +
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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