Contacts of the helix formed by residues 47 - 65 (chain I) in PDB entry 2DYY
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 ILE 47 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46I ASP* 1.3 105.2 - - - +
48I LYS* 1.3 68.9 + - + +
49I ASP 3.1 1.6 - - - -
50I GLN* 3.2 6.6 + - - +
51I THR* 2.8 38.7 + - - +
79I LEU* 5.0 7.2 - - + -
116I LEU* 3.4 44.9 - - + +
117I ILE* 4.6 10.1 - - + -
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Residues in contact with LYS 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46I ASP* 4.2 4.0 + - + +
47I ILE* 1.3 88.1 - - + +
49I ASP* 1.3 56.5 + - - +
51I THR* 3.9 6.9 - - - -
52I ARG* 2.9 40.1 + - - +
91I VAL* 4.3 20.1 - - + +
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Residues in contact with ASP 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43I VAL* 3.6 22.3 - - + +
44I LYS 4.4 2.0 - - - +
45I GLY* 3.6 33.0 - - - -
46I ASP* 4.1 2.9 + - - +
47I ILE 3.1 0.8 - - - +
48I LYS* 1.3 78.5 - - - +
50I GLN* 1.3 58.8 + - - +
52I ARG* 3.6 7.9 - - - +
53I GLN* 2.9 28.1 + - - +
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Residues in contact with GLN 50 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I PRO* 3.4 34.9 - - + +
42I ILE* 3.7 13.7 - - + +
43I VAL* 4.3 1.3 - - + -
44I LYS 3.6 24.4 - - - +
45I GLY 4.7 0.5 - - - +
46I ASP 4.3 9.4 - - - +
47I ILE* 3.2 7.7 + - + +
49I ASP* 1.3 76.2 - - - +
51I THR* 1.3 60.7 + - - +
53I GLN* 3.6 0.7 - - - +
54I VAL* 2.7 36.4 + - - +
115I VAL* 4.8 2.5 - - - -
116I LEU* 2.9 51.3 + - - +
117I ILE* 3.8 8.8 - - + +
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Residues in contact with THR 51 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I ILE* 2.8 27.5 + - - +
48I LYS* 3.9 6.4 - - - -
50I GLN* 1.3 76.7 - - - +
52I ARG* 1.3 64.9 + - - +
54I VAL* 3.1 4.9 + - - +
55I LEU* 2.9 41.5 + - + +
91I VAL* 3.5 22.7 - - + -
92I TYR* 3.7 37.0 + - + -
117I ILE* 4.0 17.0 - - + +
119I ILE* 5.1 0.7 - - + -
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Residues in contact with ARG 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I LYS* 2.9 26.1 + - - +
49I ASP* 3.6 12.5 - - - +
51I THR* 1.3 77.3 - - - +
53I GLN* 1.3 61.1 + - - +
55I LEU* 3.5 1.4 + - - +
56I GLU* 3.2 30.8 + - + +
91I VAL* 4.0 29.3 - - - +
94I GLU* 2.8 40.1 + - - -
95I TYR* 3.5 20.2 + - - +
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Residues in contact with GLN 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I PRO* 3.8 15.0 - - + -
35I ILE 3.9 6.9 + - - +
36I ASP* 4.6 9.0 + - - +
37I PRO* 3.8 17.8 - - - +
43I VAL* 3.7 30.4 - - + +
49I ASP 2.9 20.0 + - - +
50I GLN 3.6 3.6 - - - +
52I ARG* 1.3 75.0 - - - +
54I VAL* 1.3 56.8 + - - +
56I GLU* 3.1 14.0 + - - +
57I ASN* 2.8 59.1 + - - +
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Residues in contact with VAL 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32I GLN* 4.0 15.5 - - + +
33I ILE* 3.9 2.5 - - - -
34I PRO* 3.5 29.8 - - + -
50I GLN 2.7 30.8 + - - +
51I THR* 3.5 5.4 - - - +
53I GLN* 1.3 71.2 - - - +
55I LEU* 1.3 65.4 + - - +
57I ASN* 2.9 21.5 + - - +
58I ILE* 2.9 20.8 + - + +
117I ILE* 3.7 17.0 - - + +
119I ILE* 3.5 39.3 - - + +
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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
----------------------------------------------------------
51I THR* 2.9 40.4 + - + +
52I ARG 3.7 0.2 - - - +
54I VAL* 1.3 75.6 - - - +
56I GLU* 1.3 57.3 + - - +
58I ILE* 3.1 13.1 + - + +
59I LYS* 2.9 26.9 + - - +
69I LEU* 5.5 1.4 - - - +
91I VAL* 4.0 10.5 - - + +
92I TYR* 4.1 8.5 - - + -
95I TYR* 3.4 50.3 - - + -
96I PHE* 3.5 37.0 - - + -
119I ILE* 4.1 17.3 - - + -
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Residues in contact with GLU 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I ASN 5.7 0.2 - - - -
52I ARG* 3.2 14.7 + - + +
53I GLN* 3.1 18.6 + - - +
55I LEU* 1.3 72.9 - - - +
57I ASN* 1.3 66.1 + - - +
59I LYS* 2.9 46.3 + - - +
60I ALA* 3.0 15.1 + - - +
95I TYR* 2.6 39.6 + - - +
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Residues in contact with ASN 57 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I ASN 4.3 4.5 - - - +
10I ALA* 3.6 8.9 - - - +
11I PRO* 3.0 27.7 - - + +
32I GLN* 4.2 19.3 - - + +
33I ILE 3.4 18.5 + - - -
35I ILE 3.2 8.0 + - - +
37I PRO* 4.0 5.7 - - - +
53I GLN* 2.8 52.2 + - - +
54I VAL* 2.9 7.5 + - - +
56I GLU* 1.3 75.7 - - - +
58I ILE* 1.3 58.7 + - - +
60I ALA* 3.7 0.7 + - - +
61I ILE* 3.0 30.8 + - - +
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Residues in contact with ILE 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29I ILE* 3.8 25.2 - - + +
32I GLN* 4.0 15.7 - - + -
54I VAL* 2.9 19.7 + - + +
55I LEU* 3.3 18.6 - - + +
56I GLU 3.0 0.2 - - - -
57I ASN* 1.3 75.6 - - - +
59I LYS* 1.3 66.3 + - - +
61I ILE* 3.2 11.4 + - - +
62I LEU* 2.9 30.8 + - + +
69I LEU* 5.5 2.5 - - + -
72I VAL* 6.0 0.9 - - + -
96I PHE* 5.4 6.3 - - + -
119I ILE* 3.4 41.3 - - + +
121I ALA* 4.5 12.8 - - + +
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Residues in contact with LYS 59 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I LEU 2.9 12.2 + - - +
56I GLU* 2.9 45.9 + - - +
58I ILE* 1.3 75.6 - - - +
60I ALA* 1.3 61.0 + - - +
62I LEU* 3.1 14.2 + - + +
63I GLU* 2.9 55.0 + - + +
69I LEU* 4.4 25.1 - - + +
95I TYR* 4.3 7.9 - - + -
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Residues in contact with ALA 60 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I THR* 4.5 5.2 + - + +
9I ASN* 3.4 46.7 - - + +
10I ALA* 4.5 1.1 - - + -
56I GLU 3.0 13.2 + - - +
57I ASN 3.8 4.5 - - - +
58I ILE 3.3 0.2 - - - -
59I LYS* 1.3 77.7 - - - +
61I ILE* 1.3 61.9 + - - +
63I GLU* 3.5 15.7 + - - +
64I ALA* 3.1 22.3 + - - +
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Residues in contact with ILE 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I ILE* 4.1 10.8 - - + +
7I THR* 4.4 7.0 - - + -
10I ALA* 3.6 17.3 - - + -
19I GLN* 4.0 17.9 - - + +
20I ALA* 3.6 30.3 - - + -
27I LEU* 4.6 1.7 - - + +
29I ILE* 4.0 15.5 - - + -
32I GLN* 3.4 37.9 - - + +
57I ASN 3.0 19.1 - - - +
58I ILE* 3.2 6.0 + - - +
60I ALA* 1.3 72.4 - - - +
62I LEU* 1.3 66.9 + - - +
64I ALA* 3.4 17.2 + - - +
65I ALA* 3.5 6.8 + - - +
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Residues in contact with LEU 62 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I LEU* 4.2 9.6 - - + -
29I ILE* 3.9 19.5 - - + +
58I ILE* 2.9 26.4 + - + +
59I LYS* 3.2 11.9 - - + +
61I ILE* 1.3 75.3 - - - +
63I GLU* 1.3 64.7 + - + +
65I ALA* 3.0 10.2 + - - +
67I TYR* 3.0 44.2 + - + +
68I SER 3.4 21.3 - - - +
69I LEU* 3.3 34.5 - - + -
72I VAL* 4.2 14.8 - - + -
123I ALA* 4.4 7.9 - - + -
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Residues in contact with GLU 63 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I ASN* 5.3 4.7 + - - -
59I LYS* 2.9 41.5 + - + +
60I ALA* 3.5 18.6 - - - +
62I LEU* 1.3 74.0 - - + +
64I ALA* 1.3 56.1 + - - +
66I GLY* 2.6 27.3 + - - -
67I TYR 3.4 13.0 + - - +
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Residues in contact with ALA 64 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I ILE* 3.6 21.0 - - + +
6I PHE 4.0 14.1 - - - +
7I THR* 4.1 11.2 - - - +
60I ALA 3.1 11.4 + - - +
61I ILE* 3.5 11.7 - - - +
62I LEU 3.3 0.2 - - - -
63I GLU* 1.3 77.4 - - - +
65I ALA* 1.3 57.1 + - - +
66I GLY 3.8 0.3 + - - -
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Residues in contact with ALA 65 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I ILE* 3.7 26.5 - - + -
22I LYS* 5.1 5.3 + - + -
27I LEU* 4.0 13.5 - - + -
61I ILE 3.5 2.9 + - - +
62I LEU 3.0 5.4 + - - +
63I GLU 2.8 2.6 + - - -
64I ALA* 1.3 76.6 - - - +
66I GLY* 1.3 59.8 + - - +
67I TYR* 3.0 34.7 - - + -
125I LYS* 4.9 2.4 - - - +
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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