Contacts of the helix formed by residues 47 - 65 (chain I) in PDB entry 2EHO
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 LYS 47 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I GLN* 5.8 3.2 + - - +
33I ALA* 4.2 27.9 - - + +
36I ASN* 4.6 12.5 + - - -
44I LEU* 5.1 15.4 - - - +
45I GLU* 4.4 25.6 - - + +
46I SER* 1.3 77.8 - - - +
48I PRO* 1.3 72.3 - - - +
49I GLU* 3.3 3.7 + - - +
50I ILE* 3.7 28.9 + - + +
51I VAL* 3.5 13.9 + - - +
92I TYR* 4.2 9.2 + - + +
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Residues in contact with PRO 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46I SER* 3.3 20.8 - - - +
47I LYS* 1.3 89.1 - - - +
49I GLU* 1.3 76.0 + - + +
51I VAL* 3.2 12.3 + - + +
52I GLU* 3.0 36.4 + - - +
123I SER* 5.3 7.6 - - - -
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Residues in contact with GLU 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I LYS* 5.0 0.9 - - - -
48I PRO* 1.3 81.5 - - + +
50I ILE* 1.3 78.9 + - + +
51I VAL 2.7 2.7 + - - -
52I GLU* 2.8 17.8 + - - +
53I CYS* 2.8 23.1 + - - +
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Residues in contact with ILE 50 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I LEU* 4.3 13.9 - - + -
29I ARG* 4.1 40.2 - - + +
30I LEU* 3.6 44.0 - - + +
33I ALA* 5.7 4.7 - - + -
47I LYS* 3.7 30.9 + - + +
48I PRO 3.5 0.2 - - - -
49I GLU* 1.3 84.7 - - + +
51I VAL* 1.3 66.2 + - + +
53I CYS* 3.9 1.4 - - - +
54I VAL* 3.0 24.3 + - + +
92I TYR* 5.8 2.2 - - + -
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Residues in contact with VAL 51 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46I SER 5.0 2.0 - - - +
47I LYS 3.5 16.6 - - - +
48I PRO* 3.2 11.4 - - + +
49I GLU 2.7 4.0 + - - -
50I ILE* 1.3 79.0 - - + +
52I GLU* 1.3 65.5 + - + +
53I CYS 3.1 0.3 + - - -
54I VAL* 3.1 10.0 + - - +
55I MSE 3.1 27.8 + - + +
89I LEU* 4.3 22.4 - - + +
92I TYR* 4.4 21.1 - - + -
93I LEU* 4.4 20.4 - - + -
128J LEU* 5.0 11.9 - - + +
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Residues in contact with GLU 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I PRO* 3.0 23.5 + - - +
49I GLU* 2.8 10.2 + - - +
51I VAL* 1.3 79.2 - - + +
53I CYS* 1.3 56.5 + - - +
55I MSE 3.7 8.6 - - + +
56I GLU* 3.1 26.9 + - - +
125I GLU* 5.0 6.8 - - - +
128J LEU 4.7 14.4 - - - +
129J GLY* 5.9 2.0 - - - -
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Residues in contact with CYS 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I LEU* 3.4 28.0 - - + +
49I GLU* 2.8 25.2 + - - +
50I ILE 3.9 2.5 - - - +
52I GLU* 1.3 75.9 - - - +
54I VAL* 1.3 67.6 + - - +
55I MSE 3.2 0.2 - - - -
56I GLU* 3.3 17.9 + - - +
57I GLN* 2.9 26.3 + - - +
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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
----------------------------------------------------------
26I LEU* 4.1 21.8 - - + +
27I ILE* 5.2 5.4 - - + -
30I LEU* 3.7 34.5 - - + -
50I ILE 3.0 19.4 + - - +
51I VAL* 3.6 4.3 - - - +
53I CYS* 1.3 75.6 - - - +
55I MSE 1.3 52.6 + - - +
57I GLN* 3.2 4.5 + - - +
58I LEU* 2.7 58.5 + - + +
85I ILE* 3.7 15.7 - - + -
89I LEU* 4.0 17.0 - - + -
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Residues in contact with MSE 55 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51I VAL* 3.1 23.7 + - + +
52I GLU* 3.7 10.5 - - + +
54I VAL* 1.3 73.7 - - - +
56I GLU* 1.3 55.6 + - - +
58I LEU* 3.0 12.7 + - + +
59I GLU* 2.7 37.1 + - - +
86I ARG* 6.4 0.2 - - + -
89I LEU* 4.0 11.4 - - + -
93I LEU* 6.3 0.2 - - - -
128J LEU* 3.8 29.2 - - - +
129J GLY* 4.7 6.3 - - - -
131J ASP* 5.6 6.5 - - - +
133J GLY 5.1 3.6 - - - +
134J LEU* 3.3 48.0 - - + +
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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
----------------------------------------------------------
52I GLU 3.1 15.7 + - - +
53I CYS* 3.4 19.7 - - - +
55I MSE 1.3 78.0 - - - +
57I GLN* 1.3 55.7 + - - +
59I GLU* 3.0 14.3 - - - +
60I HIS* 2.8 64.5 + - + +
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Residues in contact with GLN 57 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I PRO* 3.8 37.0 - - + +
26I LEU* 4.6 12.4 - - + +
27I ILE* 5.9 4.5 - - + -
53I CYS* 2.9 17.2 + - - +
54I VAL* 3.4 8.1 - - - +
56I GLU* 1.3 77.1 - - - +
58I LEU* 1.3 68.8 + - + +
60I HIS* 3.4 13.6 + - - +
61I MSE 3.0 31.0 + - + +
29K ILE* 4.8 21.2 - - + +
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Residues in contact with LEU 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54I VAL* 2.7 51.6 + - + +
55I MSE 3.4 17.7 - - + +
57I GLN* 1.3 73.2 - - + +
59I GLU* 1.3 53.7 + - - +
61I MSE 4.1 2.8 - - - +
62I GLU* 2.7 45.8 + - - +
82I MSE 3.8 45.0 - - + +
85I ILE* 3.4 19.7 - - + -
86I ARG* 4.7 15.0 - - + +
89I LEU* 5.6 1.3 - - + -
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Residues in contact with GLU 59 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I MSE 2.7 12.8 + - - +
56I GLU* 3.0 18.8 - - - +
58I LEU* 1.3 73.2 - - - +
60I HIS* 1.3 78.9 + - - +
62I GLU* 2.9 16.9 + - - +
63I GLU* 3.1 26.6 + - - +
131J ASP* 5.6 5.6 - - - +
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Residues in contact with HIS 60 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I GLU* 2.8 55.3 + - + +
57I GLN* 3.6 18.8 - - - +
59I GLU* 1.3 82.7 + - - +
61I MSE 1.3 54.9 + - - +
63I GLU* 2.8 2.7 + - - +
64I ASN* 2.4 48.1 + - + +
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Residues in contact with MSE 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57I GLN* 3.0 18.9 + - - +
58I LEU* 4.1 2.2 - - - +
60I HIS* 1.3 76.0 - - - +
62I GLU* 1.3 55.3 + - - +
63I GLU 2.7 13.9 + - - -
64I ASN* 3.2 22.5 + - - +
65I LEU* 3.7 24.1 + - + +
66I ARG* 4.1 3.1 + - - +
78I HIS* 3.4 31.9 - - + +
81I GLU* 5.5 0.4 - - - +
82I MSE 3.9 22.0 - - + -
27K TYR 3.9 19.5 - - - +
29K ILE* 3.6 34.8 - - + +
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Residues in contact with GLU 62 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58I LEU* 2.7 33.7 + - - +
59I GLU* 2.9 11.2 + - - +
61I MSE 1.3 72.0 - - - +
63I GLU* 1.3 51.3 + - + +
66I ARG* 2.4 77.5 + - - +
79I GLN* 5.2 3.6 + - - -
82I MSE 3.0 39.6 - - - +
86I ARG* 5.2 5.7 + - - -
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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
----------------------------------------------------------
59I GLU* 3.1 23.3 + - - +
60I HIS* 2.8 7.2 + - - +
61I MSE 2.7 3.9 + - - -
62I GLU* 1.3 74.3 - - + +
64I ASN* 1.3 69.3 + - - +
65I LEU 3.3 2.0 - - - -
66I ARG* 2.6 32.9 + - - +
67I ARG* 2.7 57.9 + - + +
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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
----------------------------------------------------------
60I HIS* 2.4 36.9 + - - +
61I MSE 3.6 22.8 + - - +
63I GLU* 1.3 72.2 - - - +
65I LEU* 1.3 74.9 + - + +
67I ARG* 3.5 14.4 - - - +
68I ALA* 3.5 5.2 - - - +
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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
----------------------------------------------------------
61I MSE 3.7 24.6 + - + +
63I GLU 3.3 0.2 - - - -
64I ASN* 1.3 88.1 - - + +
66I ARG* 1.3 64.5 + - - +
67I ARG 2.8 7.1 + - - -
68I ALA* 2.9 29.2 + - + +
69I LYS 3.9 1.0 + - - -
70I ARG* 4.5 23.9 + - + +
74I LYS* 3.7 20.9 - - + +
75I VAL* 5.3 7.2 - - + +
78I HIS* 3.6 32.5 - - + +
27K TYR* 6.4 1.6 - - + -
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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