Contacts of the helix formed by residues 47 - 66 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ALA* 4.3 15.7 - - + -
44A LEU* 6.3 0.7 - - - -
45A GLU* 3.0 44.5 + - - +
46A SER* 1.3 77.8 + - - +
48A PRO* 1.3 52.7 - - - +
49A GLU* 2.7 19.5 + - - -
50A ILE* 3.3 32.6 + - + -
51A VAL* 3.4 15.2 + - - +
92A TYR* 4.0 19.8 + - - +
96A ARG* 5.1 0.2 - - - -
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Residues in contact with PRO 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A SER* 2.9 30.0 - - - +
47A LYS* 1.3 82.8 - - - +
49A GLU* 1.3 67.7 + - + +
51A VAL* 4.1 10.3 - - + +
52A GLU* 2.6 48.9 + - - +
123A SER* 5.1 9.0 - - - -
124A PRO* 6.0 2.0 - - + -
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Residues in contact with GLU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LYS* 2.7 9.1 + - - +
48A PRO* 1.3 94.5 - - + +
50A ILE* 1.3 68.8 + - + +
51A VAL 2.7 5.2 + - - -
52A GLU* 2.9 22.8 + - - +
53A CYS* 2.8 33.9 + - - +
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Residues in contact with ILE 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 4.0 19.2 - - + +
29A ARG* 3.2 35.0 - - + -
30A LEU* 3.3 42.8 - - + +
33A ALA* 4.0 22.9 - - + -
47A LYS* 3.9 23.8 - - + +
49A GLU* 1.3 81.5 - - + +
51A VAL* 1.3 58.1 + - + +
54A VAL* 3.0 35.4 + - - +
92A TYR* 6.2 0.2 - - + -
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Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 5.0 1.1 - - + -
47A LYS 3.5 19.1 - - - +
48A PRO* 4.2 7.0 - - + +
49A GLU 2.7 4.2 + - - -
50A ILE* 1.3 73.9 - - + +
52A GLU* 1.3 67.4 + - + +
53A CYS 3.1 1.6 - - - -
54A VAL* 3.0 22.7 - - - +
55A MSE 3.0 19.8 + - + +
89A LEU* 4.2 13.5 - - + -
92A TYR* 3.5 34.8 - - + +
93A LEU* 4.3 17.0 - - + -
128B LEU* 5.8 4.9 - - + +
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Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PRO* 2.6 32.6 + - - +
49A GLU* 2.9 33.9 + - - +
51A VAL* 1.3 78.6 - - + +
53A CYS* 1.3 61.2 + - - +
55A MSE 3.3 10.7 - - - +
56A GLU* 3.0 25.3 + - - +
128B LEU 5.6 2.5 - - - +
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Residues in contact with CYS 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 6.0 6.1 - - - -
26A LEU* 3.7 24.7 - - + -
49A GLU* 2.8 24.3 + - - +
50A ILE 4.1 2.0 - - - +
52A GLU* 1.3 78.8 - - - +
54A VAL* 1.3 54.5 + - - +
55A MSE 2.9 0.9 - - - -
56A GLU* 2.6 36.2 + - - +
57A GLN* 2.7 18.2 + - - +
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Residues in contact with VAL 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 3.6 28.0 - - + +
27A ILE* 4.3 14.1 - - + -
30A LEU* 3.7 27.4 - - + -
50A ILE 3.0 16.4 + - - +
51A VAL 3.0 17.9 - - - +
53A CYS* 1.3 74.6 - - - +
55A MSE 1.3 61.1 + - - +
57A GLN* 3.9 4.6 - - - +
58A LEU* 3.0 31.3 + - - +
85A ILE* 4.9 5.8 - - + -
89A LEU* 3.6 29.4 - - + -
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Residues in contact with MSE 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A VAL* 3.1 28.3 - - + +
52A GLU* 3.3 10.5 - - - +
53A CYS 2.9 0.4 - - - -
54A VAL* 1.3 82.9 - - - +
56A GLU* 1.3 60.7 + - - +
58A LEU* 3.9 7.3 - - - +
59A GLU* 3.3 25.4 + - - +
89A LEU* 3.5 27.4 - - + -
128B LEU* 3.0 33.7 - - + +
129B GLY* 3.5 18.2 - - - +
133B GLY 4.1 6.5 - - - +
134B LEU* 3.7 25.6 - - + -
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Residues in contact with GLU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLU 3.0 13.9 + - - +
53A CYS* 2.6 27.7 + - - +
55A MSE 1.3 70.5 - - - +
57A GLN* 1.3 61.9 + - - +
59A GLU* 2.7 40.5 - - - +
60A HIS* 3.0 10.8 + - + +
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Residues in contact with GLN 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PRO* 2.8 42.8 - - + +
26A LEU* 4.7 10.6 - - + +
27A ILE* 5.9 2.7 - - + -
53A CYS 2.7 17.1 + - - +
54A VAL* 3.9 9.0 - - - +
56A GLU* 1.3 72.5 + - - +
58A LEU* 1.3 65.4 + - + +
60A HIS* 3.0 33.5 + - - +
61A MSE 3.2 8.5 + - - +
85A ILE* 6.5 0.4 - - + -
29C ILE* 4.2 28.0 - - + +
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Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A VAL 3.0 21.2 + - - +
55A MSE 3.9 7.0 - - - +
57A GLN* 1.3 73.1 - - + +
59A GLU* 1.3 58.1 + - - +
61A MSE 2.6 29.4 + - - +
62A GLU* 3.0 10.2 + - - +
82A MSE 3.6 30.2 - - + +
85A ILE* 3.3 43.1 - - + +
86A ARG* 3.4 41.5 - - + +
89A LEU* 4.7 14.4 - - + -
134B LEU* 6.3 0.4 - - + -
29C ILE* 4.5 6.1 - - + -
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Residues in contact with GLU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A MSE 3.3 12.8 + - - +
56A GLU* 2.7 47.8 - - - +
58A LEU* 1.3 78.8 - - - +
60A HIS* 1.3 63.6 + - + +
62A GLU* 3.3 11.6 + - - +
63A GLU* 3.2 19.9 + - - +
86A ARG* 5.8 2.2 - - - +
130B GLY* 5.3 8.1 + - - -
131B ASP* 5.6 1.6 - - - +
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Residues in contact with HIS 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A GLU* 3.0 14.3 + - + +
57A GLN* 3.0 29.3 + - - +
59A GLU* 1.3 76.7 - - - +
61A MSE 1.3 72.5 + - + +
63A GLU* 3.1 26.9 + - - +
64A ASN* 3.4 32.5 + - - -
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Residues in contact with MSE 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLN 3.2 3.9 + - - +
58A LEU* 2.6 15.5 + - - +
60A HIS* 1.3 79.9 - - + +
62A GLU* 1.3 55.1 + - - +
63A GLU 2.6 17.0 + - - -
64A ASN* 3.0 34.8 + - + +
65A LEU* 2.8 31.5 + - + +
78A HIS* 3.6 43.3 - - + +
81A GLU* 5.3 0.4 - - - +
82A MSE 3.5 18.6 - - + -
27C TYR 5.7 1.1 - - - +
29C ILE* 3.9 29.2 - - + -
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Residues in contact with GLU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LEU 3.0 7.0 + - - +
59A GLU* 3.7 14.1 - - - +
61A MSE 1.3 77.4 - - - +
63A GLU* 1.3 62.4 + - - +
65A LEU* 3.8 9.6 - - - +
66A ARG* 3.4 17.9 + - + +
82A MSE 4.1 16.0 - - + +
86A ARG* 3.5 22.9 + - - +
131B ASP* 5.8 0.3 - - - +
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Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLU 3.2 9.2 + - - +
60A HIS* 3.1 16.8 + - - +
61A MSE 2.6 4.9 + - - -
62A GLU* 1.3 70.4 - - - +
64A ASN* 1.3 75.6 + - - +
65A LEU 2.7 14.1 + - - -
66A ARG 2.7 29.8 + - - +
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Residues in contact with ASN 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A HIS* 3.4 31.3 + - - -
61A MSE 3.0 23.3 + - + +
63A GLU* 1.3 97.0 + - - +
65A LEU* 1.3 60.1 + - - +
66A ARG 4.7 0.8 - - - +
75A VAL* 5.9 0.3 - - - +
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Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A MSE 2.8 19.8 + - + +
62A GLU* 3.8 8.7 - - - +
63A GLU 2.7 1.0 + - - -
64A ASN* 1.3 82.2 - - - +
66A ARG* 1.3 69.7 + - + +
75A VAL* 3.7 44.0 - - + +
78A HIS* 3.5 31.2 - - + -
79A GLN* 3.3 37.2 - - + +
82A MSE 4.1 22.0 - - + -
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Residues in contact with ARG 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLU 3.4 9.9 + - - +
63A GLU* 2.7 25.9 + - - +
64A ASN 4.7 1.0 - - - +
65A LEU* 1.3 90.5 - - + +
75A VAL* 5.2 6.0 - - + +
79A GLN* 4.1 28.2 + - - +
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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