Contacts of the helix formed by residues 54 - 68 (chain A) in PDB entry 2EE4
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 ASN 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A GLY* 1.3 66.4 - - - +
55A LYS* 1.3 68.6 + - - +
56A THR* 3.0 27.1 + - - +
57A ASP* 3.0 31.9 + - - +
58A GLN* 3.6 6.6 + - - +
79A THR* 5.5 6.3 - - + +
81A ASN* 5.1 1.2 - - - +
82A ALA* 4.4 3.6 - - - +
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Residues in contact with LYS 55 (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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52A SER 5.8 0.9 - - - +
53A GLY 2.6 9.1 + - - +
54A ASN* 1.3 71.4 + - - +
56A THR* 1.3 66.0 + - - +
58A GLN* 2.7 48.1 + - - +
59A ASP* 2.8 19.8 + - + +
62A GLN* 5.8 3.0 + - - +
89A ALA* 5.4 6.9 - - - +
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Residues in contact with THR 56 (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 ASN* 3.2 24.4 + - - +
55A LYS* 1.3 78.7 - - - +
57A ASP* 1.3 67.6 + - - +
59A ASP* 3.1 19.3 - - - +
60A ASN* 3.5 5.6 + - - +
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Residues in contact with ASP 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ASN* 3.0 32.5 + - - +
55A LYS 2.9 1.0 + - - -
56A THR* 1.3 74.0 - - - +
58A GLN* 1.3 59.1 + - - +
60A ASN* 2.7 42.4 + - - +
61A ILE* 2.8 17.1 + - + +
77A GLU 5.5 0.5 - - - +
78A VAL* 4.8 14.2 - - + +
79A THR* 4.5 8.0 - - - +
82A ALA* 3.6 22.9 - - + +
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Residues in contact with GLN 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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52A SER 3.6 8.4 + - - +
53A GLY* 3.0 32.9 - - - +
54A ASN 4.4 0.4 - - - +
55A LYS* 2.7 44.3 + - + +
57A ASP* 1.3 75.3 - - - +
59A ASP* 1.3 61.7 + - - +
60A ASN 3.4 0.2 + - - -
61A ILE* 3.5 10.6 - - - +
62A GLN* 3.4 29.9 + - - +
81A ASN 3.8 0.2 - - - +
82A ALA* 3.0 31.0 - - + +
85A GLY* 3.1 27.5 + - - -
86A ALA* 3.4 10.4 - - + +
89A ALA* 5.0 2.0 - - - +
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Residues in contact with ASP 59 (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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8A TRP* 3.6 13.2 - - - -
55A LYS* 2.8 16.4 + - + +
56A THR* 3.1 17.7 - - - +
58A GLN* 1.3 78.4 - - - +
60A ASN* 1.3 56.7 + - - +
62A GLN* 4.3 2.4 - - - +
63A LYS* 3.2 47.3 + - - +
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Residues in contact with ASN 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 THR* 3.5 3.4 + - - +
57A ASP* 2.7 42.8 + - - +
59A ASP* 1.3 72.3 - - - +
61A ILE* 1.3 84.9 + - - +
62A GLN 2.8 2.7 + - - -
63A LYS* 2.9 8.0 + - - -
64A GLN* 2.7 46.4 + - + +
76A MET* 3.0 25.5 - - - +
78A VAL* 4.9 4.5 - - - +
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Residues in contact with ILE 61 (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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30A PHE* 3.9 12.0 - - + -
34A CYS* 4.6 8.3 - - - -
57A ASP* 2.8 15.1 + - + +
58A GLN* 3.5 25.8 - - - +
60A ASN* 1.3 85.2 + - - +
62A GLN* 1.3 58.4 + - - +
65A PHE* 3.1 23.4 + - - +
71A ILE* 4.1 4.7 - - + +
73A LEU* 4.6 15.5 - - + -
76A MET* 4.7 4.9 - - - -
78A VAL* 4.4 13.5 - - + -
82A ALA* 3.6 14.1 - - + +
83A VAL* 3.5 39.0 - - + +
86A ALA* 3.8 15.5 - - + -
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Residues in contact with GLN 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A TRP* 4.5 16.5 - - + -
13A PHE* 3.1 32.6 - - + -
30A PHE* 3.4 23.1 - - + -
55A LYS* 5.8 3.5 + - - +
58A GLN* 3.4 15.1 + - - +
59A ASP* 4.3 3.4 - - - +
60A ASN 2.8 1.0 + - - -
61A ILE* 1.3 76.8 - - - +
63A LYS* 1.3 67.5 + - - +
65A PHE* 3.2 2.1 + - - +
66A ASP 2.9 19.1 + - - -
86A ALA* 3.2 36.7 + - + +
89A ALA* 4.2 11.3 - - - +
90A PHE* 4.5 3.9 - - - +
93A ASP* 4.6 10.1 + - - +
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Residues in contact with LYS 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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8A TRP* 3.1 50.1 - - + -
59A ASP* 3.2 31.4 + - - +
60A ASN* 2.9 6.8 + - - +
62A GLN* 1.3 77.5 - - - +
64A GLN* 1.3 65.7 + - + +
66A ASP* 2.9 17.2 + - - +
67A GLN* 3.0 26.3 + - - +
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Residues in contact with GLN 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 ASN* 2.7 40.2 + - + +
63A LYS* 1.3 74.7 - - + +
65A PHE* 1.3 52.1 + - - +
66A ASP 3.2 0.2 + - - -
67A GLN* 3.3 13.5 + - - +
68A ASP* 2.7 43.3 + - - +
71A ILE* 4.1 13.4 - - + +
76A MET* 3.1 41.7 - - + +
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Residues in contact with PHE 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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12A TYR* 4.4 14.4 - + - -
13A PHE* 3.7 18.4 - + - -
29A LEU* 3.9 16.2 - - + -
30A PHE* 3.3 54.1 - + + -
33A LYS* 3.5 32.5 - - + -
61A ILE 3.1 22.3 + - - +
62A GLN 3.2 3.3 + - - +
64A GLN* 1.3 78.1 - - - +
66A ASP* 1.3 59.4 + - - +
68A ASP 2.5 28.1 - - - +
69A HIS* 3.2 39.5 - + - -
71A ILE* 3.7 10.9 - - + +
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Residues in contact with ASP 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A TRP* 4.8 3.4 + - - +
10A SER* 3.4 21.2 - - - -
11A ASN* 3.6 24.4 + - - +
12A TYR* 3.3 24.8 - - - +
13A PHE* 3.2 35.0 + - + -
62A GLN 2.9 7.5 + - - +
63A LYS* 2.9 12.3 + - - +
65A PHE* 1.3 79.6 - - - +
67A GLN* 1.3 66.7 + - + +
69A HIS* 3.1 19.3 + - - -
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Residues in contact with GLN 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASN* 5.7 3.6 - - - +
63A LYS* 3.0 37.5 + - - +
64A GLN* 3.4 13.2 - - - +
66A ASP* 1.3 79.1 - - + +
68A ASP* 1.3 75.4 + - - +
69A HIS* 4.4 1.2 + - - -
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Residues in contact with ASP 68 (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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64A GLN* 2.7 26.2 + - - +
65A PHE* 2.5 23.6 - - - +
67A GLN* 1.3 99.1 + - - +
69A HIS* 1.3 55.9 + - - +
70A ASN* 3.2 10.7 + - + +
71A ILE* 3.5 22.0 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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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