Contacts of the helix formed by residues 63 - 73 (chain A) in PDB entry 4EDY
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 GLN 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A LYS* 6.3 1.0 - - - +
52A PRO 3.9 7.1 + - - -
62A HIS* 1.3 98.7 + - - +
64A SER* 1.3 65.3 + - - +
65A LEU* 3.3 2.6 + - - +
66A ALA* 3.2 15.8 + - + +
67A ILE* 3.0 20.1 + - - +
202A GSH 2.9 36.1 + - - +
90B ALA* 3.4 21.3 - - - +
93B ASP* 3.5 20.6 - - + +
94B THR* 3.1 26.3 + - - +
97B ASP* 3.0 22.4 + - - -
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Residues in contact with SER 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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14A ARG* 3.1 31.3 + - - +
17A ILE* 4.3 3.3 - - - +
18A ILE* 3.9 17.2 - - - +
52A PRO* 3.7 15.1 - - - +
63A GLN* 1.3 72.6 - - - +
65A LEU* 1.3 70.9 + - - +
67A ILE* 3.5 2.3 + - - +
68A ALA* 2.9 27.9 + - - +
96A ASP* 5.3 0.5 + - - -
152A TYR* 5.1 2.8 + - - -
202A GSH 2.7 30.5 + - - -
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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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17A ILE* 4.2 7.2 - - + -
63A GLN* 3.3 2.2 + - - +
64A SER* 1.3 86.4 + - - +
66A ALA* 1.3 60.8 + - - +
68A ALA* 3.7 3.8 - - - +
69A ARG* 2.9 39.8 + - - +
92A VAL* 3.4 31.9 - - + -
93A ASP* 3.8 16.2 - - - +
96A ASP* 3.7 30.7 - - + +
148A TRP* 3.8 16.5 - - + -
152A TYR* 3.9 23.1 - - + +
202A GSH 4.8 1.8 + - - +
93B ASP* 4.2 14.4 - - - +
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Residues in contact with ALA 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 HIS 3.9 3.6 - - - +
63A GLN* 3.2 14.5 + - + +
65A LEU* 1.3 78.7 - - - +
67A ILE* 1.3 56.1 + - - +
69A ARG* 3.5 14.3 + - - +
70A TYR* 3.1 27.9 + - - +
86B CYS* 3.6 12.9 - - - +
89B ASP* 3.7 10.7 - - + +
90B ALA* 3.6 35.4 - - - +
93B ASP* 4.6 4.1 + - - +
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Residues in contact with ILE 67 (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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18A ILE* 3.7 23.1 - - + -
52A PRO 4.6 2.0 - - - +
53A ILE* 4.4 4.5 - - - -
54A LEU* 3.5 49.6 - - + +
61A LEU* 4.0 15.5 - - + -
62A HIS* 3.7 27.6 - - - +
63A GLN 3.0 24.4 + - - +
64A SER* 3.6 4.3 - - - +
66A ALA* 1.3 73.5 - - - +
68A ALA* 1.3 65.5 + - - +
70A TYR* 3.1 4.5 + - + +
71A LEU* 2.9 31.3 + - + +
86B CYS* 4.2 7.2 - - - -
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Residues in contact with ALA 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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17A ILE* 4.1 11.4 - - + -
18A ILE* 4.5 3.8 - - + +
21A ILE* 3.5 24.9 - - + +
64A SER 2.9 18.7 + - - +
65A LEU* 3.7 2.7 - - - +
67A ILE* 1.3 77.1 - - - +
69A ARG* 1.3 60.6 + - - +
71A LEU* 3.4 2.9 + - - +
72A THR* 3.0 32.0 + - - +
148A TRP* 3.7 24.2 - - + -
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Residues in contact with ARG 69 (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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65A LEU* 2.9 34.0 + - - +
66A ALA* 3.7 6.1 - - - +
68A ALA* 1.3 75.9 - - - +
70A TYR* 1.3 63.3 + - - +
72A THR* 3.2 9.2 + - - +
73A LYS* 3.1 44.6 + - - +
89A ASP* 2.9 33.2 + - - +
92A VAL* 5.5 0.6 - - - +
93A ASP* 4.8 10.1 + - - -
148A TRP* 4.0 23.7 - - + +
69B ARG* 3.4 42.9 - - - +
73B LYS* 6.0 1.1 - - - +
89B ASP* 3.1 36.3 + - - +
93B ASP* 5.2 4.2 + - - -
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Residues in contact with TYR 70 (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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4A TYR* 4.4 15.8 + + - -
54A LEU* 5.6 0.2 - - + -
56A VAL* 5.1 3.6 - - + +
61A LEU* 4.3 14.4 - - + -
66A ALA 3.1 14.7 + - - +
67A ILE* 3.1 8.2 + - + +
69A ARG* 1.3 77.6 - - - +
71A LEU* 1.3 81.3 + - + +
73A LYS* 3.4 27.8 + - + +
82B GLU* 3.5 49.4 + - + +
83B MET* 3.2 33.8 - - + +
86B CYS* 3.8 19.3 - - + +
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Residues in contact with LEU 71 (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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4A TYR* 3.9 25.1 - - + +
18A ILE* 3.8 21.3 - - + -
21A ILE* 3.8 21.3 - - + -
22A PHE* 3.8 41.1 - - + -
25A LEU* 3.5 18.6 - - + +
27A ILE* 5.3 5.6 - - + -
54A LEU* 4.4 2.0 - - + -
67A ILE* 2.9 28.8 + - + +
68A ALA* 3.9 3.8 - - - +
69A ARG 3.3 0.2 - - - -
70A TYR* 1.3 88.8 - - + +
72A THR* 1.3 60.8 + - - +
73A LYS 3.4 1.3 - - - +
75A THR* 3.7 6.2 - - - +
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Residues in contact with THR 72 (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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21A ILE* 3.5 33.9 - - + -
25A LEU* 5.0 0.2 - - - -
68A ALA 3.0 17.7 + - - +
69A ARG* 3.2 8.7 + - - +
70A TYR 3.3 0.2 - - - -
71A LEU* 1.3 74.9 - - - +
73A LYS* 1.3 65.2 + - - +
74A ASN 3.3 0.7 + - - -
75A THR* 2.7 29.7 + - - -
77A LEU* 3.9 20.6 - - + -
78A ALA* 3.4 13.7 - - - +
148A TRP* 3.4 28.3 + - + -
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Residues in contact with LYS 73 (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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69A ARG* 3.1 42.9 + - - +
70A TYR* 3.4 21.9 + - + +
71A LEU 4.4 1.7 - - - +
72A THR* 1.3 76.2 - - - +
74A ASN* 1.3 82.6 + - - +
75A THR* 3.3 7.8 + - - +
78A ALA* 4.9 3.4 - - - -
85A GLN* 6.0 2.5 - - - +
69B ARG* 6.0 1.0 - - - +
73B LYS* 5.0 17.0 - - - +
82B GLU* 4.5 17.8 + - + +
85B GLN* 3.3 37.4 + - - +
86B CYS* 5.5 0.6 - - - +
89B ASP* 4.8 4.2 + - - -
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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
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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