Contacts of the helix formed by residues 79 - 89 (chain A) in PDB entry 1ZTD
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 SER 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A TRP* 3.9 5.2 - - - -
78A ILE* 1.3 78.5 - - - +
80A GLU* 1.3 63.2 + - - +
81A ARG* 3.8 6.8 + - - +
82A GLU* 3.2 28.0 + - - +
83A ALA* 3.0 24.4 + - - +
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Residues in contact with GLU 80 (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 PHE* 3.4 21.4 - - + -
18A LEU* 3.8 22.6 - - + +
21A LEU* 3.1 24.9 - - - +
73A TRP* 3.3 30.1 - - + -
79A SER* 1.3 72.7 - - - +
81A ARG* 1.3 60.5 + - - +
83A ALA* 3.2 3.6 + - - +
84A VAL* 2.9 39.1 + - + +
17B PHE* 5.5 1.0 - - - -
73B TRP* 4.2 9.5 - - - -
80B GLU* 5.1 5.5 - - - +
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Residues in contact with ARG 81 (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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79A SER* 3.3 5.9 + - - +
80A GLU* 1.3 81.3 - - - +
82A GLU* 1.3 64.0 + - - +
84A VAL* 3.4 8.0 + - - +
85A GLU* 3.1 46.5 + - + +
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Residues in contact with GLU 82 (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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78A ILE* 3.5 13.0 - - + +
79A SER* 3.2 24.9 + - - +
81A ARG* 1.3 78.0 - - - +
83A ALA* 1.3 63.2 + - - +
85A GLU* 3.4 6.6 + - - +
86A ILE* 3.1 43.8 + - + +
115A ILE* 5.8 0.2 - - - +
119A ARG* 2.6 48.0 + - - -
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Residues in contact with ALA 83 (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 LEU* 3.9 26.9 - - + -
73A TRP* 6.4 0.2 - - + -
78A ILE* 4.2 8.3 - - + +
79A SER 3.0 17.5 + - - +
80A GLU 3.6 3.8 - - - +
82A GLU* 1.3 76.0 - - - +
84A VAL* 1.3 63.5 + - - +
86A ILE* 3.4 2.8 + - - +
87A ILE* 3.0 30.8 + - - +
112A LEU* 4.0 26.4 - - + +
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Residues in contact with VAL 84 (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 LEU* 4.2 17.5 - - + +
21A LEU* 4.1 24.7 - - + -
22A ALA* 3.7 27.0 - - - +
25A GLU* 3.6 25.4 - - - +
80A GLU* 2.9 28.7 + - + +
81A ARG* 3.7 7.4 - - - +
82A GLU 3.3 0.2 - - - -
83A ALA* 1.3 77.6 - - - +
85A GLU* 1.3 59.4 + - - +
87A ILE* 3.4 5.0 + - - +
88A LYS* 2.9 30.8 + - - +
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Residues in contact with GLU 85 (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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25A GLU* 4.1 4.2 - - - +
81A ARG* 3.1 36.6 + - + +
82A GLU* 3.8 6.7 - - - +
83A ALA 3.3 0.2 - - - -
84A VAL* 1.3 74.1 - - - +
86A ILE* 1.3 66.6 + - + +
88A LYS* 3.3 32.0 + - - +
89A LYS* 3.1 58.0 + - - +
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Residues in contact with ILE 86 (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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78A ILE* 4.4 4.7 - - + -
82A GLU* 3.1 34.7 + - + +
83A ALA* 3.6 6.3 - - - +
84A VAL 3.3 0.2 - - - -
85A GLU* 1.3 78.2 - - + +
87A ILE* 1.3 59.7 + - - +
89A LYS* 3.5 8.8 + - - +
90A ASN* 2.7 30.1 + - - +
111A PRO* 4.1 14.8 - - + +
112A LEU* 3.8 46.4 - - + +
115A ILE* 3.3 30.7 - - + -
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Residues in contact with ILE 87 (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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15A ILE* 4.5 1.3 - - + -
18A LEU* 4.1 34.5 - - + +
19A TYR* 4.1 14.8 - - + +
22A ALA* 3.7 15.3 - - + -
83A ALA 3.0 19.1 + - - +
84A VAL* 3.7 3.6 - - - +
86A ILE* 1.3 76.5 - - - +
88A LYS* 1.3 64.6 + - - +
90A ASN* 3.0 16.3 + - - +
91A LEU* 3.3 26.6 + - + +
108A ALA* 4.0 17.5 - - + +
109A LEU* 4.2 17.0 - - + -
112A LEU* 4.2 24.0 - - + -
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Residues in contact with LYS 88 (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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22A ALA* 4.0 15.5 - - + +
25A GLU* 2.7 48.2 + - + +
26A PHE* 4.2 25.4 - - + +
84A VAL* 2.9 23.3 + - - +
85A GLU* 3.3 31.5 + - - +
87A ILE* 1.3 75.1 - - - +
89A LYS* 1.3 59.7 + - + +
90A ASN 3.1 5.1 + - - -
91A LEU* 3.2 24.1 + - - +
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Residues in contact with LYS 89 (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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85A GLU* 3.1 46.9 + - - +
86A ILE* 4.0 9.0 - - - +
87A ILE 3.2 0.4 + - - -
88A LYS* 1.3 74.5 - - + +
90A ASN* 1.3 64.8 + - - +
91A LEU 3.6 1.6 - - - +
92A TYR* 5.4 3.8 + - - -
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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