Contacts of the helix formed by residues 90 - 98 (chain B) in PDB entry 1EAK
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 ASP 90 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78B GLN* 3.6 0.2 + - - -
84B PRO* 5.2 3.1 - - - +
86B THR* 3.1 32.4 + - - +
88B ASP* 3.1 6.7 - - + +
89B LEU* 1.3 76.3 - - - +
91B GLN* 1.3 58.6 + - - +
92B ASN* 2.9 28.7 + - - +
93B THR* 2.5 58.9 + - - +
94B ILE* 2.8 16.8 + - - +
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Residues in contact with GLN 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B ASP* 1.3 71.0 - - - +
92B ASN* 1.3 61.6 + - - +
94B ILE* 3.7 17.8 - - - +
95B GLU* 3.1 69.7 + - - +
98B ARG* 6.3 0.6 - - - -
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Residues in contact with ASN 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B LEU* 3.5 26.7 - - + +
84B PRO* 3.6 27.2 - - + +
90B ASP* 2.6 20.9 + - - +
91B GLN* 1.3 77.8 - - - +
93B THR* 1.3 57.0 + - + +
95B GLU* 4.1 12.9 - - - +
96B THR* 2.9 27.0 + - - -
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Residues in contact with THR 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B LEU* 4.5 4.9 - - - +
77B MET* 3.3 22.9 - - - +
78B GLN* 3.5 20.2 - - + +
83B LEU* 3.9 12.3 - - + -
84B PRO* 6.3 0.4 - - + -
88B ASP 3.9 0.9 - - - +
89B LEU* 4.2 7.3 - - - +
90B ASP* 2.5 55.9 + - - +
92B ASN* 1.3 73.7 - - + +
94B ILE* 1.3 59.1 + - - -
96B THR* 3.8 1.4 - - - -
97B MET* 3.0 39.2 + - - +
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Residues in contact with ILE 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ASP* 3.1 43.3 - - + +
49B LEU* 5.0 3.4 - - + -
89B LEU* 3.6 31.2 - - + +
90B ASP* 2.8 33.4 + - - +
91B GLN* 3.7 15.0 - - - +
93B THR* 1.3 74.7 - - - +
95B GLU* 1.3 64.9 + - - +
96B THR 3.0 4.0 - - - -
97B MET* 3.1 19.4 + - + +
98B ARG* 3.1 40.1 + - + +
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Residues in contact with GLU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B GLN* 3.1 46.9 + - - +
92B ASN* 4.1 16.5 - - - +
94B ILE* 1.3 79.5 - - - +
96B THR* 1.3 63.5 + - - +
98B ARG* 3.8 17.9 + - - +
99B LYS* 4.1 18.4 + - - +
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Residues in contact with THR 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B TYR* 4.7 0.8 + - - +
77B MET* 4.9 2.7 - - + -
81B PHE* 4.4 24.2 - - + -
83B LEU* 3.8 25.8 - - + +
92B ASN 2.9 22.3 + - - -
93B THR 3.8 4.5 - - - +
94B ILE 3.0 1.0 - - - -
95B GLU* 1.3 80.5 - - - +
97B MET* 1.3 60.8 + - - +
98B ARG 3.1 1.8 - - - -
99B LYS* 3.1 44.3 + - + +
424B ILE* 3.9 15.5 - - + +
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Residues in contact with MET 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ASP 4.6 1.8 - - - +
49B LEU* 4.1 18.7 - - + +
50B ALA* 3.3 47.6 - - + +
53B TYR* 3.2 58.6 - - + -
54B LEU* 5.0 2.7 - - - -
74B LEU* 4.9 7.2 - - - -
77B MET* 4.3 14.4 - - + +
89B LEU* 4.4 3.4 - - + -
93B THR* 3.0 32.4 + - - +
94B ILE* 3.1 13.2 + - + +
96B THR* 1.3 78.8 - - + +
98B ARG* 1.3 56.7 + - - +
99B LYS 3.2 4.7 + - - +
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Residues in contact with ARG 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ASP* 2.9 39.8 + - - +
49B LEU* 3.4 24.1 - - + +
91B GLN* 6.3 0.7 - - - -
94B ILE* 3.1 26.9 + - - +
95B GLU* 4.2 10.7 - - - +
96B THR 3.1 1.6 - - - -
97B MET* 1.3 76.0 - - - +
99B LYS* 1.3 61.4 + - - +
100B PRO* 3.8 6.2 - - - +
189B GLY* 5.8 2.6 + - - -
369B SER* 4.6 13.9 + - - -
370B ASP* 5.4 4.6 - - - +
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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
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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