Contacts of the helix formed by residues 89 - 96 (chain B) in PDB entry 1HXD
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 89 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87B ILE* 2.9 9.0 - - - +
88B ASP* 1.4 84.0 - - - +
90B THR* 1.3 55.3 + - - +
91B ASN* 3.3 9.2 + - - +
92B GLN* 3.3 20.7 + - - +
93B TYR* 2.6 35.9 + - - +
112B GLN* 3.5 5.6 - - - -
114B ALA 3.6 9.0 - - - -
116B ARG* 4.1 7.3 + - - -
501B BTN 2.8 30.8 + - - -
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Residues in contact with THR 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LEU* 5.7 0.2 - - + -
87B ILE* 3.7 3.5 - - + +
89B SER* 1.3 69.8 - - - +
91B ASN* 1.3 56.5 + - - +
93B TYR* 3.1 20.3 - - - +
94B LEU* 3.2 14.9 + - - +
107B CYS* 4.0 21.9 - - - +
109B ALA* 3.8 30.3 - - + +
112B GLN* 2.9 16.0 + - - +
132B TYR* 3.8 19.5 - - + +
133B LEU 4.0 0.5 - - - -
134B SER* 2.5 28.9 + - - -
501B BTN 2.9 26.0 + - - +
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Residues in contact with ASN 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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89B SER* 3.1 9.4 + - - +
90B THR* 1.3 80.6 + - - +
92B GLN* 1.3 61.7 + - - +
94B LEU* 3.0 2.9 + - - +
95B LEU* 2.7 31.0 + - - +
116B ARG* 4.6 5.6 - - - +
134B SER* 2.5 34.2 + - - -
188B LEU* 3.6 22.0 + - - +
190B GLU* 2.3 38.0 + - - +
202B VAL* 3.5 17.1 - - + +
204B GLY* 2.9 13.4 + - - +
501B BTN 3.8 9.2 + - - +
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Residues in contact with GLN 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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88B ASP* 3.8 17.9 - - - +
89B SER* 3.2 17.9 + - - +
91B ASN* 1.3 77.5 - - - +
93B TYR* 1.3 70.0 + - - +
94B LEU 3.2 0.5 + - - -
95B LEU* 3.2 22.2 + - - +
96B ASP* 3.1 48.2 + - - +
116B ARG* 2.7 36.1 + - - +
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Residues in contact with TYR 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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82B ALA* 3.9 16.9 - - + +
84B LEU* 4.0 16.2 - - + +
87B ILE* 4.0 24.5 - - + -
88B ASP* 4.9 2.0 + - - -
89B SER 2.6 17.8 + - - +
90B THR* 3.1 12.1 - - - +
92B GLN* 1.3 75.1 - - - +
94B LEU* 1.3 93.8 + - + +
96B ASP* 3.2 18.1 - - - +
97B ARG* 3.2 53.0 + - - +
101B LEU* 5.8 3.1 - - + -
107B CYS* 3.4 18.2 - - + -
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Residues in contact with LEU 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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90B THR 3.2 8.5 + - - +
91B ASN 3.0 5.1 + - - +
93B TYR* 1.3 112.0 - - + +
95B LEU* 1.4 57.0 + - - +
96B ASP 2.8 6.5 - - - -
97B ARG* 2.8 19.5 + - - +
98B ILE* 3.2 16.4 + - - +
101B LEU* 3.6 23.7 - - + +
105B ASP 4.4 3.8 - - - +
106B ALA 5.0 2.7 - - - -
107B CYS* 3.5 14.6 - - + +
134B SER* 3.9 35.7 - - - +
135B MET* 4.1 15.5 - - - +
136B PHE* 4.2 9.2 - - + +
202B VAL* 4.3 11.4 - - + -
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Residues in contact with LEU 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 ASN 2.7 26.3 + - - +
92B GLN* 3.2 19.7 + - - +
94B LEU* 1.4 73.2 - - - +
96B ASP* 1.3 61.4 + - - +
97B ARG 3.5 0.7 + - - -
98B ILE* 3.6 21.8 - - + +
116B ARG* 4.7 7.0 - - - +
190B GLU* 3.9 43.7 - - + +
191B LEU 6.1 1.1 - - - -
192B THR* 5.8 10.3 - - + -
200B GLN 5.5 3.4 - - - +
202B VAL* 3.5 24.0 - - + +
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Residues in contact with ASP 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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88B ASP* 5.8 0.2 - - - +
92B GLN* 3.1 42.1 + - - +
93B TYR* 3.2 13.4 - - - +
95B LEU* 1.3 78.7 - - - +
97B ARG* 1.3 75.0 + - + +
98B ILE* 3.7 1.6 - - - -
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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