Contacts of the helix formed by residues 89 - 101 (chain B) in PDB entry 3LIO
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 THR 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 ALA* 3.9 8.5 - - + +
88B PRO* 1.3 80.3 - - - +
90B GLY* 1.3 67.2 + - - +
92B VAL* 4.2 0.5 - - - +
93B ALA* 3.2 13.9 + - - -
184B TRP* 4.1 14.0 - - + +
185B GLU* 4.4 9.8 + - - +
188B ASN* 3.0 28.2 + - - -
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Residues in contact with GLY 90 (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 THR* 1.3 73.9 - - - +
91B ALA* 1.3 66.8 + - - -
93B ALA* 3.2 4.7 + - - +
94B ASP* 3.2 26.3 + - - +
188B ASN* 4.1 4.9 - - - -
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Residues in contact with ALA 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 GLY* 1.3 73.3 - - - -
92B VAL* 1.4 58.8 + - - +
94B ASP* 3.3 9.8 + - - +
95B ALA* 2.9 29.3 + - - +
188B ASN* 3.2 9.3 + - - +
191B PHE* 3.7 27.9 - - + -
192B ALA* 5.8 5.6 - - + -
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Residues in contact with VAL 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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89B THR 4.2 1.6 - - - +
91B ALA* 1.4 74.3 - - - +
93B ALA* 1.3 60.2 + - - +
95B ALA* 3.2 6.1 + - - +
96B ILE* 2.8 49.5 + - + +
125B LEU* 4.5 10.8 - - + -
133B LEU* 4.5 2.5 - - + -
153B ILE* 4.6 2.7 - - + -
184B TRP* 4.0 20.2 - - + -
187B ALA* 3.7 21.3 - - + +
188B ASN* 2.9 24.4 + - - +
191B PHE* 3.6 32.3 - - + -
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Residues in contact with ALA 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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88B PRO* 3.7 33.9 - - + +
89B THR* 3.2 19.5 + - - +
90B GLY 3.2 9.7 + - - +
92B VAL* 1.3 81.6 - - - +
94B ASP* 1.3 65.7 + - - +
96B ILE* 3.4 3.6 + - - +
97B ASN* 3.0 30.9 + - - +
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Residues in contact with ASP 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 GLY 3.2 14.6 + - - +
91B ALA* 3.6 11.1 - - - +
93B ALA* 1.3 82.3 - - - +
95B ALA* 1.4 57.8 + - - +
97B ASN* 3.1 11.8 + - - +
98B ALA* 2.8 27.9 + - - +
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Residues in contact with ALA 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 ALA 2.9 17.1 + - - +
92B VAL 3.2 1.1 + - - +
94B ASP* 1.4 72.8 - - - +
96B ILE* 1.3 65.2 + - - +
98B ALA* 3.2 7.7 + - - +
99B LYS* 3.1 24.1 + - - +
131B GLY 5.1 3.1 - - - +
132B SER* 5.9 0.7 - - - -
133B LEU* 3.6 26.4 + - + +
191B PHE* 3.7 24.5 - - + -
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Residues in contact with ILE 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 PRO* 4.0 13.0 - - + -
92B VAL* 2.8 37.0 + - + +
93B ALA* 3.5 5.2 - - - +
95B ALA* 1.3 77.2 - - - +
97B ASN* 1.3 64.6 + - - +
99B LYS 3.3 0.3 + - - -
100B TRP* 3.0 35.9 + - + +
102B SER 4.1 1.1 + - - +
103B PHE* 3.9 20.2 - - + +
106B PHE* 3.5 46.4 - - + -
125B LEU* 5.0 0.4 - - + -
133B LEU* 3.5 15.3 - - + -
184B TRP* 3.9 20.9 - - + -
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Residues in contact with ASN 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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93B ALA* 3.0 20.9 + - - +
94B ASP* 3.1 13.2 + - - +
96B ILE* 1.3 77.6 - - - +
98B ALA* 1.3 60.3 + - - +
101B GLY* 2.8 35.4 + - - +
102B SER* 3.3 25.7 - - - +
103B PHE* 3.5 11.9 - - - +
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Residues in contact with ALA 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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94B ASP 2.8 14.2 + - - +
95B ALA* 3.6 11.2 - - - +
96B ILE 3.1 0.4 - - - -
97B ASN* 1.3 81.4 - - - +
99B LYS* 1.3 59.7 + - + +
101B GLY 4.7 0.5 + - - -
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Residues in contact with LYS 99 (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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95B ALA 3.1 12.2 + - - +
98B ALA* 1.3 79.7 - - + +
100B TRP* 1.3 105.4 + - + +
101B GLY 3.6 0.2 - - - -
132B SER* 5.3 7.6 - - - +
133B LEU* 3.0 28.3 - - + +
134B ASP* 3.8 20.3 + - - -
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Residues in contact with TRP 100 (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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96B ILE* 3.0 23.2 + - - +
99B LYS* 1.3 120.8 - - + +
101B GLY* 1.3 57.0 + - - +
102B SER 3.1 9.0 + - - +
105B ALA* 3.3 19.2 - - + +
106B PHE* 3.5 54.3 - + + +
109B ALA* 3.7 26.0 - - + +
125B LEU* 3.9 6.7 - - + -
133B LEU* 3.7 34.3 - - + -
134B ASP* 4.0 5.8 - - - -
135B ILE* 3.5 27.9 - - + +
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Residues in contact with GLY 101 (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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97B ASN* 2.8 30.2 + - - +
98B ALA 4.5 0.4 + - - -
99B LYS 3.6 1.2 - - - -
100B TRP* 1.3 74.9 - - - +
102B SER* 1.3 61.2 + - - +
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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