Contacts of the helix formed by residues 99 - 107 (chain A) in PDB entry 5LO6
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 99 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A MET* 1.4 75.7 - - - +
100A LYS* 1.4 57.8 + - - +
101A ALA* 3.6 9.0 + - - +
102A ASP* 3.0 35.3 + - - +
103A LEU* 2.9 27.9 + - - +
154A HIS* 3.6 29.6 - - + +
156A ASP* 4.5 7.2 - - + -
157A ASP* 3.4 27.6 - - + -
160A TYR* 4.8 1.8 - - - -
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Residues in contact with LYS 100 (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 GLU* 2.9 34.8 + - - -
20A PHE* 5.4 2.5 - - - -
99A THR* 1.4 70.1 - - - +
101A ALA* 1.4 58.1 + - - +
103A LEU* 3.3 7.3 + - - +
104A ILE* 2.9 44.3 + - + +
157A ASP* 2.9 18.7 + - - +
160A TYR* 3.6 45.5 + - + +
172A VAL* 4.7 9.9 - - + -
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Residues in contact with ALA 101 (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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99A THR* 3.2 8.2 + - - +
100A LYS* 1.4 76.1 - - - +
102A ASP* 1.4 55.7 + - - +
104A ILE* 3.3 7.8 + - - +
105A ASN* 2.8 51.4 + - - +
157A ASP* 4.7 0.4 + - - -
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Residues in contact with ASP 102 (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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97A GLY 4.6 0.9 - - - +
98A MET* 3.9 12.7 - - + -
99A THR* 3.0 47.7 + - - +
101A ALA* 1.4 73.9 - - - +
103A LEU* 1.3 55.4 + - - +
105A ASN* 3.8 7.9 + - - +
106A ASN* 2.8 44.6 + - - +
154A HIS* 4.0 13.7 + - - -
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Residues in contact with LEU 103 (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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98A MET* 4.1 27.6 - - + +
99A THR 2.9 16.7 + - - +
100A LYS* 3.4 7.6 - - - +
102A ASP* 1.3 78.1 - - - +
104A ILE* 1.3 61.9 + - + +
106A ASN* 3.5 7.8 + - - +
107A LEU* 3.1 22.5 + - + +
150A VAL* 5.1 1.6 - - + -
152A THR* 4.7 8.7 - - + -
160A TYR* 4.4 17.0 - - + -
162A TRP* 4.0 32.1 - - + +
172A VAL* 4.1 26.2 - - + -
301A 70O 3.8 26.9 - - + -
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Residues in contact with ILE 104 (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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20A PHE* 4.1 28.5 - - + -
100A LYS* 2.9 35.9 + - + +
101A ALA* 3.3 8.5 + - - +
103A LEU* 1.3 76.0 - - + +
105A ASN* 1.4 69.4 + - - +
107A LEU* 3.2 18.0 + - - +
108A GLY* 3.3 9.4 + - - -
170A PHE* 4.7 10.4 - - + -
172A VAL* 4.0 28.0 - - + -
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Residues in contact with ASN 105 (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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101A ALA* 2.8 38.5 + - - +
102A ASP* 3.8 7.5 + - - +
104A ILE* 1.4 77.6 - - - +
106A ASN* 1.4 58.2 + - - +
108A GLY* 3.2 18.7 + - - +
109A THR 4.5 0.3 + - - -
110A ILE* 3.9 18.5 + - + +
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Residues in contact with ASN 106 (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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98A MET* 3.6 18.6 - - - +
102A ASP* 2.8 33.6 + - - +
103A LEU 3.8 1.1 - - - +
104A ILE 3.3 0.8 - - - -
105A ASN* 1.4 75.8 - - - +
107A LEU* 1.3 58.6 + - - +
108A GLY 3.3 1.2 + - - -
110A ILE* 4.5 16.6 - - - +
111A ALA* 3.8 16.6 - - - +
139A TYR* 4.9 2.1 + - - -
301A 70O 3.7 55.4 - - + +
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Residues in contact with LEU 107 (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 PHE* 4.1 12.1 - - + -
23A GLN* 4.7 7.8 + - - +
26A ILE* 3.4 20.9 - - + +
103A LEU* 3.1 28.0 + - + +
104A ILE* 3.2 9.8 + - - +
106A ASN* 1.3 75.5 - - - +
108A GLY* 1.3 59.3 + - - +
139A TYR* 3.3 27.4 - - - +
162A TRP* 3.2 52.9 - - + +
170A PHE* 4.0 24.3 - - + -
301A 70O 3.9 15.7 - - + -
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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