Contacts of the helix formed by residues 99 - 109 (chain B) in PDB entry 5LEK
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 ILE 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B GLU* 3.7 37.7 + - + +
37B TYR* 4.8 8.1 - - - +
38B CYS* 5.0 0.9 - - + +
70B MET* 3.8 19.7 - - + -
72B GLY* 3.6 16.8 - - - +
73B PHE 3.2 28.0 - - - +
74B ILE* 4.3 9.8 - - + +
77B GLU* 3.9 28.8 - - + +
97B ILE 3.5 4.4 + - - -
98B LYS* 1.3 73.4 - - - +
100B ASN* 1.3 66.7 + - + +
102B LEU* 3.7 16.4 - - + +
103B LYS* 3.7 6.9 + - - +
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Residues in contact with ASN 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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77B GLU* 2.9 29.0 - - - +
98B LYS* 3.2 4.6 - - + +
99B ILE* 1.3 82.9 - - + +
101B GLU* 1.3 64.6 + - - +
103B LYS* 3.1 24.1 + - - +
104B GLU* 3.7 12.0 + - - +
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Residues in contact with GLU 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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15B ASN* 4.3 13.5 - - - +
17B ILE* 4.3 19.6 - - - +
97B ILE* 4.9 3.7 - - + +
98B LYS* 3.3 19.8 + - + +
100B ASN* 1.3 76.5 - - - +
102B LEU* 1.3 57.1 + - - +
104B GLU* 2.8 39.2 + - + +
105B LEU* 3.0 27.6 + - + +
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Residues in contact with LEU 102 (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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8B PHE* 5.1 6.5 - - + -
12B LEU* 5.8 0.2 - - + -
38B CYS* 3.6 27.8 - - + -
70B MET* 3.5 33.2 - - + -
74B ILE* 3.6 13.9 - - + -
97B ILE* 3.8 29.9 - - + +
98B LYS 3.2 7.3 + - - +
99B ILE* 3.7 12.1 - - + +
100B ASN 3.3 0.2 - - - -
101B GLU* 1.3 75.8 - - - +
103B LYS* 1.3 63.1 + - - +
105B LEU* 3.1 19.5 + - + -
106B LEU* 3.1 42.5 + - + +
116B VAL* 5.5 2.7 - - + -
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Residues in contact with LYS 103 (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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114A PHE* 3.7 30.6 - - + -
74B ILE* 3.1 38.8 + - + +
75B ASP* 3.2 35.6 + - - +
77B GLU* 4.5 13.4 + - - +
99B ILE 3.7 4.9 + - - +
100B ASN* 3.1 16.9 + - - +
101B GLU 3.0 0.4 - - - -
102B LEU* 1.3 80.1 - - - +
104B GLU* 1.3 56.7 + - + +
106B LEU* 3.9 1.2 + - - +
107B SER* 2.8 31.0 + - - -
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Residues in contact with GLU 104 (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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100B ASN* 4.4 13.0 + - - +
101B GLU* 2.8 21.3 + - + +
103B LYS* 1.3 78.2 - - + +
105B LEU* 1.3 62.6 + - + +
107B SER* 3.7 6.1 + - - -
108B LYS* 3.1 27.4 + - + +
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Residues in contact with LEU 105 (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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8B PHE* 6.5 0.2 - - + -
11B TYR* 2.7 40.6 + - + +
12B LEU* 4.2 18.2 - - + -
15B ASN* 3.8 36.6 - - + +
17B ILE* 4.0 19.1 - - + -
97B ILE* 4.4 9.9 - - + -
101B GLU* 3.0 34.6 + - + +
102B LEU* 3.1 16.7 + - + +
104B GLU* 1.3 78.3 - - + +
106B LEU* 1.3 66.9 + - + +
108B LYS* 3.4 11.8 + - - -
109B ASN 3.5 4.5 + - - +
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Residues in contact with LEU 106 (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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114A PHE* 5.2 3.8 - - + -
117A PHE* 5.3 4.0 - - + -
8B PHE* 4.3 11.7 - - + -
11B TYR* 5.9 0.7 - - + -
74B ILE* 5.1 6.5 - - + -
102B LEU* 3.1 42.4 + - + +
103B LYS 4.5 2.5 - - - +
105B LEU* 1.3 80.1 - - + +
107B SER* 1.3 62.8 + - - +
109B ASN 2.9 21.2 - - - +
110B LEU* 4.3 1.4 + - - +
112B HIS* 3.7 33.0 - - + +
113B PHE* 3.5 43.7 - - + +
116B VAL* 4.0 22.7 - - + -
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Residues in contact with SER 107 (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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110A LEU* 3.8 30.9 - - - +
114A PHE* 3.4 19.1 - - - -
103B LYS* 2.8 23.2 + - - +
104B GLU* 4.1 7.4 - - - -
105B LEU 3.3 1.0 - - - -
106B LEU* 1.3 78.6 - - - +
108B LYS* 1.3 63.9 + - - +
110B LEU* 4.8 6.1 - - - +
113B PHE* 5.0 2.5 - - - -
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Residues in contact with LYS 108 (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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11B TYR* 3.3 23.5 - - + +
15B ASN* 2.9 25.9 + - - +
104B GLU* 3.1 19.7 - - + +
105B LEU* 4.5 6.9 - - - +
106B LEU 3.2 0.8 - - - -
107B SER* 1.3 80.7 - - - +
109B ASN* 1.3 58.9 + - + +
110B LEU* 4.0 3.5 + - - +
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Residues in contact with ASN 109 (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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11B TYR* 3.9 27.0 - - + +
105B LEU 3.5 2.4 + - - +
106B LEU* 2.9 19.7 - - - +
108B LYS* 1.3 76.6 - - + +
110B LEU* 1.3 60.7 + - - +
111B THR* 2.8 37.0 + - - -
112B HIS* 3.2 31.6 + - + +
113B PHE 3.4 12.0 + - - -
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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