Contacts of the helix formed by residues 70 - 92 (chain B) in PDB entry 2LUX
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 70 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B PHE* 4.8 2.7 - - - -
27B LYS* 5.1 13.7 - - - +
64B ASN* 4.8 8.0 - - - +
66B ASP* 5.5 2.4 - - - +
68B GLU* 5.2 2.6 - - - +
69B VAL* 1.3 81.5 + - - +
71B PHE* 1.3 67.8 + - - +
72B GLN* 3.0 9.2 - - + +
73B GLU* 2.8 17.9 + - + +
74B TYR* 2.8 22.2 + - - +
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Residues in contact with PHE 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A THR* 4.3 17.9 - - + -
83A VAL* 4.3 30.5 - - + -
86A ASN* 4.4 28.5 - - + +
11B LEU* 4.7 6.3 - - + -
12B ILE* 3.7 44.4 - - + -
15B PHE* 4.1 36.8 - + + -
70B ASP* 1.3 72.7 - - - +
72B GLN* 1.3 63.5 + - - +
74B TYR* 3.1 12.7 + + - +
75B VAL* 2.9 29.4 + - + +
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Residues in contact with GLN 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A VAL* 4.0 35.5 - - + +
70B ASP* 3.0 7.5 - - + +
71B PHE* 1.3 80.4 - - - +
73B GLU* 1.3 66.2 + - + +
75B VAL* 3.2 19.2 - - + +
76B VAL* 3.6 11.0 - - + +
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Residues in contact with GLU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 4.1 14.3 - - + +
62B ASP* 2.8 23.8 + - - +
63B GLU* 4.2 2.8 + - - +
64B ASN* 3.1 9.0 - - - +
68B GLU 3.2 2.5 - - - +
69B VAL* 3.2 29.5 - - + +
70B ASP* 2.8 22.6 + - + +
72B GLN* 1.3 79.0 - - + +
74B TYR* 1.3 59.0 + - - +
76B VAL* 2.8 28.3 - - - +
77B LEU* 2.8 15.2 + - + +
102B CA 2.4 30.0 - - - -
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Residues in contact with TYR 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.4 26.1 - - + +
11B LEU* 4.8 11.0 - - + -
14B VAL* 4.6 3.6 - - - +
15B PHE* 3.5 48.5 - + + -
28B LEU* 4.4 0.7 - - + -
33B LEU* 3.4 34.8 - - + -
36B LEU* 3.5 22.1 - - + +
37B LEU* 4.2 5.0 - - + +
69B VAL* 4.7 6.8 - - + +
70B ASP 2.8 10.9 + - - +
71B PHE* 3.4 15.7 - + - +
73B GLU* 1.3 74.5 - - - +
75B VAL* 1.3 68.8 + - - +
77B LEU* 3.0 7.0 + - + +
78B VAL* 2.9 48.1 + - + +
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Residues in contact with VAL 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ALA* 3.5 40.2 - - + +
80A ALA* 5.3 0.2 - - - -
82A THR* 3.9 21.3 - - + +
83A VAL* 4.0 9.9 - - + -
11B LEU* 4.3 15.0 - - + -
71B PHE* 2.9 22.3 + - + +
72B GLN* 3.2 15.0 - - + +
74B TYR* 1.3 80.6 - - - +
76B VAL* 1.3 72.7 + - + +
78B VAL* 3.0 24.5 - - - +
79B ALA* 3.2 10.6 + - - +
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Residues in contact with VAL 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A VAL* 5.4 12.1 - - + +
79A ALA* 4.4 10.1 - - + -
80A ALA* 5.4 3.1 - - + +
61B LEU* 4.7 20.5 - - + +
72B GLN* 3.6 14.6 - - + +
73B GLU* 2.8 33.4 - - - +
75B VAL* 1.3 87.2 - - + +
77B LEU* 1.3 65.9 + - - +
79B ALA* 3.1 8.9 + - - +
80B ALA* 3.1 23.2 + - - +
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 3.4 15.3 - - + -
37B LEU* 3.4 33.4 - - + -
57B VAL* 5.4 4.9 - - + -
58B MET* 3.2 35.7 - - + -
61B LEU* 3.2 29.9 - - + +
69B VAL* 4.9 4.9 - - + -
73B GLU 2.8 17.7 + - - +
74B TYR* 3.0 9.4 + - - +
76B VAL* 1.3 80.1 - - - +
78B VAL* 1.3 66.3 + - + +
80B ALA* 3.6 7.8 + - - +
81B LEU* 3.4 20.5 + - + +
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Residues in contact with VAL 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 4.4 17.3 - - + -
8A MET* 4.8 1.2 - - - +
11B LEU* 4.6 18.6 - - + -
37B LEU* 4.7 8.1 - - + -
41B LEU* 6.3 1.8 - - + -
74B TYR* 2.9 52.1 + - + +
75B VAL* 3.0 26.5 - - - +
77B LEU* 1.3 81.6 - - + +
79B ALA* 1.3 56.4 + - - +
81B LEU* 3.1 11.2 + - + +
82B THR* 2.8 36.4 + - - +
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Residues in contact with ALA 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A VAL* 3.5 48.6 - - + +
76A VAL* 4.4 5.6 - - + -
79A ALA* 4.2 4.5 - - + -
75B VAL 3.4 13.7 - - - +
76B VAL* 3.1 10.9 + - - +
78B VAL* 1.3 84.2 - - + +
80B ALA* 1.3 62.8 + - - +
82B THR* 3.2 22.7 + - - -
83B VAL* 3.5 2.4 + - - +
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Residues in contact with ALA 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A VAL* 5.3 0.7 - - - -
76A VAL* 5.4 2.9 - - - +
61B LEU* 5.5 9.6 - - + -
76B VAL 3.1 11.6 + - - +
77B LEU* 3.8 10.5 - - - +
78B VAL 3.2 0.2 - - - -
79B ALA* 1.3 76.3 - - - +
81B LEU* 1.3 68.4 + - + +
83B VAL* 3.2 22.9 + - - +
84B ALA* 3.8 2.6 + - - +
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Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A MET* 5.2 1.6 - - + -
37B LEU* 3.6 32.1 - - + -
41B LEU* 3.7 31.9 - - + +
57B VAL* 6.1 5.4 - - + -
77B LEU* 3.4 18.8 - - + +
78B VAL* 3.1 10.5 + - - +
80B ALA* 1.3 77.4 - - + +
82B THR* 1.3 58.5 + - - +
84B ALA* 2.7 37.9 + - + +
85B MET* 3.4 3.3 + - - +
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Residues in contact with THR 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A MET* 3.2 46.5 - - + +
11A LEU* 4.7 7.7 - - + +
12A ILE* 5.5 3.4 - - + +
71A PHE* 4.3 15.7 - - + -
75A VAL* 3.9 17.2 - - + +
78B VAL* 2.8 23.3 + - - +
79B ALA* 3.2 15.3 + - - -
81B LEU* 1.3 76.0 - - - +
83B VAL* 1.3 62.4 + - - +
85B MET* 3.1 15.1 + - + +
86B ASN* 3.4 8.8 + - - +
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Residues in contact with VAL 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PHE* 4.3 16.2 - - + -
72A GLN* 4.0 45.5 - - + +
75A VAL* 4.0 8.5 - - + -
79B ALA 3.8 13.0 - - - +
80B ALA* 3.4 12.8 - - - +
81B LEU 3.1 0.2 - - - -
82B THR* 1.3 77.0 - - - +
84B ALA* 1.3 63.7 + - - +
86B ASN* 3.0 21.6 + - + +
87B ASN* 3.1 6.7 + - + +
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Residues in contact with ALA 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ALA 3.8 1.7 + - - +
81B LEU* 2.7 27.9 + - + +
83B VAL* 1.3 71.5 - - - +
85B MET* 1.3 63.7 + - - +
87B ASN* 2.9 21.0 + - - +
88B PHE* 2.9 12.2 + - - +
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Residues in contact with MET 85 (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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5A GLU* 5.0 5.8 - - - +
8A MET* 3.8 25.4 - - - +
9A GLU* 3.9 34.1 - - + +
12A ILE* 3.2 35.0 - - + -
81B LEU 3.4 2.9 + - - +
82B THR 3.1 11.3 + - - +
84B ALA* 1.3 78.4 - - - +
86B ASN* 1.3 58.7 + - - +
88B PHE* 2.9 17.6 + - + +
89B PHE* 2.8 37.1 + - + +
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Residues in contact with ASN 86 (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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12A ILE* 4.4 22.1 - - + +
71A PHE* 4.4 29.9 - - + +
82B THR 3.4 5.3 + - - +
83B VAL* 3.0 21.6 + - + +
85B MET* 1.3 79.8 - - - +
87B ASN* 1.3 60.9 + - - +
89B PHE* 3.1 28.5 + - - +
90B TRP* 3.3 6.1 + - - +
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Residues in contact with ASN 87 (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 VAL* 3.1 6.2 + - + +
84B ALA* 2.9 16.3 + - - +
86B ASN* 1.3 78.5 - - - +
88B PHE* 1.3 62.8 + - - +
90B TRP* 3.1 25.9 + - - +
91B GLU* 3.8 5.8 + - - +
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Residues in contact with PHE 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B SER* 6.2 0.2 - - - -
84B ALA 2.9 11.0 + - - +
85B MET* 2.9 19.5 + - + +
87B ASN* 1.3 75.1 - - - +
89B PHE* 1.3 58.1 + - - +
91B GLU* 2.7 65.7 + - + +
92B ASN* 3.6 10.1 + - + -
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Residues in contact with PHE 89 (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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12A ILE* 5.8 10.3 - - + -
85B MET* 2.8 21.5 + - + +
86B ASN* 3.1 25.1 + - - +
88B PHE* 1.3 80.1 - - - +
90B TRP* 1.3 58.0 + + - +
92B ASN* 2.5 51.2 + - + +
93B SER* 4.1 18.4 - - - -
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Residues in contact with TRP 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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86B ASN 3.3 3.8 + - - +
87B ASN* 3.1 24.7 + - - +
88B PHE 3.1 0.2 - - - -
89B PHE* 1.3 85.0 - + - +
91B GLU* 1.3 64.6 + - + +
92B ASN 3.2 3.9 + - - +
93B SER* 4.0 9.0 - - - +
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Residues in contact with GLU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ASN 4.3 4.9 - - - +
88B PHE* 2.7 57.1 + - + +
90B TRP* 1.3 77.5 - - + +
92B ASN* 1.3 56.8 + - + +
93B SER* 4.0 3.3 + - - +
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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
----------------------------------------------------------
88B PHE* 3.6 10.3 + - + +
89B PHE* 2.5 37.8 + - + +
90B TRP* 3.9 1.6 - - - +
91B GLU* 1.3 77.8 - - + +
93B SER* 1.3 93.6 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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