Contacts of the helix formed by residues 70 - 92 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A PHE* 4.8 2.7 - - - -
27A LYS* 5.1 14.4 - - - +
64A ASN* 4.8 8.3 - - - +
66A ASP* 5.5 2.6 - - - +
68A GLU* 5.2 2.9 - - - +
69A VAL* 1.3 82.2 - - - +
71A PHE* 1.3 69.6 + - - +
72A GLN* 3.0 9.6 - - + +
73A GLU* 2.8 17.9 + - + +
74A TYR* 2.8 21.6 + - - +
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Residues in contact with PHE 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.7 5.8 - - + -
12A ILE* 3.7 44.6 - - + -
15A PHE* 4.1 37.0 - + + -
70A ASP* 1.3 72.4 - - - +
72A GLN* 1.3 63.4 + - - +
74A TYR* 3.1 13.1 + + - +
75A VAL* 2.9 29.6 + - + +
82B THR* 4.3 24.0 - - + -
83B VAL* 4.3 25.1 - - + -
86B ASN* 4.4 27.8 - - + +
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Residues in contact with GLN 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ASP* 3.0 7.0 - - + +
71A PHE* 1.3 80.8 - - - +
73A GLU* 1.3 66.8 + - + +
75A VAL* 3.2 19.4 - - + +
76A VAL* 3.6 11.2 - - + +
83B VAL* 4.0 35.8 - - + +
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Residues in contact with GLU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 4.2 13.8 - - + +
62A ASP* 2.8 23.0 + - - +
63A GLU* 4.2 2.9 + - - +
64A ASN* 3.1 8.5 - - - +
68A GLU 3.2 2.1 - - - +
69A VAL* 3.2 29.2 - - + +
70A ASP* 2.8 22.1 + - + +
72A GLN* 1.3 79.7 - - + +
74A TYR* 1.3 58.5 + - - +
76A VAL* 2.8 28.2 - - - +
77A LEU* 2.8 15.0 + - + +
202A CA 2.4 30.5 - - - -
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Residues in contact with TYR 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.8 11.2 - - + -
14A VAL* 4.6 3.5 - - - +
15A PHE* 3.5 49.1 - + + -
28A LEU* 4.4 0.7 - - + -
33A LEU* 3.4 34.5 - - + -
36A LEU* 3.5 22.1 - - + +
37A LEU* 4.2 5.3 - - + +
69A VAL* 4.7 7.5 - - + +
70A ASP 2.8 11.5 + - - +
71A PHE* 3.4 15.3 - + - +
73A GLU* 1.3 75.3 - - - +
75A VAL* 1.3 69.6 + - - +
77A LEU* 3.4 6.4 - - + +
78A VAL* 2.9 46.4 + - + +
4B LEU* 3.4 26.2 - - + +
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Residues in contact with VAL 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.4 15.3 - - + -
71A PHE* 2.9 22.9 + - + +
72A GLN* 3.2 15.3 - - + +
74A TYR* 1.3 80.5 - - - +
76A VAL* 1.3 71.5 + - + +
78A VAL* 3.0 24.3 - - - +
79A ALA* 3.1 10.4 + - - +
79B ALA* 3.5 39.4 - - + +
80B ALA* 5.3 0.2 - - - -
82B THR* 3.9 20.9 - - + +
83B VAL* 4.0 10.1 - - + -
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Residues in contact with VAL 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 4.6 20.5 - - + +
72A GLN* 3.6 14.8 - - + +
73A GLU* 2.8 33.9 - - - +
75A VAL* 1.3 86.1 - - + +
77A LEU* 1.3 66.9 + - - +
79A ALA* 3.1 8.6 + - - +
80A ALA* 3.1 23.2 + - - +
76B VAL* 5.4 12.1 - - + +
79B ALA* 4.4 10.1 - - + -
80B ALA* 5.4 3.6 - - + +
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Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.4 16.6 - - + -
37A LEU* 3.4 32.8 - - + -
57A VAL* 5.4 4.7 - - + -
58A MET* 3.2 35.0 - - + -
61A LEU* 3.2 30.2 - - + +
69A VAL* 4.9 4.9 - - + -
73A GLU 2.8 20.0 + - - +
74A TYR* 3.4 9.2 - - + +
76A VAL* 1.3 78.6 - - - +
78A VAL* 1.3 65.3 - - + +
80A ALA* 3.5 8.2 + - - +
81A LEU* 3.4 19.7 + - + +
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Residues in contact with VAL 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.6 19.1 - - + -
37A LEU* 4.7 8.1 - - + -
74A TYR* 2.9 52.1 + - + +
75A VAL* 3.0 26.5 - - - +
77A LEU* 1.3 81.9 - - + +
79A ALA* 1.3 56.2 + - - +
81A LEU* 3.1 10.1 + - - +
82A THR* 2.8 36.0 + - - +
4B LEU* 4.4 16.8 - - + -
8B MET* 4.8 1.8 - - + +
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Residues in contact with ALA 79 (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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75A VAL 3.4 14.4 - - - +
76A VAL* 3.1 10.7 + - - +
78A VAL* 1.3 84.1 - - + +
80A ALA* 1.3 63.2 + - - +
82A THR* 3.2 22.5 + - - -
83A VAL* 3.5 2.6 + - - +
75B VAL* 3.5 47.9 - - + +
76B VAL* 4.4 5.4 - - + -
79B ALA* 4.2 4.9 - - + -
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Residues in contact with ALA 80 (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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61A LEU* 5.5 9.6 - - + -
76A VAL 3.1 11.8 + - - +
77A LEU* 3.8 10.3 - - - +
79A ALA* 1.3 76.4 - - - +
81A LEU* 1.3 67.7 + - + +
83A VAL* 3.2 24.1 + - - +
84A ALA* 3.8 2.6 + - - +
75B VAL* 5.3 0.7 - - - -
76B VAL* 5.4 4.0 - - + +
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Residues in contact with LEU 81 (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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37A LEU* 3.6 32.5 - - + -
41A LEU* 3.7 30.8 - - + +
57A VAL* 6.1 5.4 - - + -
77A LEU* 3.4 19.5 - - + +
78A VAL* 3.1 9.4 + - - +
80A ALA* 1.3 77.4 - - + +
82A THR* 1.3 57.8 + - - +
84A ALA* 2.7 37.7 + - + +
85A MET* 3.4 3.1 + - - +
8B MET* 5.2 1.6 - - + -
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Residues in contact with THR 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A VAL* 2.8 22.9 + - - +
79A ALA* 3.2 14.8 + - - -
81A LEU* 1.3 75.2 - - - +
83A VAL* 1.3 62.7 + - - +
85A MET* 3.1 14.4 + - - +
86A ASN* 3.4 8.8 + - - +
8B MET* 3.2 46.9 - - + +
11B LEU* 4.7 6.8 - - + +
12B ILE* 5.4 3.5 - - + +
71B PHE* 4.3 15.9 - - + -
75B VAL* 3.9 19.1 - - + +
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Residues in contact with VAL 83 (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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79A ALA 3.8 13.0 - - - +
80A ALA* 3.4 12.1 - - - +
81A LEU 3.1 1.0 - - - -
82A THR* 1.3 77.0 - - - +
84A ALA* 1.3 63.9 + - - +
86A ASN* 3.0 20.4 + - + +
87A ASN* 3.1 6.8 + - + +
71B PHE* 4.3 16.8 - - + -
72B GLN* 4.0 45.5 - - + +
75B VAL* 4.0 9.0 - - + -
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Residues in contact with ALA 84 (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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80A ALA 3.8 1.7 + - - +
81A LEU* 2.7 28.7 + - + +
83A VAL* 1.3 71.1 - - - +
85A MET* 1.3 62.9 + - - +
87A ASN* 2.9 20.3 + - + +
88A PHE* 2.9 12.6 + - - +
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Residues in contact with MET 85 (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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81A LEU 3.4 2.9 + - - +
82A THR 3.1 11.4 + - - +
84A ALA* 1.3 77.1 - - - +
86A ASN* 1.3 58.4 + - - +
88A PHE* 2.9 18.0 + - + +
89A PHE* 2.8 36.7 + - + +
5B GLU* 5.0 5.4 - - - +
8B MET* 3.8 27.1 - - - +
9B GLU* 3.9 33.2 - - + +
12B ILE* 3.2 35.0 - - + -
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Residues in contact with ASN 86 (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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82A THR 3.4 4.8 + - - +
83A VAL* 3.0 22.0 + - + +
85A MET* 1.3 79.5 - - - +
87A ASN* 1.3 60.8 + - - +
89A PHE* 3.1 28.1 + - - +
90A TRP* 3.3 5.5 + - - +
12B ILE* 4.4 23.0 - - + +
71B PHE* 4.4 28.7 - - + +
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Residues in contact with ASN 87 (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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83A VAL* 3.1 6.2 + - + +
84A ALA* 2.9 16.5 + - - +
86A ASN* 1.3 79.0 - - - +
88A PHE* 1.3 63.1 + - - +
90A TRP* 3.1 25.5 + - - +
91A GLU* 3.8 5.8 + - - +
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Residues in contact with PHE 88 (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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84A ALA 2.9 11.2 + - - +
85A MET* 2.9 20.6 + - + +
87A ASN* 1.3 75.1 - - - +
89A PHE* 1.3 59.0 + - - +
91A GLU* 2.7 64.9 + - + +
92A ASN* 3.6 9.8 + - + -
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Residues in contact with PHE 89 (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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85A MET* 2.8 22.6 + - + +
86A ASN* 3.1 23.8 - - - +
88A PHE* 1.3 80.1 - - - +
90A TRP* 1.3 57.7 + + - +
92A ASN* 2.5 50.3 + - + +
93A SER* 4.1 19.1 - - - -
12B ILE* 5.8 10.5 - - + -
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Residues in contact with TRP 90 (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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86A ASN 3.3 4.2 + - - +
87A ASN* 3.1 23.7 + - - +
88A PHE 3.1 0.4 - - - -
89A PHE* 1.3 85.8 - + - +
91A GLU* 1.3 63.9 + - + +
92A ASN 3.2 3.9 + - - +
93A SER* 4.0 9.5 - - - +
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Residues in contact with GLU 91 (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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87A ASN 4.3 5.6 - - - +
88A PHE* 2.7 56.2 + - + +
90A TRP* 1.3 76.5 - - + +
92A ASN* 1.3 58.0 + - + +
93A SER* 3.9 3.5 + - - +
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Residues in contact with ASN 92 (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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88A PHE* 3.6 11.0 + - + +
89A PHE* 2.5 36.7 + - + +
90A TRP* 3.9 1.3 - - - +
91A GLU* 1.3 79.2 - - + +
93A SER* 1.3 93.9 + - - +
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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