Contacts of the helix formed by residues 52 - 62 (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 52 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B LYS* 2.8 29.6 + - - +
51B VAL* 1.3 88.9 - - - +
53B ALA* 1.3 56.3 + - - +
54B VAL* 4.6 1.3 - - - -
55B ASP* 2.8 35.7 + - - +
56B LYS* 3.7 9.9 + - - +
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Residues in contact with ALA 53 (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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49B LYS 4.3 0.2 + - - -
50B ASP* 2.8 16.0 + - - +
52B ASP* 1.3 78.8 - - - +
54B VAL* 1.3 54.6 + - - +
56B LYS* 2.7 41.6 + - + +
57B VAL* 2.9 22.3 + - + +
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Residues in contact with VAL 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LYS* 5.8 2.9 - - + -
33B LEU* 5.9 3.6 - - + -
34B LYS* 4.4 33.7 - - + -
37B LEU* 5.7 11.0 - - + -
50B ASP 4.1 0.4 + - - -
51B VAL* 2.7 30.4 + - + +
52B ASP* 4.6 0.2 - - - -
53B ALA* 1.3 78.8 - - - +
55B ASP* 1.3 81.0 + - - +
57B VAL* 3.1 28.7 - - + +
58B MET* 3.2 20.5 - - + +
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Residues in contact with ASP 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LYS* 3.9 21.5 - - + +
34B LYS* 5.0 4.9 - - - +
52B ASP* 2.8 19.7 + - - +
54B VAL* 1.3 97.0 - - - +
56B LYS* 1.3 63.8 + - + +
58B MET* 3.4 17.7 + - - +
59B LYS* 3.7 6.4 + - - +
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Residues in contact with LYS 56 (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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52B ASP* 4.3 7.9 - - - +
53B ALA* 2.7 33.6 + - + +
55B ASP* 1.3 74.3 - - + +
57B VAL* 1.3 61.2 + - + +
59B LYS* 3.5 17.3 + - - +
60B GLU* 4.0 9.9 + - - +
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Residues in contact with VAL 57 (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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53B ALA* 2.9 17.1 + - + +
54B VAL* 3.1 24.5 - - + +
56B LYS* 1.3 76.2 - - + +
58B MET* 1.3 75.0 + - + +
60B GLU* 3.2 13.3 + - - +
61B LEU* 3.2 35.8 + - + +
77B LEU* 5.4 3.8 - - + -
81B LEU* 6.1 5.8 - - + -
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Residues in contact with MET 58 (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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30B LYS* 4.0 36.6 - - + -
33B LEU* 3.4 17.0 - - + -
54B VAL* 3.2 21.7 + - + +
55B ASP 3.6 8.5 - - - +
56B LYS 3.3 0.8 - - - -
57B VAL* 1.3 79.0 - - + +
59B LYS* 1.3 56.9 + - - +
61B LEU* 3.3 4.5 + - - +
62B ASP* 2.9 34.8 + - + +
67B GLY* 4.3 12.3 - - - +
69B VAL* 3.1 33.2 - - + -
77B LEU* 3.2 31.2 - - - -
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Residues in contact with LYS 59 (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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55B ASP 3.7 6.0 + - - +
56B LYS* 3.5 13.3 + - - +
57B VAL 3.2 0.8 - - - -
58B MET* 1.3 80.0 - - - +
60B GLU* 1.3 62.1 + - + +
62B ASP* 3.0 26.0 - - - +
65B GLY* 5.5 5.7 - - - -
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Residues in contact with GLU 60 (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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56B LYS 4.3 11.2 - - - +
57B VAL* 3.2 12.3 + - - +
59B LYS* 1.3 81.5 - - + +
61B LEU* 1.3 67.7 + - + +
62B ASP 3.5 3.3 + - - -
63B GLU* 4.6 1.4 + - - -
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Residues in contact with LEU 61 (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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57B VAL* 3.2 24.8 + - + +
58B MET* 3.8 5.2 - - - +
60B GLU* 1.3 81.5 - - + +
62B ASP* 1.3 58.3 + - - +
63B GLU* 3.3 7.3 + - - +
69B VAL* 6.0 1.8 - - + -
73B GLU* 4.1 23.9 - - + +
76B VAL* 4.7 19.0 - - + +
77B LEU* 3.2 53.8 - - + +
80B ALA* 5.5 9.2 - - + -
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Residues in contact with ASP 62 (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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58B MET* 2.9 18.4 + - + +
59B LYS* 3.0 16.4 - - - +
60B GLU 3.3 1.5 - - - +
61B LEU* 1.3 75.4 - - - +
63B GLU* 1.3 62.2 + - - +
64B ASN* 3.1 8.3 + - - +
65B GLY* 2.8 13.8 + - - +
66B ASP* 2.3 45.3 + - - +
67B GLY* 2.8 7.9 + - - +
68B GLU 3.8 2.5 - - - +
69B VAL* 5.3 3.4 - - + -
73B GLU* 2.8 13.7 - - - +
102B CA 2.2 23.2 - - - -
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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