Contacts of the helix formed by residues 42 - 60 (chain R) in PDB entry 3LUE
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 ALA 42 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43R TRP* 1.3 79.7 + - - +
44R GLU* 3.1 6.8 + - - +
45R LYS* 3.2 10.1 + - - +
46R GLN* 2.7 37.8 + - + +
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Residues in contact with TRP 43 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I ARG 6.0 1.8 - - - -
92I ASN 4.6 8.5 - - - -
93I GLU* 4.2 22.0 - - - +
42R ALA* 1.3 88.7 - - - +
44R GLU* 1.3 89.9 + - + +
46R GLN* 3.2 8.9 + - - +
47R GLN* 2.8 77.3 + - + +
135R LYS* 4.7 28.0 - - + -
138R LEU* 5.1 4.9 - - + -
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Residues in contact with GLU 44 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42R ALA 3.1 4.0 - - - +
43R TRP* 1.3 108.9 + - + +
45R LYS* 1.3 62.6 + - - +
47R GLN* 4.6 1.1 - - - -
48R ARG* 3.1 25.0 + - - +
134R LEU* 3.2 36.9 - - + +
135R LYS* 3.7 31.4 + - + +
138R LEU* 3.9 12.5 - - + +
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Residues in contact with LYS 45 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42R ALA* 3.2 6.2 + - - +
44R GLU* 1.3 78.0 - - - +
46R GLN* 1.3 78.3 + - - +
48R ARG* 3.5 11.2 + - - +
49R LYS* 3.2 21.3 + - - +
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Residues in contact with GLN 46 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42R ALA* 2.7 38.7 + - + +
43R TRP* 3.2 7.8 + - - +
45R LYS* 1.3 90.5 - - - +
47R GLN* 1.3 65.7 + - - +
49R LYS* 2.9 18.6 + - - +
50R THR* 2.9 29.3 + - - +
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Residues in contact with GLN 47 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92I ASN 4.3 1.8 + - - +
93I GLU 4.4 2.2 + - - -
95I ARG* 2.3 60.7 + - + +
43R TRP* 2.8 55.8 + - - +
44R GLU 4.0 3.1 - - - +
46R GLN* 1.3 73.2 - - - +
48R ARG* 1.3 57.2 + - - +
50R THR* 4.6 3.6 - - - +
51R PHE* 2.9 53.1 + - + -
138R LEU* 4.0 16.5 - - + +
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Residues in contact with ARG 48 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44R GLU 3.1 17.8 + - - +
45R LYS* 3.6 11.1 + - - +
46R GLN 3.1 0.8 - - - -
47R GLN* 1.3 77.9 - - - +
49R LYS* 1.3 56.8 + - - +
51R PHE* 4.2 0.2 - - - +
52R THR* 2.5 41.0 + - - +
67R GLU 4.6 2.1 + - - -
68R ASN* 3.0 29.8 - - - +
69R ILE* 3.7 17.5 - - + +
70R GLU* 2.5 43.5 + - - -
134R LEU* 4.2 16.4 - - - -
138R LEU* 3.9 15.2 - - + +
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Residues in contact with LYS 49 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45R LYS* 3.2 9.4 + - + +
46R GLN* 2.9 19.8 + - - +
48R ARG* 1.3 83.0 - - - +
50R THR* 1.3 74.0 + - - +
52R THR* 3.6 4.3 - - - -
53R ALA* 3.0 31.4 + - + +
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Residues in contact with THR 50 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46R GLN* 2.9 17.6 + - - +
47R GLN* 4.1 5.1 - - - -
49R LYS* 1.3 90.0 + - - +
51R PHE* 1.3 68.8 + - + +
53R ALA* 3.3 7.1 + - + +
54R TRP* 2.9 30.9 + - + +
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Residues in contact with PHE 51 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95I ARG* 0.8 150.1 - - + -
47R GLN* 2.9 39.9 + - + +
50R THR* 1.3 82.2 - - + +
52R THR* 1.3 58.1 + - - +
54R TRP* 3.2 5.9 + - - +
55R CYS* 2.8 33.8 + - - -
69R ILE* 4.0 16.4 - - + -
138R LEU* 3.3 29.4 - - + -
141R ILE* 4.0 13.9 - - + -
142R TRP* 3.7 3.6 - + + -
145R ILE* 3.7 15.3 - - + -
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Residues in contact with THR 52 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48R ARG* 2.5 28.9 + - - +
49R LYS* 3.6 5.4 - - - -
51R PHE* 1.3 77.3 - - - +
53R ALA* 1.3 64.2 + - - +
55R CYS* 3.2 2.6 + - - +
56R ASN* 2.9 38.7 + - - +
66R ILE* 4.0 17.3 - - + +
67R GLU 4.0 20.9 + - - +
69R ILE* 3.6 25.1 + - + +
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Residues in contact with ALA 53 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49R LYS* 3.0 19.0 + - + +
50R THR* 3.6 5.8 - - - +
52R THR* 1.3 76.7 - - - +
54R TRP* 1.3 64.0 + - - +
56R ASN* 3.4 7.2 + - - +
57R SER* 3.0 23.9 + - - -
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Residues in contact with TRP 54 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50R THR* 2.9 17.2 + - + +
51R PHE* 3.5 9.6 - - - +
52R THR 3.2 0.2 - - - -
53R ALA* 1.3 77.1 - - - +
55R CYS* 1.3 85.6 + - - +
57R SER* 2.7 25.6 + - - -
58R HIS* 3.5 35.8 + + - -
82R LEU* 4.1 24.9 - - + -
86R ILE* 4.1 26.0 - - + -
141R ILE* 4.9 1.1 - - + -
144R ILE* 4.2 6.1 - - + -
145R ILE* 3.6 46.6 - - + +
149R ALA* 4.2 25.3 - - + +
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Residues in contact with CYS 55 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51R PHE 2.8 26.7 + - - +
52R THR 3.6 4.0 - - - +
54R TRP* 1.3 82.6 - - - +
56R ASN* 1.3 58.8 + - - +
58R HIS* 3.1 5.7 + - - +
59R LEU* 2.9 34.9 + - + +
66R ILE* 4.1 14.6 - - + -
69R ILE* 4.7 2.0 - - - -
73R PHE* 3.9 13.7 - - + -
82R LEU* 3.7 26.3 - - + +
141R ILE* 3.8 31.2 - - - -
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Residues in contact with ASN 56 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52R THR* 2.9 26.9 + - - +
53R ALA* 3.7 7.3 - - - +
55R CYS* 1.3 72.9 - - - +
57R SER* 1.3 55.8 + - - +
58R HIS 3.0 5.6 - - - -
59R LEU* 4.2 4.0 - - - +
60R ARG* 3.0 18.9 + - - +
65R GLN* 2.7 49.3 + - - +
66R ILE* 2.7 54.2 - - - +
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Residues in contact with SER 57 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53R ALA 3.0 14.2 + - - -
54R TRP* 2.7 26.0 + - - -
56R ASN* 1.3 74.5 - - - +
58R HIS* 1.3 65.2 + - - +
60R ARG* 2.9 44.1 + - - +
61R LYS* 3.5 11.6 + - - -
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Residues in contact with HIS 58 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54R TRP* 3.5 56.8 + + - -
55R CYS 3.1 6.4 + - - +
56R ASN 3.0 0.6 - - - -
57R SER* 1.3 84.7 + - - +
59R LEU* 1.3 66.6 + - - +
60R ARG 3.1 1.8 - - - -
61R LYS* 3.0 48.2 + - - +
62R ALA 4.1 0.3 + - - -
82R LEU* 3.8 13.7 - - + -
85R VAL* 3.6 16.3 - - + +
86R ILE* 3.5 20.0 - - + +
149R ALA* 5.8 1.2 - - - +
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Residues in contact with LEU 59 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55R CYS* 2.9 23.7 + - + +
56R ASN* 3.4 11.0 + - - +
58R HIS* 1.3 77.0 - - - +
60R ARG* 1.3 53.6 + - - +
62R ALA* 2.7 29.5 + - - +
63R GLY 3.3 6.4 + - - -
64R THR* 3.3 36.3 + - + +
65R GLN* 4.2 1.1 - - - +
66R ILE* 3.8 29.6 - - + +
73R PHE* 4.4 13.9 - - + -
78R LYS* 3.6 12.6 - - + +
81R LEU* 4.3 8.5 - - + +
82R LEU* 3.6 35.9 - - + +
85R VAL* 5.0 1.8 - - + -
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Residues in contact with ARG 60 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56R ASN 3.0 19.1 + - - +
57R SER* 2.9 37.1 + - - +
59R LEU* 1.3 76.4 - - - +
61R LYS* 1.3 66.8 + - + +
62R ALA 3.1 0.2 - - - -
63R GLY* 3.1 18.1 + - - +
64R THR 3.3 10.7 + - - +
65R GLN* 3.5 12.8 - - - +
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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