Contacts of the helix formed by residues 42 - 60 (chain Q) 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 Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43Q TRP* 1.3 78.5 + - - +
44Q GLU* 3.1 6.7 + - - +
45Q LYS* 3.2 10.3 + - - +
46Q GLN* 2.7 37.6 + - + +
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Residues in contact with TRP 43 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F ARG 6.0 1.6 - - - -
92F ASN 4.6 8.5 - - - -
93F GLU* 4.2 23.1 - - - +
42Q ALA* 1.3 88.3 - - - +
44Q GLU* 1.3 89.7 + - + +
46Q GLN* 3.3 8.8 + - - +
47Q GLN* 2.8 77.5 + - - +
135Q LYS* 4.7 26.9 - - + -
138Q LEU* 5.1 4.7 - - + -
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Residues in contact with GLU 44 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42Q ALA 3.1 3.5 - - - +
43Q TRP* 1.3 108.7 + - + +
45Q LYS* 1.3 61.4 + - - +
47Q GLN* 4.6 1.3 - - - -
48Q ARG* 3.1 25.2 + - - +
134Q LEU* 3.2 37.8 - - + +
135Q LYS* 3.7 31.2 + - + +
138Q LEU* 3.9 12.7 - - + +
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Residues in contact with LYS 45 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42Q ALA* 3.2 6.6 + - - +
44Q GLU* 1.3 79.1 - - - +
46Q GLN* 1.3 76.5 + - - +
48Q ARG* 3.5 11.0 + - - +
49Q LYS* 3.2 21.5 + - + +
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Residues in contact with GLN 46 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42Q ALA* 2.7 39.7 + - + +
43Q TRP* 3.3 8.0 + - - +
45Q LYS* 1.3 92.0 - - - +
47Q GLN* 1.3 65.6 + - - +
49Q LYS* 2.9 18.8 + - - +
50Q THR* 2.9 29.4 + - - +
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Residues in contact with GLN 47 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F ASN 4.3 2.0 + - - +
93F GLU 4.4 2.0 + - - -
95F ARG* 2.3 60.9 + - + +
43Q TRP* 2.8 56.0 + - - +
44Q GLU* 4.0 3.6 - - - +
46Q GLN* 1.3 73.4 - - - +
48Q ARG* 1.3 56.6 + - - +
50Q THR* 4.6 3.4 - - - +
51Q PHE* 2.9 53.8 + - + -
138Q LEU* 4.0 17.1 - - + +
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Residues in contact with ARG 48 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44Q GLU 3.1 18.2 + - - +
45Q LYS* 3.6 11.3 + - - +
46Q GLN 3.1 0.8 - - - -
47Q GLN* 1.3 76.1 - - - +
49Q LYS* 1.3 56.7 + - - +
51Q PHE* 4.2 0.2 - - - +
52Q THR* 2.5 41.4 + - - +
67Q GLU 4.6 2.1 + - - -
68Q ASN* 3.0 30.2 - - - +
69Q ILE* 3.7 17.2 - - + +
70Q GLU* 2.5 42.2 + - - -
134Q LEU* 4.2 16.4 - - - -
138Q LEU* 3.9 16.8 - - + +
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Residues in contact with LYS 49 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45Q LYS 3.2 9.2 + - - +
46Q GLN* 2.9 20.0 + - - +
48Q ARG* 1.3 82.4 - - - +
50Q THR* 1.3 73.4 + - - +
52Q THR* 3.6 4.4 - - - -
53Q ALA* 3.0 31.1 + - + +
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Residues in contact with THR 50 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46Q GLN* 2.9 17.8 + - - +
47Q GLN* 4.1 4.7 - - - -
49Q LYS* 1.3 90.1 + - - +
51Q PHE* 1.3 69.4 + - + +
53Q ALA* 3.3 6.3 + - - +
54Q TRP* 2.9 30.1 + - + +
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Residues in contact with PHE 51 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F ARG* 0.9 148.3 - - + -
47Q GLN* 2.9 39.9 + - + +
50Q THR* 1.3 82.7 - - + +
52Q THR* 1.3 58.1 + - - +
54Q TRP* 3.2 6.7 + - - +
55Q CYS* 2.8 33.8 + - - -
69Q ILE* 4.0 15.9 - - + -
138Q LEU* 3.3 29.6 - - + -
141Q ILE* 4.0 13.7 - - + -
142Q TRP* 3.7 3.8 - + + -
145Q ILE* 3.7 15.5 - - + -
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Residues in contact with THR 52 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48Q ARG* 2.5 28.3 + - - +
49Q LYS* 3.6 5.2 - - - -
51Q PHE* 1.3 76.7 - - - +
53Q ALA* 1.3 63.7 + - - +
55Q CYS* 3.2 2.3 + - - +
56Q ASN* 2.9 39.4 + - - +
66Q ILE* 4.0 16.6 - - + +
67Q GLU 4.0 20.8 + - - +
69Q ILE* 3.6 25.5 + - + +
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Residues in contact with ALA 53 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49Q LYS* 3.0 19.6 + - + +
50Q THR* 3.6 6.5 - - - +
52Q THR* 1.3 76.6 - - - +
54Q TRP* 1.3 62.6 + - - +
56Q ASN* 3.4 6.9 + - - +
57Q SER* 3.0 24.8 + - - -
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Residues in contact with TRP 54 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50Q THR* 2.9 17.0 + - + +
51Q PHE* 3.5 9.4 - - - +
52Q THR 3.2 0.2 - - - -
53Q ALA* 1.3 77.5 - - - +
55Q CYS* 1.3 85.9 + - - +
57Q SER* 2.7 25.9 + - - -
58Q HIS* 3.5 36.8 + + - -
82Q LEU* 4.1 25.8 - - + -
86Q ILE* 4.1 25.6 - - + -
141Q ILE* 4.9 1.1 - - + -
144Q ILE* 4.2 5.4 - - + -
145Q ILE* 3.6 46.6 - - + +
148Q PHE* 5.9 0.2 - - + -
149Q ALA* 4.2 24.4 - - + +
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Residues in contact with CYS 55 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51Q PHE 2.8 26.8 + - - +
52Q THR 3.6 4.3 - - - +
54Q TRP* 1.3 82.0 - - - +
56Q ASN* 1.3 58.6 + - - +
58Q HIS* 3.1 5.4 + - - +
59Q LEU* 2.9 34.5 + - + +
66Q ILE* 4.1 14.4 - - + -
69Q ILE* 4.7 2.0 - - - -
73Q PHE* 3.9 13.9 - - + -
82Q LEU* 3.7 26.8 - - + +
141Q ILE* 3.8 31.0 - - - -
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Residues in contact with ASN 56 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52Q THR* 2.9 26.7 + - - +
53Q ALA* 3.7 7.2 - - - +
55Q CYS* 1.3 71.6 - - - +
57Q SER* 1.3 56.4 + - - +
58Q HIS 3.0 5.6 - - - -
59Q LEU* 4.2 4.5 - - - +
60Q ARG* 3.0 20.0 + - - +
65Q GLN* 2.7 49.0 + - - +
66Q ILE* 2.7 54.6 - - - +
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Residues in contact with SER 57 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53Q ALA 3.0 14.8 + - - -
54Q TRP* 2.7 25.7 + - - -
56Q ASN* 1.3 75.4 - - - +
58Q HIS* 1.3 65.8 + - - +
60Q ARG* 2.9 43.3 + - - +
61Q LYS* 3.5 11.8 + - - -
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Residues in contact with HIS 58 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54Q TRP* 3.5 56.4 + + - -
55Q CYS 3.1 6.6 + - - +
56Q ASN 3.0 0.2 - - - -
57Q SER* 1.3 84.9 + - - +
59Q LEU* 1.3 66.1 + - - +
60Q ARG 3.1 1.6 - - - -
61Q LYS* 3.0 48.4 + - - +
62Q ALA 4.1 0.7 + - - -
82Q LEU* 3.8 14.1 - - + -
85Q VAL* 3.6 17.3 - - + +
86Q ILE* 3.5 21.2 - - + +
149Q ALA* 5.8 1.4 - - - +
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Residues in contact with LEU 59 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55Q CYS* 2.9 24.2 + - + +
56Q ASN* 4.2 10.8 - - - +
58Q HIS* 1.3 76.2 - - - +
60Q ARG* 1.3 54.2 + - - +
62Q ALA* 2.7 29.5 + - - +
63Q GLY 3.3 6.1 + - - -
64Q THR* 3.3 35.4 + - + +
65Q GLN* 4.2 2.0 - - - +
66Q ILE* 3.8 29.2 - - + +
73Q PHE* 4.4 13.7 - - + -
78Q LYS* 3.6 11.7 - - + +
81Q LEU* 4.3 8.7 - - + +
82Q LEU* 3.6 35.4 - - + +
85Q VAL* 5.0 1.8 - - + -
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Residues in contact with ARG 60 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56Q ASN 3.0 18.5 + - - +
57Q SER* 2.9 38.1 + - - +
59Q LEU* 1.3 77.0 - - - +
61Q LYS* 1.3 66.8 + - + +
62Q ALA 3.1 0.4 - - - -
63Q GLY* 3.1 17.9 + - - +
64Q THR 3.3 10.5 + - - +
65Q 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
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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