Contacts of the helix formed by residues 42 - 60 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43S TRP* 1.3 78.0 + - - +
44S GLU* 3.1 5.9 + - - +
45S LYS* 3.2 10.3 + - - +
46S GLN* 2.7 38.5 + - + +
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Residues in contact with TRP 43 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H ARG 6.0 1.6 - - - -
92H ASN 4.6 8.5 - - - -
93H GLU* 4.2 22.4 - - - +
42S ALA* 1.3 88.3 - - - +
44S GLU* 1.3 91.3 + - + +
46S GLN* 3.3 8.8 + - - +
47S GLN* 2.8 76.9 + - - +
135S LYS* 4.7 26.9 - - + -
138S LEU* 5.1 5.2 - - + -
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Residues in contact with GLU 44 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42S ALA 3.1 3.6 - - - +
43S TRP* 1.3 109.3 + - + +
45S LYS* 1.3 61.0 + - - +
47S GLN* 4.6 1.1 - - - -
48S ARG* 3.1 25.0 + - - +
134S LEU* 3.2 37.8 - - + +
135S LYS* 3.7 30.2 + - + +
138S LEU* 3.9 12.8 - - + +
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Residues in contact with LYS 45 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42S ALA* 3.2 5.8 + - - +
44S GLU* 1.3 79.2 - - - +
46S GLN* 1.3 78.3 + - - +
48S ARG* 3.5 10.8 + - - +
49S LYS* 3.2 21.5 + - + +
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Residues in contact with GLN 46 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42S ALA* 2.7 39.1 + - + +
43S TRP* 3.6 7.2 - - - +
45S LYS* 1.3 91.6 - - - +
47S GLN* 1.3 68.1 + - - +
49S LYS* 2.9 20.0 + - - +
50S THR* 2.9 27.8 + - - +
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Residues in contact with GLN 47 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92H ASN 4.3 1.2 + - - +
93H GLU 4.4 2.4 + - - -
95H ARG* 2.3 61.0 + - + +
43S TRP* 2.8 55.5 + - + +
44S GLU 4.0 3.1 - - - +
46S GLN* 1.3 73.6 - - - +
48S ARG* 1.3 56.5 + - - +
50S THR* 4.6 4.0 - - - +
51S PHE* 2.9 52.3 + - + -
138S LEU* 4.0 16.9 - - + +
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Residues in contact with ARG 48 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44S GLU 3.1 17.6 + - - +
45S LYS* 3.6 11.2 + - - +
46S GLN 3.1 0.8 - - - -
47S GLN* 1.3 77.3 - - - +
49S LYS* 1.3 55.1 + - - +
51S PHE* 4.2 0.3 - - - +
52S THR* 2.5 41.2 + - - +
67S GLU 4.6 1.9 + - - -
68S ASN* 3.0 29.8 - - - +
69S ILE* 3.7 18.0 - - + +
70S GLU* 2.5 44.2 + - - -
134S LEU* 4.2 15.9 - - - -
138S LEU* 3.9 15.6 - - + +
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Residues in contact with LYS 49 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45S LYS* 3.2 9.0 + - + +
46S GLN* 2.9 19.3 + - - +
48S ARG* 1.3 82.9 - - - +
50S THR* 1.3 75.0 + - - +
52S THR* 3.6 4.6 - - - -
53S ALA* 3.0 31.4 + - + +
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Residues in contact with THR 50 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46S GLN* 2.9 17.5 + - - +
47S GLN* 4.1 4.5 - - - -
49S LYS* 1.3 89.6 + - - +
51S PHE* 1.3 68.6 + - + +
53S ALA* 3.3 7.3 + - + +
54S TRP* 2.9 31.4 + - + +
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Residues in contact with PHE 51 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95H ARG* 0.8 148.1 - - + -
47S GLN* 2.9 40.4 + - + +
50S THR* 1.3 83.3 - - + +
52S THR* 1.3 57.8 + - - +
54S TRP* 3.2 5.7 + - - +
55S CYS* 2.8 34.0 + - - -
69S ILE* 4.0 16.2 - - + -
138S LEU* 3.3 30.7 - - + -
141S ILE* 4.0 13.9 - - + -
142S TRP* 3.7 3.6 - + + -
145S ILE* 3.7 15.9 - - + -
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Residues in contact with THR 52 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48S ARG* 2.5 28.7 + - - +
49S LYS* 3.6 5.6 - - - -
51S PHE* 1.3 77.3 - - - +
53S ALA* 1.3 62.8 + - - +
55S CYS* 3.2 2.6 + - - +
56S ASN* 2.9 38.5 + - - +
66S ILE* 4.0 17.7 - - + +
67S GLU 4.0 19.9 + - - +
69S ILE* 3.6 25.4 + - + +
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Residues in contact with ALA 53 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49S LYS* 3.0 19.6 + - + +
50S THR* 3.6 6.5 - - - +
52S THR* 1.3 78.0 - - - +
54S TRP* 1.3 61.9 + - - +
56S ASN* 3.4 6.5 + - - +
57S SER* 3.0 24.9 + - - -
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Residues in contact with TRP 54 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50S THR* 2.9 18.0 + - + +
51S PHE* 3.5 9.4 - - - +
53S ALA* 1.3 77.2 - - - +
55S CYS* 1.3 85.8 + - - +
57S SER* 2.7 26.4 + - - -
58S HIS* 3.5 34.3 + + - -
82S LEU* 4.1 24.7 - - + -
86S ILE* 4.1 26.0 - - + -
141S ILE* 4.9 0.9 - - + -
144S ILE* 4.2 4.7 - - + -
145S ILE* 3.6 47.5 - - + +
148S PHE 5.8 0.4 - - - -
149S ALA* 4.2 25.3 - - + +
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Residues in contact with CYS 55 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51S PHE 2.8 26.7 + - - +
52S THR 3.6 4.0 - - - +
54S TRP* 1.3 83.6 - - - +
56S ASN* 1.3 58.0 + - - +
58S HIS* 3.1 5.9 + - - +
59S LEU* 2.9 34.4 + - + +
66S ILE* 4.1 14.6 - - + -
69S ILE* 4.7 2.5 - - - -
73S PHE* 3.9 14.1 - - + -
82S LEU* 3.7 25.0 - - + +
141S ILE* 3.8 31.0 - - - -
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Residues in contact with ASN 56 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52S THR* 2.9 25.8 + - - +
53S ALA* 3.7 7.6 - - - +
54S TRP 3.2 0.2 - - - -
55S CYS* 1.3 72.7 - - - +
57S SER* 1.3 55.5 + - - +
58S HIS 3.0 5.2 - - - -
59S LEU* 4.2 3.9 - - - +
60S ARG* 3.0 19.8 + - - +
65S GLN* 2.7 50.7 + - - +
66S ILE* 2.7 54.6 - - - +
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Residues in contact with SER 57 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53S ALA 3.0 13.8 + - - -
54S TRP* 2.7 25.2 + - - -
56S ASN* 1.3 76.4 - - - +
58S HIS* 1.3 64.7 + - - +
60S ARG* 2.9 44.0 + - - +
61S LYS* 3.5 11.6 + - - -
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Residues in contact with HIS 58 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54S TRP* 3.5 56.1 + + - -
55S CYS 3.1 6.6 + - - +
56S ASN 3.0 0.4 - - - -
57S SER* 1.3 85.8 + - - +
59S LEU* 1.3 66.1 + - - +
60S ARG 3.1 1.3 - - - -
61S LYS* 3.0 47.3 + - - +
62S ALA 4.1 0.3 + - - -
82S LEU* 3.8 13.5 - - + -
85S VAL* 3.6 17.8 - - + +
86S ILE* 3.5 20.3 - - + +
149S ALA* 5.8 1.2 - - - +
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Residues in contact with LEU 59 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55S CYS* 2.9 23.1 + - + +
56S ASN* 3.4 10.7 + - - +
58S HIS* 1.3 76.7 - - - +
60S ARG* 1.3 53.8 + - - +
62S ALA* 2.7 28.8 + - - +
63S GLY 3.3 6.6 + - - -
64S THR* 3.3 35.3 + - + +
65S GLN* 4.2 1.3 - - - +
66S ILE* 3.8 29.4 - - + +
73S PHE* 4.4 14.1 - - + -
78S LYS* 3.6 12.6 - - + +
81S LEU* 4.3 8.5 - - + -
82S LEU* 3.6 35.4 - - + +
85S VAL* 5.0 2.5 - - + -
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Residues in contact with ARG 60 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56S ASN 3.0 20.2 + - - +
57S SER* 2.9 36.6 + - - +
59S LEU* 1.3 76.1 - - - +
61S LYS* 1.3 67.2 + - + +
62S ALA 3.1 0.2 - - - -
63S GLY* 3.1 17.5 + - - +
64S THR 3.3 10.2 + - - +
65S GLN* 3.5 12.6 - - - +
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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