Contacts of the helix formed by residues 42 - 60 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43O TRP* 1.3 78.6 + - - +
44O GLU* 3.1 6.3 + - - +
45O LYS* 3.2 10.6 + - - +
46O GLN* 2.7 38.8 + - + +
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Residues in contact with TRP 43 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D ARG 6.0 1.6 - - - -
92D ASN 4.6 8.3 - - - -
93D GLU* 4.2 22.4 - - - +
42O ALA* 1.3 88.3 - - - +
44O GLU* 1.3 90.8 + - + +
46O GLN* 3.2 8.9 + - - +
47O GLN* 2.8 77.3 + - + +
135O LYS* 4.7 26.9 - - + -
138O LEU* 5.1 5.2 - - + -
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Residues in contact with GLU 44 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42O ALA 3.1 4.0 - - - +
43O TRP* 1.3 107.9 + - + +
45O LYS* 1.3 61.8 + - - +
47O GLN* 3.6 1.3 + - - -
48O ARG* 3.1 25.1 + - - +
134O LEU* 3.2 37.4 - - + +
135O LYS* 3.7 30.4 + - - +
138O LEU* 3.9 12.1 - - + +
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Residues in contact with LYS 45 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42O ALA* 3.2 6.4 + - - +
44O GLU* 1.3 79.2 - - - +
46O GLN* 1.3 78.6 + - - +
48O ARG* 3.5 11.6 + - - +
49O LYS* 3.2 21.2 + - + +
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Residues in contact with GLN 46 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42O ALA* 2.7 38.7 + - + +
43O TRP* 3.2 7.4 + - - +
45O LYS* 1.3 92.0 - - - +
47O GLN* 1.3 66.5 + - - +
49O LYS* 2.9 19.8 + - - +
50O THR* 2.9 28.4 + - - +
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Residues in contact with GLN 47 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D ASN 4.3 1.6 + - - +
93D GLU 4.4 2.4 + - - -
95D ARG* 2.3 60.3 + - + +
43O TRP* 2.8 55.9 + - - +
44O GLU 4.0 3.1 - - - +
46O GLN* 1.3 73.2 - - - +
48O ARG* 1.3 57.3 + - - +
50O THR* 4.6 3.8 - - - +
51O PHE* 2.9 51.9 + - + -
138O LEU* 4.0 16.1 - - + +
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Residues in contact with ARG 48 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44O GLU 3.1 18.0 + - - +
45O LYS* 3.6 10.9 + - - +
46O GLN 3.1 0.8 - - - -
47O GLN* 1.3 78.1 - - - +
49O LYS* 1.3 55.6 + - - +
51O PHE* 4.2 0.3 - - - +
52O THR* 2.5 41.2 + - - +
67O GLU 4.6 2.1 + - - -
68O ASN* 3.0 29.8 - - - +
69O ILE* 3.7 18.7 - - + +
70O GLU* 2.5 42.9 + - - -
134O LEU* 4.2 16.4 - - - -
138O LEU* 3.9 15.2 - - + +
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Residues in contact with LYS 49 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45O LYS* 3.2 8.7 + - + +
46O GLN* 2.9 18.8 + - - +
48O ARG* 1.3 82.5 - - - +
50O THR* 1.3 74.5 + - - +
52O THR* 3.4 4.6 + - - -
53O ALA* 3.0 30.8 + - + +
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Residues in contact with THR 50 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46O GLN* 2.9 17.0 + - - +
47O GLN* 4.1 4.5 - - - -
49O LYS* 1.3 89.8 + - - +
51O PHE* 1.3 69.1 + - + +
53O ALA* 3.3 7.5 + - + +
54O TRP* 2.9 30.7 + - + +
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Residues in contact with PHE 51 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D ARG* 0.9 147.4 - - + -
47O GLN* 2.9 40.9 + - + +
50O THR* 1.3 82.9 - - + +
52O THR* 1.3 57.1 + - - +
54O TRP* 3.2 6.1 + - - +
55O CYS* 2.8 34.0 + - - -
69O ILE* 4.0 16.6 - - + -
138O LEU* 3.3 30.3 - - + -
141O ILE* 4.0 13.7 - - + -
142O TRP* 3.7 3.4 - + + -
145O ILE* 3.7 15.7 - - + -
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Residues in contact with THR 52 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48O ARG* 2.5 28.1 + - - +
49O LYS* 3.6 5.6 - - - -
51O PHE* 1.3 77.3 - - - +
53O ALA* 1.3 63.9 + - - +
55O CYS* 3.2 2.4 + - - +
56O ASN* 2.9 38.7 + - - +
66O ILE* 4.0 17.7 - - + +
67O GLU 4.0 19.8 + - - +
69O ILE* 3.6 25.8 + - + +
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Residues in contact with ALA 53 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49O LYS* 3.0 19.8 + - + +
50O THR* 3.6 6.3 - - + +
52O THR* 1.3 77.2 - - - +
54O TRP* 1.3 62.0 + - - +
56O ASN* 3.4 7.0 + - - +
57O SER* 3.0 24.3 + - - -
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Residues in contact with TRP 54 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50O THR* 2.9 17.8 + - + +
51O PHE* 3.5 9.4 - - - +
53O ALA* 1.3 76.3 - - - +
55O CYS* 1.3 85.5 + - - +
57O SER* 2.7 26.4 + - - -
58O HIS* 3.5 34.8 + + - -
82O LEU* 4.1 25.4 - - + -
86O ILE* 4.1 25.6 - - + -
141O ILE* 4.9 1.1 - - + -
144O ILE* 4.2 4.5 - - + -
145O ILE* 3.6 47.9 - - + +
148O PHE 5.8 0.4 - - - -
149O ALA* 4.2 25.3 - - + +
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Residues in contact with CYS 55 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51O PHE 2.8 27.3 + - - +
52O THR 3.6 4.0 - - - +
54O TRP* 1.3 84.1 - - - +
56O ASN* 1.3 57.5 + - - +
58O HIS* 3.1 5.9 + - - +
59O LEU* 2.9 34.6 + - + +
66O ILE* 4.1 14.8 - - + -
69O ILE* 4.7 2.2 - - - -
73O PHE* 3.9 13.7 - - + -
82O LEU* 3.7 25.0 - - + +
141O ILE* 3.8 31.2 - - - -
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Residues in contact with ASN 56 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52O THR* 2.9 26.5 + - - +
53O ALA* 3.7 7.2 - - - +
54O TRP 3.2 0.2 - - - -
55O CYS* 1.3 73.8 - - - +
57O SER* 1.3 56.4 + - - +
58O HIS 3.0 4.9 - - - -
59O LEU* 4.2 3.5 - - - +
60O ARG* 3.0 20.0 + - - +
65O GLN* 2.7 49.2 + - - +
66O ILE* 2.7 54.9 - - - +
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Residues in contact with SER 57 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53O ALA 3.0 13.4 + - - -
54O TRP* 2.7 25.4 + - - -
56O ASN* 1.3 75.7 - - - +
58O HIS* 1.3 64.9 + - - +
60O ARG* 2.9 43.8 + - - +
61O LYS* 3.5 11.8 + - - -
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Residues in contact with HIS 58 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54O TRP* 3.5 56.8 + + - -
55O CYS 3.1 6.8 + - - +
56O ASN 3.0 0.2 - - - -
57O SER* 1.3 85.0 + - - +
59O LEU* 1.3 66.5 + - - +
60O ARG 3.1 1.3 - - - -
61O LYS* 3.0 46.9 + - - +
62O ALA 4.1 0.5 + - - -
82O LEU* 3.8 13.9 - - + -
85O VAL* 3.6 17.5 - - + +
86O ILE* 3.5 19.9 - - + +
149O ALA* 5.8 1.4 - - - +
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Residues in contact with LEU 59 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55O CYS* 2.9 23.3 + - + +
56O ASN* 3.4 10.5 + - - +
58O HIS* 1.3 77.2 - - - +
60O ARG* 1.3 53.7 + - - +
62O ALA* 2.7 28.9 + - - +
63O GLY 3.3 6.6 + - - -
64O THR* 3.3 34.7 + - + +
65O GLN* 4.2 1.6 - - - +
66O ILE* 3.8 29.8 - - + +
73O PHE* 4.4 14.1 - - + -
78O LYS* 3.6 12.8 - - + +
81O LEU* 4.3 9.0 - - + +
82O LEU* 3.6 35.2 - - + +
85O VAL* 5.0 1.8 - - + -
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Residues in contact with ARG 60 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56O ASN 3.0 19.6 + - - +
57O SER* 2.9 35.8 + - - +
59O LEU* 1.3 75.5 - - - +
61O LYS* 1.3 66.8 + - + +
63O GLY* 3.1 17.5 + - - +
64O THR 3.3 10.5 + - - +
65O 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
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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