Contacts of the helix formed by residues 42 - 60 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43M TRP* 1.3 78.4 + - - +
44M GLU* 3.1 6.1 + - - +
45M LYS* 3.2 10.2 + - - +
46M GLN* 2.7 39.0 + - + +
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Residues in contact with TRP 43 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ARG 6.0 1.3 - - - -
92B ASN 4.6 8.7 - - - -
93B GLU* 4.2 23.1 - - - -
42M ALA* 1.3 88.1 - - - +
44M GLU* 1.3 89.2 + - + +
46M GLN* 3.2 8.7 + - - +
47M GLN* 2.8 77.4 + - - +
135M LYS* 4.7 26.5 - - + -
138M LEU* 5.1 5.6 - - + -
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Residues in contact with GLU 44 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42M ALA 3.1 3.5 - - - +
43M TRP* 1.3 108.7 + - + +
45M LYS* 1.3 61.8 + - - +
47M GLN* 4.6 1.3 - - - -
48M ARG* 3.1 25.1 + - - +
134M LEU* 3.2 37.8 - - + +
135M LYS* 3.7 30.5 + - + +
138M LEU* 3.9 13.1 - - + +
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Residues in contact with LYS 45 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42M ALA* 3.2 6.2 + - - +
44M GLU* 1.3 78.6 - - - +
46M GLN* 1.3 77.2 + - - +
48M ARG* 3.5 11.0 + - - +
49M LYS* 3.2 21.0 + - - +
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Residues in contact with GLN 46 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42M ALA* 2.7 39.5 + - + +
43M TRP* 3.2 7.6 + - - +
45M LYS* 1.3 91.6 - - - +
47M GLN* 1.3 66.1 - - - +
49M LYS* 2.9 18.7 + - - +
50M THR* 2.9 29.2 + - - +
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Residues in contact with GLN 47 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ASN 4.3 1.6 + - - +
93B GLU 4.4 2.2 + - - -
95B ARG* 2.3 61.1 + - + +
43M TRP* 2.8 55.4 + - - +
44M GLU* 4.0 3.8 - - - +
46M GLN* 1.3 72.5 - - - +
48M ARG* 1.3 56.5 + - - +
50M THR* 4.6 3.1 - - - +
51M PHE* 2.9 53.6 + - + -
138M LEU* 4.0 16.9 - - + +
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Residues in contact with ARG 48 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44M GLU 3.1 18.0 + - - +
45M LYS* 3.6 11.1 + - - +
46M GLN 3.1 0.6 - - - -
47M GLN* 1.3 77.6 - - - +
49M LYS* 1.3 55.9 + - - +
51M PHE* 4.2 0.2 - - - +
52M THR* 2.5 40.7 + - - +
67M GLU 4.6 2.1 + - - -
68M ASN* 3.0 29.8 - - - +
69M ILE* 3.7 17.0 - - + +
70M GLU* 2.5 43.1 + - - -
134M LEU* 4.2 16.4 - - + -
138M LEU* 3.9 15.0 - - + +
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Residues in contact with LYS 49 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45M LYS* 3.2 9.4 + - + +
46M GLN* 2.9 19.1 + - - +
48M ARG* 1.3 82.2 - - - +
50M THR* 1.3 73.2 + - - +
52M THR* 3.6 4.4 - - - -
53M ALA* 3.0 30.8 + - + +
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Residues in contact with THR 50 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46M GLN* 2.9 17.4 + - - +
47M GLN* 4.1 4.5 - - - -
49M LYS* 1.3 89.9 + - - +
51M PHE* 1.3 70.8 + - + +
53M ALA* 3.3 6.9 + - - +
54M TRP* 2.9 29.9 + - + +
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Residues in contact with PHE 51 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ARG* 0.9 146.3 - - + -
47M GLN* 2.9 40.8 + - + +
50M THR* 1.3 80.9 - - + +
52M THR* 1.3 57.9 + - - +
54M TRP* 3.2 6.7 + - - +
55M CYS* 2.8 33.3 + - - -
69M ILE* 4.0 16.2 - - + -
138M LEU* 3.3 30.3 - - + -
141M ILE* 4.0 13.2 - - + -
142M TRP* 3.7 3.6 - + + -
145M ILE* 3.7 16.4 - - + -
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Residues in contact with THR 52 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48M ARG* 2.5 28.9 + - - +
49M LYS* 3.6 5.3 - - - -
51M PHE* 1.3 76.7 - - - +
53M ALA* 1.3 62.9 + - - +
55M CYS* 3.2 2.3 + - - +
56M ASN* 2.9 39.3 + - - +
66M ILE* 4.0 16.4 - - + +
67M GLU 4.0 20.4 + - - +
69M ILE* 3.6 25.7 + - + +
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Residues in contact with ALA 53 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49M LYS* 3.0 19.6 + - + +
50M THR* 3.6 7.0 - - - +
52M THR* 1.3 76.3 - - - +
54M TRP* 1.3 62.8 + - - +
56M ASN* 3.4 7.1 + - - +
57M SER* 3.0 24.4 + - - -
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Residues in contact with TRP 54 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50M THR* 2.9 16.5 + - + +
51M PHE* 3.5 9.4 - - - +
53M ALA* 1.3 78.0 - - - +
55M CYS* 1.3 85.6 + - - +
57M SER* 2.7 26.3 + - - -
58M HIS* 3.5 35.8 + + - -
82M LEU* 4.1 24.9 - - + -
86M ILE* 4.1 25.6 - - + -
141M ILE* 4.9 0.9 - - + -
144M ILE* 4.2 5.4 - - + -
145M ILE* 3.6 47.0 - - + +
148M PHE 5.8 0.2 - - - -
149M ALA* 4.2 24.2 - - + +
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Residues in contact with CYS 55 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51M PHE 2.8 26.8 + - - +
52M THR 3.6 3.8 - - - +
54M TRP* 1.3 82.6 - - - +
56M ASN* 1.3 59.0 + - - +
58M HIS* 3.1 5.9 + - - +
59M LEU* 2.9 34.1 + - + +
66M ILE* 4.1 14.8 - - + -
69M ILE* 4.7 2.0 - - - -
73M PHE* 3.9 14.6 - - + -
82M LEU* 3.7 25.9 - - + +
141M ILE* 3.8 30.7 - - - -
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Residues in contact with ASN 56 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52M THR* 2.9 26.3 + - - +
53M ALA* 3.7 7.2 - - - +
55M CYS* 1.3 72.8 - - - +
57M SER* 1.3 55.8 + - - +
58M HIS 3.0 5.4 - - - -
59M LEU* 4.2 4.3 - - - +
60M ARG* 3.0 19.6 + - - +
65M GLN* 2.7 49.2 + - - +
66M ILE* 2.7 54.3 - - - +
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Residues in contact with SER 57 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53M ALA 3.0 14.2 + - - -
54M TRP* 2.7 25.5 + - - -
56M ASN* 1.3 75.0 - - - +
58M HIS* 1.3 66.1 + - - +
60M ARG* 2.9 43.5 + - - +
61M LYS* 3.5 11.4 + - - -
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Residues in contact with HIS 58 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54M TRP* 3.5 56.4 + + - -
55M CYS 3.1 7.0 + - - +
56M ASN 3.0 0.2 - - - -
57M SER* 1.3 84.0 + - - +
59M LEU* 1.3 66.1 + - - +
60M ARG 3.1 1.6 - - - -
61M LYS* 3.0 48.6 + - - +
62M ALA 4.1 0.7 + - - -
82M LEU* 3.8 14.1 - - + -
85M VAL* 3.6 16.2 - - + +
86M ILE* 3.5 21.0 - - + +
149M ALA* 5.8 1.4 - - - +
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Residues in contact with LEU 59 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55M CYS* 2.9 23.3 + - + +
56M ASN* 4.2 10.8 - - - +
58M HIS* 1.3 77.1 - - - +
60M ARG* 1.3 54.8 + - - +
62M ALA* 2.7 29.5 + - - +
63M GLY 3.3 5.9 + - - -
64M THR* 3.3 35.7 + - + +
65M GLN* 4.2 1.6 - - - +
66M ILE* 3.8 28.9 - - + +
73M PHE* 4.4 13.5 - - + -
78M LYS* 3.6 11.9 - - + +
81M LEU* 4.3 8.7 - - + -
82M LEU* 3.6 36.1 - - + +
85M VAL* 5.0 1.8 - - + -
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Residues in contact with ARG 60 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56M ASN 3.0 18.5 + - - +
57M SER* 2.9 37.8 + - - +
59M LEU* 1.3 77.2 - - - +
61M LYS* 1.3 66.8 + - + +
63M GLY* 3.1 17.8 + - - +
64M THR 3.3 10.9 + - - +
65M GLN* 3.5 13.5 - - - +
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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
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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