Contacts of the helix formed by residues 56 - 74 (chain F) in PDB entry 5WC9
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 SER 56 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55F LEU* 1.3 79.3 - - - +
57F PHE* 1.3 54.7 - - - +
58F LYS* 3.8 18.1 - - - +
59F ASN* 3.1 17.9 + - - +
60F ALA* 2.8 33.3 + - - +
147F LYS* 3.7 21.1 - - - -
148F ARG* 4.5 0.4 - - - +
182H A 2.8 27.4 + - - -
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Residues in contact with PHE 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F GLU* 3.5 44.4 - - + -
6F ILE* 4.6 12.1 - - + -
9F LEU* 3.9 20.2 - - + -
55F LEU 3.8 0.4 + - - -
56F SER* 1.3 73.8 - - - +
58F LYS* 1.3 75.1 + - + +
60F ALA* 3.1 7.1 + - - +
61F CYS* 2.9 53.0 + - - -
147F LYS 4.6 2.6 + - - -
149F VAL* 4.5 14.9 - - + +
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Residues in contact with LYS 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F SER* 3.8 23.2 - - - +
57F PHE* 1.3 92.1 - - + +
59F ASN* 1.3 61.0 + - - +
61F CYS* 3.3 7.1 + - - +
62F LYS* 3.0 23.0 + - - +
147F LYS* 4.8 10.9 + - - +
181H A 5.1 10.6 + - - -
182H A 4.4 13.4 + - - +
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Residues in contact with ASN 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F LEU* 3.7 24.5 - - + +
56F SER* 3.1 25.4 + - - +
58F LYS* 1.3 78.6 - - - +
60F ALA* 1.3 56.1 + - - +
62F LYS* 3.3 12.6 + - - +
63F LEU* 2.9 39.5 + - - +
182H A 3.9 28.6 + - - +
183H T 2.9 33.4 + - - +
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Residues in contact with ALA 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F LEU* 3.7 27.4 - - + -
50F PHE* 3.7 11.7 - - + -
53F LEU* 5.7 2.7 - - + -
55F LEU* 3.5 19.2 - - + +
56F SER 2.8 17.4 + - - +
57F PHE* 3.1 7.2 + - - +
59F ASN* 1.3 74.6 - - - +
61F CYS* 1.3 55.0 + - - +
63F LEU 3.3 0.7 + - - +
64F LYS* 2.7 37.5 + - - +
149F VAL* 5.0 4.0 - - + -
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Residues in contact with CYS 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F GLU* 5.7 0.7 - - - -
9F LEU* 4.6 9.9 - - - -
57F PHE* 2.9 51.5 + - - -
58F LYS* 3.7 9.2 - - - +
60F ALA* 1.3 76.5 - - - +
62F LYS* 1.3 62.8 + - - +
64F LYS* 3.8 6.7 - - - +
65F ALA* 3.2 22.2 + - - +
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Residues in contact with LYS 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F HIS* 5.0 7.2 - - - -
58F LYS 3.0 13.8 + - - +
59F ASN* 3.4 20.9 - - - +
60F ALA 3.2 0.2 - - - -
61F CYS* 1.3 76.4 - - - +
63F LEU* 1.3 65.1 + - + +
65F ALA* 3.1 8.9 + - - +
66F ILE* 3.1 44.9 + - + +
182H A 4.1 11.4 + - - -
183H T 3.1 25.6 + - - -
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Residues in contact with LEU 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F LEU* 5.5 0.2 - - + -
42F PHE* 3.5 35.9 - - + -
46F THR* 4.7 9.4 - - + -
47F ILE* 5.3 3.4 - - + -
50F PHE* 3.6 27.8 - - + -
55F LEU* 4.6 8.5 - - + -
59F ASN* 2.9 44.1 + - - +
60F ALA* 4.6 0.2 - - - -
62F LYS* 1.3 80.4 - - + +
64F LYS* 1.3 56.9 + - - +
66F ILE* 3.2 8.4 + - + +
67F LEU* 2.7 53.2 + - + +
183H T 3.9 10.1 - - - +
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Residues in contact with LYS 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F LEU* 4.6 12.6 - - + -
12F PHE* 4.0 15.3 - - + -
50F PHE* 3.7 19.4 - - + -
60F ALA 2.7 21.4 + - - +
61F CYS* 3.8 8.3 - - - +
63F LEU* 1.3 72.0 - - - +
65F ALA* 1.3 56.7 + - - +
67F LEU* 4.5 1.6 - - - +
68F SER* 2.9 32.9 + - - -
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Residues in contact with ALA 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F CYS 3.2 12.4 + - - +
62F LYS* 3.1 12.1 + - - +
64F LYS* 1.3 74.3 - - - +
66F ILE* 1.3 65.0 + - + +
68F SER* 2.9 19.2 + - - -
69F LYS* 3.3 12.3 + - - +
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Residues in contact with ILE 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F LEU* 4.4 16.8 - - + -
37F VAL* 4.6 13.4 - - + +
38F HIS* 3.4 50.5 - - + +
42F PHE* 4.6 8.5 - - + -
62F LYS* 3.1 38.0 + - + +
63F LEU* 3.8 11.2 - - + +
65F ALA* 1.3 77.0 - - + +
67F LEU* 1.3 61.5 + - + +
69F LYS* 3.6 4.4 + - - +
70F TRP* 3.1 21.9 + - + +
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Residues in contact with LEU 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F PHE* 4.5 5.4 - - + -
16F PHE* 3.7 36.8 - - + -
30F VAL* 4.5 12.1 - - + -
34F LEU* 4.6 14.6 - - + -
47F ILE* 4.6 14.6 - - + -
50F PHE* 3.5 42.4 - - + -
63F LEU* 2.7 34.9 + - + +
64F LYS* 4.3 3.4 - - - +
66F ILE* 1.3 71.0 - - + +
68F SER* 1.3 60.3 + - - +
70F TRP* 3.3 11.8 + - + +
71F LEU* 2.9 30.8 + - - +
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Residues in contact with SER 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F PHE* 3.4 29.5 - - - -
64F LYS 2.9 17.7 + - - -
65F ALA* 2.9 17.0 + - - -
67F LEU* 1.3 78.0 - - - +
69F LYS* 1.3 64.9 + - - +
71F LEU* 3.5 5.4 + - - +
72F GLU* 3.4 20.8 + - - +
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Residues in contact with LYS 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F VAL* 3.7 21.8 - - + -
65F ALA 3.3 12.9 + - - +
66F ILE* 4.0 1.8 - - - +
68F SER* 1.3 82.9 + - - +
70F TRP* 1.3 61.7 + - - +
72F GLU* 3.7 5.8 + - - +
73F GLU* 3.2 29.2 + - - +
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Residues in contact with TRP 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F PHE* 4.3 14.4 - + - -
20F ARG* 6.4 2.0 - - + -
23F LEU* 5.8 4.3 - - + -
25F TYR* 4.6 24.7 - + - -
30F VAL* 3.6 36.6 - - + -
33F ALA* 2.3 46.8 + - + +
34F LEU* 3.5 20.9 - - + -
36F ALA* 5.6 2.2 - - + -
37F VAL* 3.8 24.0 - - + +
66F ILE* 3.1 18.1 + - + +
67F LEU* 3.7 12.1 - - + +
68F SER 3.2 0.2 - - - -
69F LYS* 1.3 76.5 - - - +
71F LEU* 1.3 84.9 + - + +
73F GLU* 3.0 4.8 + - + +
74F ALA* 2.8 48.1 + - + +
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Residues in contact with LEU 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F PHE* 5.8 5.2 - - + -
15F GLU 6.1 0.2 - - - -
16F PHE* 4.1 27.4 - - + +
19F ARG* 4.3 31.2 - - + +
20F ARG 5.8 0.2 - - - +
23F LEU* 5.9 7.0 - - + -
67F LEU 2.9 17.5 + - - +
68F SER* 3.8 7.4 - - - +
69F LYS 3.4 0.2 - - - -
70F TRP* 1.3 91.7 - - + +
72F GLU* 1.3 65.2 + - - +
74F ALA* 3.1 23.9 + - - +
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Residues in contact with GLU 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F SER 3.4 9.7 + - - +
69F LYS* 3.8 11.0 - - - +
70F TRP 3.3 0.4 - - - -
71F LEU* 1.3 85.8 - - + +
73F GLU* 1.3 62.9 + - + +
74F ALA 3.2 0.7 + - - -
75F GLU* 3.0 27.7 + - - +
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Residues in contact with GLU 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F ALA* 4.8 10.6 - - - +
37F VAL* 3.6 29.5 - - + +
69F LYS* 3.2 14.7 + - - +
70F TRP* 3.0 11.9 + - + +
72F GLU* 1.3 77.4 - - + +
74F ALA* 1.3 56.3 + - - +
75F GLU* 3.3 17.7 + - - +
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Residues in contact with ALA 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F LEU* 4.1 18.8 - - + +
25F TYR* 4.7 13.5 - - + +
70F TRP* 2.8 48.4 + - + +
71F LEU 3.1 15.2 + - - +
73F GLU* 1.3 74.0 - - - +
75F GLU* 1.3 62.2 + - - +
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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