Contacts of the helix formed by residues 56 - 74 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55E LEU* 1.3 78.5 - - - +
57E PHE* 1.3 65.4 + - - +
58E LYS* 3.8 3.9 + - - +
59E ASN* 3.1 13.2 + - - +
60E ALA* 2.9 22.2 + - - +
147E LYS* 3.6 23.7 + - - -
149E VAL* 4.2 0.4 - - - -
173H A 5.3 4.3 - - - -
174H A 2.2 31.4 + - - -
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Residues in contact with PHE 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E SER* 5.5 1.6 - - - -
5E GLU* 3.5 36.6 - - + -
6E ILE* 4.1 22.4 - - + -
9E LEU* 4.3 7.9 - - + -
56E SER* 1.3 73.6 - - - +
58E LYS* 1.3 66.5 + - + +
60E ALA* 3.4 2.4 + - - +
61E CYS* 3.2 38.4 + - - -
147E LYS 4.7 2.0 + - - -
148E ARG 5.3 0.4 - - - -
149E VAL* 3.6 26.7 - - + +
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Residues in contact with LYS 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E SER* 3.2 4.4 + - - +
57E PHE* 1.3 84.4 - - + +
59E ASN* 1.3 60.8 + - - +
61E CYS* 3.4 7.6 + - - +
62E LYS* 3.2 21.6 + - + +
173H A 4.2 10.0 + - - +
174H A 3.2 25.0 + - - +
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Residues in contact with ASN 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E THR* 5.8 0.8 - - - +
55E LEU* 3.6 34.3 - - + +
56E SER* 3.1 23.3 + - - +
58E LYS* 1.3 76.2 - - - +
60E ALA* 1.3 63.0 + - - +
62E LYS* 3.3 12.0 + - - +
63E LEU* 3.0 28.8 + - - +
174H A 3.5 32.3 + - - +
175H T 3.2 29.4 + - - +
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Residues in contact with ALA 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E LEU* 3.6 28.0 - - + +
50E PHE* 3.5 8.6 - - + -
53E LEU* 4.5 14.6 - - + -
55E LEU* 4.4 16.1 - - + +
56E SER 2.9 18.3 + - - +
57E PHE* 3.8 2.5 - - - +
58E LYS 3.3 0.2 - - - -
59E ASN* 1.3 77.0 - - - +
61E CYS* 1.3 61.9 + - - +
63E LEU 3.4 0.3 + - - -
64E LYS* 3.0 26.7 + - - +
149E VAL* 5.1 2.9 - - + -
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Residues in contact with CYS 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E GLU* 4.4 16.2 - - - -
9E LEU* 4.5 13.0 - - - -
57E PHE* 3.2 43.6 + - - -
58E LYS* 3.7 8.5 - - - +
59E ASN 3.3 0.4 - - - -
60E ALA* 1.3 77.6 - - - +
62E LYS* 1.3 64.8 + - - +
64E LYS* 3.7 4.8 + - - +
65E ALA* 3.4 19.4 + - - +
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Residues in contact with LYS 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E HIS* 4.9 14.5 + - - -
42E PHE* 4.9 6.5 - - - -
58E LYS* 3.2 11.2 + - + +
59E ASN* 3.5 18.4 - - - +
61E CYS* 1.3 79.2 - - - +
63E LEU* 1.3 66.9 + - - +
65E ALA* 3.1 16.6 + - - +
66E ILE* 3.1 29.6 + - + +
174H A 3.9 9.6 + - - +
175H T 2.2 33.0 + - - +
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Residues in contact with LEU 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E LEU* 5.4 2.7 - - + -
42E PHE* 3.8 35.0 - - + -
46E THR* 3.7 25.6 - - + +
47E ILE* 5.4 3.6 - - + -
50E PHE* 3.8 20.6 - - + -
55E LEU* 3.6 28.0 - - + -
59E ASN* 3.0 25.9 + - - +
60E ALA 3.4 0.2 + - - -
62E LYS* 1.3 78.1 - - + +
64E LYS* 1.3 55.9 + - - +
66E ILE* 3.1 12.6 + - + +
67E LEU* 2.7 50.4 + - + +
175H T 4.9 0.4 - - - +
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Residues in contact with LYS 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E GLU* 4.2 15.8 + - - -
8E GLU* 4.6 15.7 + - - +
9E LEU* 3.8 21.4 - - + +
12E PHE* 3.8 37.1 - - + -
50E PHE* 3.4 20.2 - - + -
60E ALA 3.0 17.9 + - - +
61E CYS* 4.0 5.6 - - - +
62E LYS 3.3 0.2 - - - -
63E LEU* 1.3 75.5 - - - +
65E ALA* 1.3 57.9 + - - +
68E SER* 2.8 37.3 + - - -
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Residues in contact with ALA 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E CYS 3.4 10.2 + - - +
62E LYS* 3.1 12.1 + - - +
64E LYS* 1.3 77.9 - - - +
66E ILE* 1.3 70.0 + - + +
68E SER* 3.1 17.8 + - - -
69E LYS* 3.4 12.5 + - - +
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Residues in contact with ILE 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E LEU* 4.5 13.6 - - + +
37E VAL* 4.0 14.4 - - + +
38E HIS* 4.0 42.4 - - + -
42E PHE* 5.3 2.9 - - + -
62E LYS* 3.2 33.0 - - + +
63E LEU* 3.1 14.5 + - + +
65E ALA* 1.3 81.0 - - + +
67E LEU* 1.3 62.9 + - + +
69E LYS* 3.6 4.9 + - - +
70E TRP* 3.3 19.4 + - - +
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Residues in contact with LEU 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E PHE* 4.2 11.4 - - + -
16E PHE* 3.8 20.4 - - + -
30E VAL* 3.8 23.1 - - + -
34E LEU* 3.7 31.0 - - + -
47E ILE* 4.3 12.1 - - + -
50E PHE* 3.6 41.3 - - + -
63E LEU* 2.7 29.5 + - + +
64E LYS 4.2 1.6 - - - +
66E ILE* 1.3 72.5 - - - +
68E SER* 1.3 59.0 + - - +
70E TRP* 3.1 6.5 + - + +
71E LEU* 2.8 30.7 + - - +
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Residues in contact with SER 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E PHE* 3.6 26.1 - - - -
64E LYS* 2.8 25.1 + - - -
65E ALA* 3.1 10.4 + - - -
67E LEU* 1.3 77.5 - - - +
69E LYS* 1.3 64.3 + - - +
71E LEU* 3.8 3.9 - - - +
72E GLU* 3.1 36.3 + - - +
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Residues in contact with LYS 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E VAL* 4.2 18.5 - - + +
65E ALA 3.4 12.0 + - - +
66E ILE* 3.9 4.9 - - - +
67E LEU 3.3 0.6 - - - -
68E SER* 1.3 82.5 + - - +
70E TRP* 1.3 61.1 + - - +
72E GLU* 3.8 11.6 + - - +
73E GLU* 3.2 23.0 + - - +
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Residues in contact with TRP 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E PHE* 3.8 26.9 - + - -
20E ARG* 5.4 3.4 - - + -
23E LEU* 5.8 0.9 - - + -
25E TYR* 3.9 34.5 - + + -
30E VAL* 3.7 28.0 - - + -
33E ALA* 2.8 37.2 + - + +
34E LEU* 3.4 24.2 - - + -
36E ALA* 6.0 1.3 - - + -
37E VAL* 4.1 15.0 - - + +
66E ILE 3.3 11.5 + - - +
67E LEU* 3.1 7.9 + - + +
69E LYS* 1.3 77.7 - - - +
71E LEU* 1.3 86.4 + - + +
73E GLU* 3.0 13.0 + - + +
74E ALA* 2.7 55.3 + - + +
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Residues in contact with LEU 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E PHE* 4.8 13.2 - - + -
15E GLU* 5.0 1.8 - - + +
16E PHE* 4.2 26.0 - - + +
19E ARG* 4.0 38.1 - - + -
20E ARG* 5.0 0.9 - - - +
23E LEU* 4.3 13.7 - - + -
67E LEU 2.8 20.0 + - - +
68E SER* 3.4 6.3 + - - +
70E TRP* 1.3 91.9 - - + +
72E GLU* 1.3 63.9 + - + +
74E ALA* 3.1 11.7 + - - -
75E GLU* 3.1 30.1 + - - +
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Residues in contact with GLU 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E SER* 3.1 22.8 + - - +
69E LYS* 3.9 8.9 - - - +
71E LEU* 1.3 77.8 - - + +
73E GLU* 1.3 62.7 + - - +
74E ALA 3.2 0.7 + - - -
75E GLU* 3.3 19.4 + - - +
76E GLN* 4.7 2.6 - - - +
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Residues in contact with GLU 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E ALA* 4.3 19.2 - - - +
37E VAL* 4.0 24.7 - - - +
69E LYS 3.2 14.4 + - - +
70E TRP* 3.0 12.9 + - + +
72E GLU* 1.3 77.9 - - - +
74E ALA* 1.3 56.3 + - - +
75E GLU 3.3 0.9 - - - -
76E GLN* 3.4 20.9 - - - +
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Residues in contact with ALA 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E LEU* 3.3 22.4 - - + +
25E TYR* 4.1 17.3 + - + +
70E TRP* 2.7 53.4 + - + +
71E LEU* 3.1 9.3 + - - +
73E GLU* 1.3 73.6 - - - +
75E GLU* 1.3 56.3 + - - +
76E GLN* 3.6 8.0 + - - -
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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