Contacts of the helix formed by residues 43 - 52 (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 43 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31E GLY* 4.8 2.5 - - - -
42E PHE* 1.3 79.6 - - - +
44E GLN* 1.3 66.2 + - - +
45E THR* 3.9 6.2 + - - -
46E THR* 3.0 23.6 + - - -
47E ILE* 3.0 17.9 + - - +
176H G 2.5 56.5 + - - +
177H A 4.9 4.0 - - - -
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Residues in contact with GLN 44 (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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27E GLN* 3.8 30.4 + - + +
28E THR* 3.4 35.6 + - + +
43E SER* 1.3 73.8 - - - +
45E THR* 1.3 58.1 + - - +
47E ILE* 4.0 1.4 - - - +
48E CYS* 2.9 28.9 + - - +
179G C 3.6 24.7 - - + +
180G A 2.7 50.3 + - - +
178H A 4.6 3.6 - - - +
179H T 5.5 0.4 + - - -
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Residues in contact with THR 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E SER* 3.1 10.3 + - - -
44E GLN* 1.3 86.3 + - - +
46E THR* 1.3 58.0 + - - +
48E CYS* 3.3 3.4 + - - +
49E ARG* 2.9 67.1 + - - +
180G A 4.2 1.2 + - - -
181G T 3.0 28.1 + - + +
176H G 3.7 7.9 - - - +
177H A 3.5 25.7 + - - +
178H A 3.8 6.9 + - - -
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Residues in contact with THR 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E PHE* 3.5 27.4 - - + -
43E SER* 3.0 9.1 + - - -
45E THR* 1.3 77.9 - - - +
47E ILE* 1.3 65.6 + - + +
49E ARG* 3.2 14.6 + - - +
50E PHE* 3.1 19.9 + - - +
55E LEU* 4.7 5.9 - - + +
59E ASN* 5.8 0.4 - - - +
63E LEU* 3.7 23.1 - - + +
175H T 3.2 18.4 - - + +
176H G 2.5 27.0 + - - -
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Residues in contact with ILE 47 (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* 4.2 22.9 - - + -
20E ARG* 5.1 0.2 - - - +
27E GLN* 3.9 37.9 - - + +
30E VAL* 4.3 9.9 - - + -
31E GLY* 4.0 15.7 - - - +
34E LEU* 4.6 3.6 - - + -
42E PHE* 4.6 11.2 - - + -
43E SER 3.0 15.3 + - - +
44E GLN 4.0 3.1 - - - +
46E THR* 1.3 80.4 - - + +
48E CYS* 1.3 63.8 + - - +
50E PHE* 3.0 16.0 + - + +
51E GLU* 3.1 15.5 + - - +
63E LEU* 5.4 3.4 - - + -
67E LEU* 4.3 27.8 - - + -
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Residues in contact with CYS 48 (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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27E GLN* 3.5 21.4 - - - +
44E GLN* 2.9 23.5 + - - +
45E THR 3.6 4.7 - - - +
47E ILE* 1.3 77.9 - - - +
49E ARG* 1.3 62.2 + - - +
51E GLU* 3.5 0.9 + - - +
52E ASN* 2.9 32.9 + - - +
54E GLN* 5.4 2.2 - - - -
180G A 3.4 52.9 - - - +
181G T 3.8 12.6 - - + -
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Residues in contact with ARG 49 (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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45E THR* 2.9 33.8 + - + +
46E THR* 3.5 16.6 + - - +
47E ILE 3.2 0.2 - - - -
48E CYS* 1.3 75.9 - - - +
50E PHE* 1.3 57.8 + - - +
52E ASN 3.5 0.3 - - - -
53E LEU* 2.8 7.1 + - - -
54E GLN* 2.5 70.9 + - + +
55E LEU* 3.6 16.7 - - + +
148E ARG* 5.2 5.6 - - - +
181G T 4.7 6.1 - - + +
182G T 3.0 31.5 + - - +
183G C 4.2 0.4 - - - +
175H T 3.7 26.3 + - - +
176H G 2.6 49.1 + - - -
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Residues in contact with PHE 50 (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* 5.5 4.5 - - + -
12E PHE* 3.6 34.3 - + - -
13E ALA* 3.9 16.3 - - + +
16E PHE* 4.4 10.5 - + - -
46E THR 3.1 11.2 + - - +
47E ILE* 3.0 12.6 + - - +
49E ARG* 1.3 74.2 - - - +
51E GLU* 1.3 66.9 + - + +
53E LEU* 2.8 32.4 + - + +
55E LEU* 4.1 15.8 - - + +
60E ALA* 3.5 17.9 - - + -
63E LEU* 3.8 18.2 - - + -
64E LYS* 3.4 32.1 - - + -
67E LEU* 3.6 24.2 - - + -
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Residues in contact with GLU 51 (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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13E ALA* 3.8 22.9 - - - +
14E ASN* 4.9 3.8 - - - +
16E PHE* 3.6 29.4 - - + -
17E LYS* 3.0 40.7 + - + +
20E ARG* 2.1 45.8 + - - -
27E GLN* 3.0 18.6 + - - +
47E ILE* 3.1 13.3 + - - +
48E CYS 4.0 3.8 - - - +
50E PHE* 1.3 81.7 - - + +
52E ASN* 1.3 60.8 + - - +
53E LEU* 3.6 1.4 + - - +
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Residues in contact with ASN 52 (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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17E LYS* 4.3 3.3 + - - +
48E CYS* 2.9 27.1 + - - +
50E PHE 3.2 0.6 - - - -
51E GLU* 1.3 78.3 - - - +
53E LEU* 1.3 70.5 + - - +
54E GLN* 3.2 27.5 + - + +
150E LYS* 3.8 9.9 - - - +
180G A 3.3 38.1 + - - -
181G T 4.8 6.5 + - - -
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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
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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