Contacts of the helix formed by residues 44 - 59 (chain E) in PDB entry 4P9U
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 THR 44 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E SER* 5.0 0.4 - - - -
43E VAL* 1.3 78.3 - - - +
45E ARG* 1.3 69.8 + - - +
46E THR* 3.9 5.1 + - - +
47E THR* 3.3 31.6 - - - +
48E LEU* 3.2 19.2 + - - +
15G C 3.3 39.0 + - + +
16G A 4.0 38.5 + - - -
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Residues in contact with ARG 45 (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 GLU* 2.9 41.0 + - + +
35E ARG* 4.0 34.2 - - - +
38E SER* 4.1 17.1 - - - +
44E THR* 1.3 77.4 + - - +
46E THR* 1.3 58.5 + - - +
48E LEU* 3.1 6.2 + - - +
49E ARG* 2.9 43.3 + - + +
18G A 4.0 8.1 - - - +
12H G 3.7 17.2 + - - -
13H G 2.9 45.2 + - - -
14H T 3.5 15.5 + - - +
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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
----------------------------------------------------------
44E THR* 3.4 9.5 + - - +
45E ARG* 1.3 77.9 - - - +
47E THR* 1.3 63.9 + - - +
49E ARG* 2.9 23.2 + - - +
50E GLU* 3.0 25.6 + - + +
46F THR* 3.6 30.0 - - + +
50F GLU* 4.9 1.5 - - - +
14G T 5.2 4.5 - - + -
15G C 4.4 17.0 - - + +
16G A 3.2 28.1 + - - -
17G A 4.7 1.7 + - - -
14H T 5.7 1.1 + - - -
15H T 4.5 3.5 + - - -
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Residues in contact with THR 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E PRO* 4.3 9.4 - - + -
9E ALA* 3.7 39.4 - - + +
43E VAL* 4.7 6.1 - - + -
44E THR* 3.3 16.1 - - - +
45E ARG 3.4 0.2 - - - -
46E THR* 1.3 77.5 - - - +
48E LEU* 1.3 63.5 + - - +
50E GLU* 3.1 12.6 + - + +
51E VAL* 3.0 22.6 + - + +
14G T 3.7 25.1 + - - +
15G C 3.2 17.3 + - - +
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Residues in contact with LEU 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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12E ALA* 4.5 8.7 - - + -
16E ILE* 3.8 28.3 - - + -
34E GLU* 4.0 28.0 - - + +
37E LEU* 4.3 15.0 - - + -
38E SER* 4.6 6.1 - - - +
41E ILE* 4.1 15.5 - - + -
43E VAL* 4.0 13.2 - - + +
44E THR 3.2 11.0 + - - +
45E ARG* 3.1 11.6 + - - +
47E THR* 1.3 78.1 - - - +
49E ARG* 1.3 58.4 + - - +
51E VAL* 3.4 4.9 + - + +
52E LEU* 2.9 54.2 + - + +
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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
----------------------------------------------------------
34E GLU* 3.0 31.3 + - + +
45E ARG* 2.9 40.3 + - + +
46E THR* 2.9 10.7 + - - +
48E LEU* 1.3 76.1 - - + +
50E GLU* 1.3 61.1 + - - +
52E LEU* 3.2 8.7 + - - +
53E GLN* 2.9 43.4 + - - +
50F GLU* 2.5 48.1 + - - +
12H G 4.0 2.6 - - - +
13H G 2.3 50.6 + - - +
14H T 3.4 28.3 - - - +
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Residues in contact with GLU 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 ALA* 6.1 0.9 - - + -
46E THR* 3.0 31.2 + - + +
47E THR* 3.1 10.7 + - + +
49E ARG* 1.3 73.2 - - - +
51E VAL* 1.3 66.3 + - - +
53E GLN* 3.3 7.5 + - - +
54E ARG* 3.0 34.5 + - - +
46F THR* 4.4 3.3 - - - +
49F ARG* 2.6 48.0 + - - +
50F GLU* 4.0 18.6 - - + +
53F GLN* 3.7 28.9 + - + +
14G T 4.4 11.9 + - - +
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Residues in contact with VAL 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E ALA* 3.3 33.4 - - + +
12E ALA* 3.7 13.5 - - + -
13E GLU* 3.6 34.1 - - + +
16E ILE* 4.2 6.7 - - + -
47E THR 3.0 19.2 + - - +
48E LEU* 3.4 9.4 - - + +
50E GLU* 1.3 76.3 - - - +
52E LEU* 1.3 57.8 + - - +
54E ARG* 3.2 19.9 + - - +
55E LEU* 2.9 38.8 + - + +
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Residues in contact with LEU 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E ILE* 3.7 27.4 - - + -
31E LEU* 3.8 14.8 - - + -
34E GLU* 3.6 32.3 - - + +
37E LEU* 5.0 1.1 - - + -
48E LEU* 2.9 43.9 + - + +
49E ARG* 3.5 7.9 - - - +
50E GLU 3.2 0.2 - - - -
51E VAL* 1.3 73.3 - - - +
53E GLN* 1.3 60.5 + - + +
55E LEU* 3.4 1.9 + - + +
56E ALA* 2.9 32.9 + - - +
61E LEU* 3.7 24.2 - - + +
63E ILE* 3.9 16.8 - - + +
69E THR* 5.1 3.4 - - - +
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Residues in contact with GLN 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E ARG* 2.9 29.7 + - - +
50E GLU* 3.7 6.3 - - - +
52E LEU* 1.3 72.7 - - - +
54E ARG* 1.3 66.7 + - + +
56E ALA* 3.9 5.7 - - - +
57E ARG* 2.9 25.6 + - - +
63E ILE* 4.7 12.7 - - - +
50F GLU* 4.0 21.9 + - + +
53F GLN* 5.6 0.2 - - + -
54F ARG* 2.9 53.8 + - + +
13H G 3.7 25.7 + - - -
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Residues in contact with ARG 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E ALA* 3.6 26.5 + - - +
10E GLY* 4.6 2.0 - - - +
13E GLU* 2.9 26.9 + - - +
50E GLU* 3.0 22.1 + - - +
51E VAL* 3.4 35.0 - - - +
53E GLN* 1.3 76.2 - - - +
55E LEU* 1.3 57.7 + - - +
57E ARG* 3.1 9.2 + - - +
58E ASP* 2.9 26.0 + - - +
53F GLN* 3.0 56.0 + - + +
54F ARG* 5.1 1.1 - - - +
57F ARG* 3.2 37.9 - - + +
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Residues in contact with LEU 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E GLU* 3.6 36.1 - - + +
16E ILE* 3.7 39.7 - - + -
17E ILE* 3.6 21.3 - - + -
51E VAL* 2.9 34.0 + - + +
52E LEU* 3.9 3.4 - - - +
54E ARG* 1.3 77.0 - - - +
56E ALA* 1.3 57.7 + - - +
58E ASP* 3.0 7.9 + - - +
59E GLY 2.9 22.0 + - - -
60E TRP* 3.1 25.9 + - + +
61E LEU* 4.2 12.6 - - + -
57F ARG* 4.8 1.6 - - - +
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Residues in contact with ALA 56 (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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52E LEU 2.9 18.6 + - - +
53E GLN* 3.9 6.5 - - - +
55E LEU* 1.3 76.6 - - - +
57E ARG* 1.3 63.1 + - - +
59E GLY* 3.1 13.7 + - - -
61E LEU* 3.9 25.1 - - + +
63E ILE* 3.8 28.9 - - + +
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Residues in contact with ARG 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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53E GLN 2.9 18.3 + - - +
54E ARG* 3.4 8.1 - - - +
56E ALA* 1.3 76.0 - - - +
58E ASP* 1.3 62.0 + - - +
59E GLY 3.6 0.2 + - - -
13F GLU* 3.0 28.9 + - - -
54F ARG* 3.1 55.9 + - + +
55F LEU* 4.7 1.0 - - - +
57F ARG* 4.7 6.5 - - + -
58F ASP* 2.8 52.1 + - - +
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Residues in contact with ASP 58 (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 GLU* 4.5 0.2 - - - +
54E ARG 2.9 7.0 + - - +
55E LEU* 3.0 11.2 + - - +
57E ARG* 1.3 79.2 - - - +
59E GLY* 1.3 56.7 + - - +
60E TRP* 3.6 17.1 + - + -
78E SER* 3.1 12.9 + - - -
79E GLY 4.5 0.2 + - - -
81E HIS* 3.0 47.8 + - + -
57F ARG* 2.5 55.6 + - - +
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Residues in contact with GLY 59 (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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55E LEU 2.9 1.8 + - - -
56E ALA 3.1 12.7 + - - -
57E ARG 3.3 0.4 - - - -
58E ASP* 1.3 78.9 - - - +
60E TRP* 1.3 63.2 + - - +
61E LEU 3.4 2.0 - - - -
72E ASN* 3.6 8.2 + - - +
74E PHE* 4.3 1.9 - - - +
77E THR* 2.3 43.8 + - - -
78E SER* 3.4 8.3 + - - -
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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
------------------------------------------------------------
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