Contacts of the helix formed by residues 44 - 60 (chain E) in PDB entry 2POZ
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 GLY 44 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D MSE 3.8 15.5 - - - -
54D ASP* 3.4 14.9 + - - +
19E HIS* 5.1 0.2 + - - -
39E ILE* 3.8 10.9 - - - +
42E GLY 4.1 0.2 + - - -
43E VAL* 1.3 78.1 - - - +
45E GLY* 1.3 70.2 + - - +
46E THR 3.1 3.1 - - - -
47E ALA* 3.0 15.1 + - - +
48E ALA* 3.0 13.5 + - - +
88E ILE* 3.9 4.5 - - - +
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Residues in contact with GLY 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D ASP* 3.6 2.4 + - - -
12E LEU* 3.9 10.8 - - - +
19E HIS* 3.5 35.6 + - - -
21E VAL* 3.5 11.3 - - - +
39E ILE* 3.9 9.4 - - - -
44E GLY* 1.3 77.6 - - - +
46E THR* 1.3 60.8 + - - +
48E ALA* 3.3 4.3 + - - +
49E ALA 3.2 17.3 + - - -
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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
----------------------------------------------------------
50D GLY* 3.7 20.1 - - - +
53D LYS* 4.5 18.1 + - + +
54D ASP* 2.6 31.5 + - - -
380D TRP* 4.1 7.4 - - + -
12E LEU* 3.9 18.3 - - + +
45E GLY* 1.3 73.2 - - - +
47E ALA* 1.3 59.5 + - - +
49E ALA* 3.5 3.4 + - - +
50E GLY* 3.0 22.7 + - - -
380E TRP* 4.0 27.2 - - + +
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Residues in contact with ALA 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D ALA* 3.2 37.0 - - - +
50D GLY 3.9 0.6 - - - -
51D MSE 3.6 22.7 - - + +
54D ASP* 3.4 3.0 + - - -
88D ILE* 4.1 4.7 - - + -
44E GLY* 3.0 12.4 + - - +
46E THR* 1.3 74.9 - - - +
48E ALA* 1.3 55.5 + - - +
50E GLY 3.1 1.0 + - - -
51E MSE 2.8 31.0 + - - +
88E ILE* 4.0 16.2 - - + -
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Residues in contact with ALA 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E VAL* 4.2 13.5 - - + -
37E ALA* 4.5 7.4 - - + -
39E ILE* 3.8 33.2 - - + -
44E GLY 3.0 7.1 + - - +
45E GLY 3.5 9.4 - - - +
46E THR 3.3 0.2 - - - -
47E ALA* 1.3 75.4 - - - +
49E ALA* 1.3 66.5 + - - +
51E MSE 3.0 4.5 + - - +
52E ILE* 3.0 25.8 + - - +
88E ILE* 4.2 12.3 - - + +
91E ALA* 5.1 2.5 - - + -
92E GLY* 5.0 1.4 - - - +
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Residues in contact with ALA 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E ILE* 3.7 21.2 - - + +
12E LEU* 4.7 7.4 - - + -
21E VAL* 3.9 11.1 - - + +
45E GLY 3.2 10.7 + - - +
46E THR* 3.8 9.0 - - - +
48E ALA* 1.3 78.0 - - - +
50E GLY* 1.3 63.8 + - - +
52E ILE* 3.2 3.9 + - - +
53E LYS* 3.1 18.4 + - - +
380E TRP* 3.6 36.0 - - + -
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Residues in contact with GLY 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D THR* 3.8 12.9 - - - -
47D ALA 4.0 9.0 - - - -
46E THR 3.0 13.4 + - - -
47E ALA 3.1 5.3 + - - -
49E ALA* 1.3 77.6 - - - +
51E MSE 1.3 55.3 + - - +
53E LYS* 3.4 1.9 + - - +
54E ASP* 3.0 33.4 + - - -
380E TRP* 3.6 20.4 - - - -
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Residues in contact with MSE 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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43D VAL* 3.3 21.5 - - + +
44D GLY* 3.8 10.8 - - - -
47D ALA* 3.9 6.7 - - + +
88D ILE* 5.5 3.4 - - - -
47E ALA 2.8 12.9 + - - +
48E ALA 3.0 8.3 + - - +
50E GLY* 1.3 74.8 - - - +
52E ILE* 1.3 66.5 + - - +
54E ASP* 3.3 23.2 + - + -
55E LEU* 2.9 39.4 + - + +
88E ILE* 3.7 29.8 - - + +
89E ILE* 3.5 29.4 - - - +
92E GLY* 4.3 2.5 - - - -
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Residues in contact with ILE 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E ILE* 3.7 15.9 - - + -
21E VAL* 4.0 26.5 - - + -
22E LEU 4.7 2.0 - - - +
23E VAL* 3.7 34.8 - - + -
37E ALA* 4.3 5.8 - - + +
48E ALA 3.0 10.5 + - - +
49E ALA 3.2 5.4 + - - +
51E MSE 1.3 75.9 - - - +
53E LYS* 1.3 56.5 + - - +
55E LEU* 3.9 6.2 - - - +
56E SER* 2.7 44.2 + - - +
92E GLY* 3.9 19.1 - - - +
95E ALA* 4.0 22.0 - - + -
96E ILE* 4.4 9.0 - - + -
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Residues in contact with LYS 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D THR* 4.5 17.3 + - + +
10E ILE* 4.3 13.9 - - + +
49E ALA 3.1 13.2 + - - +
50E GLY 3.6 7.4 - - - +
52E ILE* 1.3 77.9 - - - +
54E ASP* 1.3 68.1 + - - +
56E SER* 3.5 1.0 + - - -
57E GLU* 2.7 67.6 + - - +
380E TRP* 4.0 21.1 - - + -
381E ALA* 4.1 13.2 - - + -
382E SER 6.2 0.2 - - - -
383E CYS* 4.1 8.0 - - - -
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Residues in contact with ASP 54 (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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43D VAL* 3.5 11.4 - - + +
44D GLY* 3.2 8.0 - - - -
45D GLY 3.2 10.2 + - - -
46D THR* 2.7 46.0 + - - -
47D ALA 3.6 0.3 + - - -
50E GLY 3.0 14.6 + - - +
51E MSE 3.3 17.2 + - + -
53E LYS* 1.3 83.6 + - - +
55E LEU* 1.3 62.3 + - - +
57E GLU* 3.6 6.7 + - - +
58E ARG* 3.2 24.9 + - - +
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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
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43D VAL* 3.8 6.3 - - + -
51E MSE 2.9 49.5 + - + +
52E ILE 3.9 0.2 - - - +
54E ASP* 1.3 76.2 - - - +
56E SER* 1.3 55.5 + - - +
58E ARG 3.1 0.3 + - - -
59E PHE* 2.7 64.7 + - + +
60E LEU* 4.8 0.4 - - - -
75E MSE 4.5 12.1 - - + -
79E SER* 4.4 3.8 - - - -
89E ILE* 4.1 13.2 - - + +
92E GLY* 3.9 6.5 - - - -
93E ILE* 3.7 33.7 - - + +
96E ILE* 3.8 17.7 - - + -
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Residues in contact with SER 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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8E VAL* 3.3 41.2 - - - +
52E ILE* 2.7 28.4 + - - +
53E LYS* 3.8 3.3 - - - -
55E LEU* 1.3 76.2 - - - +
57E GLU* 1.3 60.2 + - - +
60E LEU* 3.0 41.1 + - - +
61E ILE* 3.0 14.4 + - - +
96E ILE* 4.3 1.1 - - - +
383E CYS* 4.3 9.2 - - - -
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Residues in contact with GLU 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 LYS* 2.7 50.6 + - - +
54E ASP* 4.1 6.8 - - - +
56E SER* 1.3 80.0 - - - +
58E ARG* 1.3 58.7 + - - +
61E ILE* 4.1 9.5 - - + +
382E SER 5.0 1.4 - - - +
383E CYS* 3.2 33.3 - - + +
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Residues in contact with ARG 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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43D VAL* 4.0 14.3 - - + +
170D GLN* 4.7 12.1 + - - +
54E ASP 3.2 17.4 + - - +
55E LEU 3.1 3.0 + - - +
56E SER 3.1 0.4 - - - -
57E GLU* 1.3 79.9 - - - +
59E PHE* 1.3 100.3 + - + +
63E LYS* 4.9 3.8 + - - -
74E THR* 5.8 0.4 - - - +
78E HIS* 4.8 10.9 + - - +
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Residues in contact with PHE 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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43D VAL* 4.0 8.3 - - + -
55E LEU* 2.7 43.1 + - + +
58E ARG* 1.3 115.5 - - + +
60E LEU* 1.3 65.8 + - + +
61E ILE 4.1 0.4 - - - -
63E LYS* 3.2 30.8 + - - +
71E LEU* 4.4 7.6 - - + +
74E THR* 3.7 27.6 - - + -
75E MSE 3.6 32.3 - - + -
78E HIS* 3.7 40.6 - - + -
79E SER* 4.0 3.1 - - - -
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Residues in contact with LEU 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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5E ILE* 3.6 26.6 - - + +
8E VAL* 4.2 13.5 - - + -
25E ILE* 4.3 9.2 - - + -
55E LEU 4.5 2.0 - - - +
56E SER* 3.0 39.4 + - - +
58E ARG 4.0 0.2 - - - -
59E PHE* 1.3 87.3 - - + +
61E ILE* 1.3 71.6 + - + +
62E GLY 3.1 0.7 + - - -
63E LYS* 2.9 21.9 + - - +
71E LEU* 4.4 19.3 - - + -
75E MSE 4.9 5.4 - - - -
96E ILE* 3.7 42.0 - - + -
100E LEU* 5.1 1.1 - - + -
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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