Contacts of the helix formed by residues 30 - 50 (chain E) in PDB entry 3O65
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 30 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17E GLN* 4.0 2.5 - - - -
29E PHE* 1.3 75.8 - - - +
31E PRO* 1.3 66.8 - - - +
32E VAL* 2.8 7.7 + - - +
33E GLU* 2.8 43.3 + - - +
34E LEU* 3.0 12.2 + - - +
27G GLU* 2.7 32.2 + - - -
28G TYR 4.0 1.8 + - - -
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Residues in contact with PRO 31 (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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14E LEU* 5.1 12.1 - - + -
17E GLN* 3.2 24.2 - - - +
30E SER* 1.3 87.7 - - - -
32E VAL* 1.3 57.1 + - + +
34E LEU* 3.8 7.8 - - + +
35E ALA* 2.9 26.7 + - - +
70E MSE 5.2 2.4 - - - +
76E PHE* 4.7 6.6 - - + -
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Residues in contact with VAL 32 (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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30E SER* 2.8 16.2 + - - +
31E PRO* 1.3 77.1 - - + +
33E GLU* 1.3 68.7 + - - +
34E LEU 3.1 1.1 - - - -
35E ALA* 2.9 9.1 + - + +
36E SER* 2.8 27.1 + - - +
25G GLN 5.2 2.0 - - - +
26G GLY* 4.5 4.3 - - - -
27G GLU* 3.7 29.4 - - + +
28G TYR* 3.3 33.0 - - + +
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Residues in contact with GLU 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E TYR 2.8 23.7 - - - +
29E PHE* 3.6 27.7 - - + -
30E SER* 2.8 29.0 + - - +
32E VAL* 1.3 78.5 - - - +
34E LEU* 1.3 58.8 + - - +
36E SER 3.3 0.3 + - - -
37E ILE* 3.0 32.4 + - - +
87E PHE* 3.8 4.0 - - - -
28G TYR* 2.7 35.2 - - + +
29G PHE* 5.5 1.2 - - - -
33G GLU* 3.1 11.3 - - - +
87G PHE* 5.0 0.7 - - - -
88G TRP* 3.3 35.6 + - + -
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Residues in contact with LEU 34 (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 ALA* 4.5 4.5 - - + -
17E GLN* 3.7 46.2 - - + +
20E LEU* 4.1 13.7 - - + -
29E PHE* 3.9 29.8 - - + -
30E SER 3.0 12.1 + - - +
31E PRO* 4.0 3.6 - - + +
33E GLU* 1.3 73.5 - - - +
35E ALA* 1.3 67.3 + - - +
37E ILE* 3.4 13.4 + - + +
38E ALA* 3.1 23.9 + - - +
76E PHE* 3.5 36.8 - - + -
80E VAL* 4.5 9.3 - - + +
84E ALA* 4.7 1.3 - - + -
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Residues in contact with ALA 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E PRO 2.9 20.2 + - - +
32E VAL* 2.9 12.1 + - + +
34E LEU* 1.3 77.0 - - - +
36E SER* 1.3 58.3 + - - +
38E ALA* 3.2 3.6 + - - +
39E HIS* 2.9 47.6 + - + +
70E MSE 4.3 20.6 - - + -
76E PHE* 4.3 0.2 - - - -
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Residues in contact with SER 36 (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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32E VAL* 2.8 19.7 + - - +
35E ALA* 1.3 72.3 - - - +
37E ILE* 1.3 62.7 + - - +
39E HIS* 4.0 9.7 - - - +
40E GLN* 2.8 37.3 + - - +
28G TYR* 2.9 26.3 + - - -
88G TRP* 3.9 19.3 - - - -
171G PRO* 4.2 11.3 - - - +
172G ASP* 5.2 4.0 + - - +
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Residues in contact with ILE 37 (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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29E PHE* 4.5 3.1 - - + -
33E GLU 3.0 20.8 + - - +
34E LEU* 3.8 13.0 - - + +
35E ALA 3.2 0.2 - - - -
36E SER* 1.3 78.1 - - - +
38E ALA* 1.3 61.9 + - - +
40E GLN* 3.5 6.9 + - - +
41E LEU* 2.9 33.4 + - + +
80E VAL* 3.5 23.8 - - + -
83E ASN* 3.6 26.7 - - + +
84E ALA* 3.6 35.2 - - + +
87E PHE* 3.9 21.8 - - + -
88G TRP* 4.1 13.0 - - + -
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Residues in contact with ALA 38 (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 3.1 17.7 + - - +
35E ALA* 3.7 3.8 - - - +
37E ILE* 1.3 75.8 - - - +
39E HIS* 1.3 60.4 + - + +
41E LEU* 3.3 3.6 + - - +
42E ASP* 2.9 34.1 + - - +
69E ASN* 3.7 31.1 - - + +
70E MSE 3.8 18.6 - - + -
76E PHE* 4.3 1.8 - - + -
80E VAL* 4.0 9.0 - - + -
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Residues in contact with HIS 39 (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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35E ALA* 2.9 41.7 + - + +
36E SER* 4.3 8.5 - - - +
38E ALA* 1.3 77.8 - - + +
40E GLN* 1.3 60.6 + - + +
42E ASP* 3.2 16.9 + - - +
43E GLU* 2.9 26.7 + - - +
70E MSE 5.2 11.8 - - + -
172G ASP* 5.2 18.2 - - + +
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Residues in contact with GLN 40 (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 SER* 2.8 25.7 + - - +
37E ILE* 3.5 9.9 + - - +
38E ALA 3.2 0.6 - - - -
39E HIS* 1.3 78.7 - - + +
41E LEU* 1.3 64.1 + - + +
43E GLU* 3.8 8.8 - - + +
44E GLU* 3.2 29.6 + - - +
83E ASN* 5.9 1.0 + - - -
88G TRP* 4.3 22.7 - - - +
169G ASP 5.4 3.8 - - - +
170G LEU 5.4 0.5 - - - +
171G PRO* 5.0 12.1 - - - +
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Residues in contact with LEU 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E ILE* 2.9 21.8 - - - +
38E ALA 3.3 4.0 + - - +
39E HIS 3.2 0.4 - - - -
40E GLN* 1.3 81.9 - - + +
42E ASP* 1.3 64.9 + - - +
43E GLU 3.2 1.6 - - - -
44E GLU* 3.9 11.4 - - - +
45E GLU* 3.3 23.6 + - - +
69E ASN* 3.5 23.7 + - - +
79E GLN* 3.4 51.4 - - + +
80E VAL* 3.8 9.4 - - + +
83E ASN* 2.9 33.7 - - + +
8F LEU* 4.0 13.8 - - + +
9F THR* 5.8 0.2 - - + -
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Residues in contact with ASP 42 (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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38E ALA* 2.9 17.2 + - - +
39E HIS* 3.2 22.3 + - - +
41E LEU* 1.3 79.8 - - - +
43E GLU* 1.3 58.3 + - - +
45E GLU* 3.7 3.4 + - - +
46E ARG* 3.0 26.3 + - - +
62E PHE* 5.2 3.3 - - - -
67E SER* 2.8 40.5 + - - -
68E GLU 4.4 0.2 + - - -
69E ASN* 2.9 20.4 + - - +
70E MSE 5.8 0.5 - - - +
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Residues in contact with GLU 43 (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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39E HIS 2.9 14.5 + - - +
40E GLN* 4.0 10.1 - - + +
41E LEU 3.2 0.2 - - - -
42E ASP* 1.3 74.5 - - - +
44E GLU* 1.3 54.2 + - + +
45E GLU 3.1 1.8 - - - -
46E ARG* 2.6 52.4 + - - +
47E MSE 2.7 38.0 + - + +
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Residues in contact with GLU 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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40E GLN 3.2 18.7 + - - +
41E LEU* 4.1 7.9 - - - +
42E ASP 3.6 0.2 - - - -
43E GLU* 1.3 78.5 - - + +
45E GLU* 1.3 56.5 + - - +
47E MSE 3.2 11.2 - - - +
48E ARG* 3.2 29.6 + - - +
8F LEU* 3.7 45.1 - - + +
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Residues in contact with GLU 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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41E LEU 3.3 14.1 + - - +
42E ASP* 4.1 3.8 - - - +
43E GLU 3.1 1.0 - - - -
44E GLU* 1.3 75.2 - - - +
46E ARG* 1.3 67.2 + - - +
47E MSE 3.0 1.3 - - - -
48E ARG* 3.3 7.8 + - + +
49E MSE 3.2 29.0 + - + +
62E PHE* 3.3 21.8 - - + -
68E GLU* 5.2 7.2 + - - +
69E ASN* 4.4 13.9 + - - -
79E GLN* 4.5 2.6 + - - -
8F LEU* 4.2 5.4 - - + +
42F ARG* 2.9 32.6 + - - -
44F ILE* 5.6 3.8 - - + -
70F VAL* 3.4 41.7 - - + +
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Residues in contact with ARG 46 (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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42E ASP 3.0 15.8 + - - +
43E GLU* 2.6 43.2 + - - +
45E GLU* 1.3 76.1 - - - +
47E MSE 1.3 82.8 + - - +
49E MSE 3.0 1.0 + - - -
50E ALA* 2.8 54.1 + - - +
59E TYR* 2.6 46.7 + - + +
62E PHE* 3.9 15.8 - - + -
63E LEU* 4.4 14.6 - - + -
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Residues in contact with MSE 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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43E GLU* 2.7 14.6 + - + +
44E GLU* 3.2 16.2 - - - +
45E GLU 3.0 0.2 - - - -
46E ARG* 1.3 99.9 - - - +
48E ARG* 1.3 76.7 + - - +
49E MSE 3.1 0.2 - - - -
50E ALA* 3.3 29.7 + - + +
51E GLU* 3.6 12.7 + - + +
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Residues in contact with ARG 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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44E GLU 3.2 14.9 + - - +
45E GLU* 3.3 9.8 + - + +
46E ARG 3.3 0.4 - - - -
47E MSE 1.3 90.8 + - - +
49E MSE 1.3 61.6 + - - +
51E GLU* 2.9 39.7 + - - +
8F LEU* 5.6 5.6 - - + -
44F ILE* 4.0 17.2 - - + +
47F GLY* 3.1 23.4 + - - -
68F HIS* 3.1 42.2 + - + -
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Residues in contact with MSE 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 GLU* 3.2 16.1 + - + +
46E ARG 3.0 6.8 + - - +
48E ARG* 1.3 82.5 - - - +
50E ALA* 1.3 52.8 + - - +
51E GLU 2.7 15.3 + - - -
52E GLY* 2.9 16.6 + - - -
53E GLY 3.8 0.5 + - - -
58E GLU* 3.2 29.6 - - + +
59E TYR* 3.2 32.4 - - + +
62E PHE* 3.8 38.8 - - + -
42F ARG* 4.8 1.8 - - - +
44F ILE* 3.5 35.4 - - + -
47F GLY* 3.9 16.0 - - - +
49F GLN* 3.7 15.5 - - + +
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Residues in contact with ALA 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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46E ARG* 2.8 36.8 + - - +
47E MSE 3.3 25.0 + - + +
49E MSE 1.3 72.0 - - - +
51E GLU* 1.3 58.9 + - - +
53E GLY 4.5 1.6 - - - -
54E VAL* 3.6 29.5 + - + +
59E TYR* 3.2 15.0 - - + -
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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