Contacts of the helix formed by residues 24 - 41 (chain E) in PDB entry 6X0A
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 24 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E ILE 3.2 8.8 + - - +
21E ALA* 3.3 4.4 + - - -
23E ASP* 1.3 89.8 - - - +
25E PRO* 1.3 71.5 - - - +
26E ARG* 3.4 11.8 + - - +
27E ALA* 3.3 26.2 + - - +
28E ALA 3.2 16.1 + - - -
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Residues in contact with PRO 25 (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 TRP* 3.4 31.2 - - + -
21E ALA* 3.6 15.1 - - + +
23E ASP 4.6 1.1 - - - +
24E SER* 1.3 84.5 - - - +
26E ARG* 1.3 64.0 + - + +
28E ALA* 3.2 4.9 + - - +
29E ASP* 3.2 20.1 + - - -
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Residues in contact with ARG 26 (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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66A ASN* 2.9 32.3 + - - +
89A ASP* 3.8 30.1 + - - +
91A SER* 5.7 0.2 + - - -
24E SER* 3.1 8.9 + - - +
25E PRO* 1.3 80.7 - - + +
27E ALA* 1.3 64.0 + - - +
29E ASP* 3.0 22.4 + - + +
30E HIS* 3.4 31.7 + - + +
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Residues in contact with ALA 27 (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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20E ILE* 4.0 14.2 - - + +
23E ASP* 5.1 5.2 - - - +
24E SER* 3.2 23.3 + - - +
26E ARG* 1.3 79.0 - - - +
28E ALA* 1.3 61.7 + - - +
30E HIS* 3.3 20.9 + - - +
31E PHE* 3.4 11.6 + - - +
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Residues in contact with ALA 28 (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 TRP* 3.2 59.2 - - + +
20E ILE* 3.7 14.1 - - + +
21E ALA* 3.9 7.0 - - - +
24E SER 3.2 11.5 + - - +
25E PRO 3.4 4.9 - - - +
26E ARG 3.1 0.6 - - - -
27E ALA* 1.3 77.3 - - - +
29E ASP* 1.3 62.9 + - - +
31E PHE* 3.3 9.5 + - - +
32E LEU* 3.5 11.3 - - - +
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Residues in contact with ASP 29 (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 TRP* 2.8 33.8 + - - +
25E PRO 3.2 9.8 + - - +
26E ARG* 3.0 14.2 + - + +
28E ALA* 1.3 79.4 - - - +
30E HIS* 1.3 63.4 + - + +
32E LEU* 3.5 3.4 + - - +
33E ASP* 3.2 30.5 + - - +
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Residues in contact with HIS 30 (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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63A THR* 6.5 0.9 - - - -
65A GLY* 4.6 16.8 - - - -
66A ASN* 4.9 8.4 + - - -
26E ARG* 3.4 43.0 + - + +
27E ALA* 3.3 12.2 + - - +
28E ALA 3.3 0.4 - - - -
29E ASP* 1.3 79.0 - - + +
31E PHE* 1.3 57.7 + - - +
33E ASP* 3.3 14.5 + - - +
34E ALA* 2.8 27.6 + - - +
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Residues in contact with PHE 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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16E ILE* 3.7 22.2 - - + -
20E ILE* 3.5 30.5 - - + -
27E ALA 3.4 5.5 + - - +
28E ALA 3.3 9.5 + - - +
29E ASP 3.2 0.8 - - - -
30E HIS* 1.3 78.3 - - - +
32E LEU* 1.3 52.1 + - + +
34E ALA* 2.8 13.1 + - + +
35E ILE* 2.7 52.4 + - + +
64E ILE* 3.5 42.0 - - + -
65E GLY* 5.7 2.2 - - - -
67E TYR* 4.9 19.5 - + + -
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Residues in contact with LEU 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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13E LEU* 3.8 38.8 - - + +
14E VAL* 5.7 0.2 - - - -
16E ILE* 4.4 11.4 - - + -
17E TRP* 3.8 31.6 - - + -
20E ILE* 5.6 0.2 - - + -
28E ALA* 3.5 15.0 - - - +
29E ASP* 3.5 6.2 + - - +
30E HIS 3.4 0.2 - - - -
31E PHE* 1.3 84.8 - - + +
33E ASP* 1.3 53.7 + - - +
35E ILE* 2.9 15.1 + - + +
36E ALA* 2.5 39.3 + - - +
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Residues in contact with ASP 33 (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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63A THR* 5.9 2.9 - - - +
29E ASP* 3.2 21.1 + - - +
30E HIS* 3.3 17.4 + - - +
32E LEU* 1.3 75.4 - - - +
34E ALA* 1.3 58.0 + - - +
36E ALA* 3.2 7.5 + - - +
37E GLU* 2.9 31.9 + - - +
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Residues in contact with ALA 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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30E HIS 2.8 12.4 + - - +
31E PHE* 2.8 23.2 + - + +
33E ASP* 1.3 72.6 - - - +
35E ILE* 1.3 58.6 + - - +
37E GLU* 3.6 10.3 + - - +
38E ARG* 3.3 26.5 + - - +
64E ILE* 4.0 13.6 - - + +
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Residues in contact with ILE 35 (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 LEU* 4.2 28.0 - - + -
16E ILE* 4.9 3.1 - - + -
31E PHE* 2.7 48.3 + - + +
32E LEU* 3.4 16.2 - - + +
34E ALA* 1.3 70.6 - - - +
36E ALA* 1.3 60.3 + - - +
38E ARG* 3.2 6.1 + - - +
39E ILE* 2.9 52.9 + - + +
64E ILE* 3.5 27.6 - - + -
69E ILE* 3.8 14.4 - - + -
83E ILE* 4.8 10.8 - - + -
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Residues in contact with ALA 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 LEU 2.5 20.4 + - - +
33E ASP* 3.5 9.6 - - - +
35E ILE* 1.3 73.1 - - - +
37E GLU* 1.3 64.2 + - - +
39E ILE* 2.8 11.5 + - - +
40E LEU* 2.8 37.9 + - + +
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Residues in contact with GLU 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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38A ARG* 2.5 44.6 + - - -
41A GLN* 3.6 12.2 + - - -
48A SER* 3.4 43.0 - - - +
33E ASP 2.9 19.7 + - - +
34E ALA* 3.9 9.9 - - - +
35E ILE 3.4 0.2 - - - -
36E ALA* 1.3 72.5 - - - +
38E ARG* 1.3 61.0 + - + +
40E LEU* 3.5 9.5 + - - +
41E GLN* 3.1 33.6 + - - +
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Residues in contact with ARG 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 ALA 3.3 12.7 + - - +
35E ILE* 3.2 8.6 + - - +
36E ALA 3.1 0.8 - - - -
37E GLU* 1.3 78.5 - - + +
39E ILE* 1.3 61.8 + - - +
41E GLN* 3.4 31.1 + - - +
42E LEU* 2.7 22.8 - - - +
62E LEU* 3.3 41.2 - - + +
63E THR* 3.3 29.2 + - - +
64E ILE* 4.2 23.7 - - - +
69E ILE* 4.5 4.4 - - + +
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Residues in contact with ILE 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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3E ILE* 3.4 20.2 - - + +
13E LEU* 5.2 10.8 - - + -
35E ILE* 2.9 39.3 + - + +
36E ALA* 2.8 11.2 + - - +
38E ARG* 1.3 79.3 - - - +
40E LEU* 1.3 62.9 + - + +
42E LEU* 3.3 24.2 - - - +
69E ILE* 3.9 27.1 - - + -
80E ILE* 3.7 35.7 - - + -
83E ILE* 5.4 1.6 - - + -
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Residues in contact with LEU 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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47A GLU 5.6 8.1 - - - +
48A SER 5.9 3.1 - - - +
50A PRO* 6.1 6.7 - - + -
3E ILE* 3.8 20.6 - - + -
36E ALA* 2.8 32.2 + - + +
37E GLU* 4.0 8.3 - - - +
39E ILE* 1.3 72.1 - - + +
41E GLN* 1.3 64.2 + - - +
42E LEU 3.1 0.9 - - - -
43E ALA* 3.1 22.9 + - - +
44E ALA* 4.2 1.0 + - - +
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Residues in contact with GLN 41 (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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41A GLN* 3.4 27.1 - - - +
45A PHE* 3.4 46.6 - - + -
48A SER* 4.1 9.2 + - - +
37E GLU* 3.1 22.3 + - - +
38E ARG* 3.5 32.7 + - - +
39E ILE 3.2 1.0 - - - -
40E LEU* 1.3 75.7 - - - +
42E LEU* 1.3 59.4 + - + +
43E ALA 3.2 0.2 - - - -
44E ALA* 3.1 8.8 + - - +
45E PHE* 3.0 28.9 + - - +
48E SER* 5.4 3.6 - - - +
62E LEU* 5.6 1.9 - - - +
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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