Contacts of the helix formed by residues 21 - 36 (chain E) in PDB entry 3ECS
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 ALA 21 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E MSE 1.3 75.4 - - - +
22E SER* 1.3 69.6 + - - +
23E ALA 4.5 0.9 - - - +
24E VAL* 2.8 32.8 + - + +
25E ALA* 3.1 8.9 + - - +
108E ARG* 3.2 17.9 - - - +
132E ARG* 3.7 14.8 - - - +
231E GLU* 4.2 8.1 - - - +
233E PHE* 4.1 15.9 - - + -
234E LYS* 5.7 2.0 - - - -
505E SO4 4.7 4.3 - - - +
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Residues in contact with SER 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E PHE* 3.7 3.0 - - - -
14E MSE 3.2 32.2 - - - +
20E MSE 3.6 3.0 + - - -
21E ALA* 1.3 71.1 - - - +
23E ALA* 1.3 64.4 + - - +
25E ALA* 3.0 4.0 + - - +
26E ALA* 3.0 21.0 + - - +
60E ASP* 3.5 27.0 + - - -
62E SER* 5.3 4.8 - - - -
64E ALA* 5.4 2.7 - - - -
65E VAL* 4.2 6.7 - - - -
132E ARG* 3.8 14.3 + - - +
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Residues in contact with ALA 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E ALA* 3.2 1.0 - - + +
22E SER* 1.3 78.2 - - - +
24E VAL* 1.3 57.6 + - - +
26E ALA* 3.2 2.0 + - - +
27E ILE* 2.8 35.8 + - - +
64E ALA* 3.5 30.1 - - + +
65E VAL* 4.2 12.7 - - - +
68E GLY* 4.7 3.1 - - - -
233E PHE* 3.3 34.8 - - + -
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Residues in contact with VAL 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E MSE 4.1 18.4 - - + -
21E ALA* 2.8 19.9 + - + +
23E ALA* 1.3 69.1 - - - +
25E ALA* 1.3 60.2 + - - +
26E ALA 3.1 1.8 - - - -
27E ILE* 3.9 7.0 - - + +
28E ARG* 2.8 35.1 + - - +
101E LEU* 4.2 10.3 - - + -
104E ILE* 3.4 35.9 - - + +
105E SER* 6.1 1.1 - - - -
233E PHE* 3.6 25.8 - - + -
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Residues in contact with ALA 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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10E PHE* 3.7 8.5 - - + -
13E GLN* 3.8 11.4 - - + +
14E MSE 3.7 27.4 - - + -
20E MSE 3.7 24.6 - - - -
21E ALA 3.1 6.5 + - - +
22E SER 3.0 9.0 + - - +
24E VAL* 1.3 76.5 - - - +
26E ALA* 1.3 53.8 + - - +
28E ARG* 3.5 6.0 - - - +
29E THR* 2.7 35.3 + - - -
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Residues in contact with ALA 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E PHE* 3.6 23.8 - - + -
22E SER 3.0 7.0 + - - +
23E ALA* 3.4 9.0 - - - +
25E ALA* 1.3 76.7 - - - +
27E ILE* 1.3 64.2 + - + +
28E ARG 2.8 4.7 - - - -
29E THR* 2.9 15.4 + - - -
30E LEU* 3.1 18.2 + - - +
57E CYS* 4.7 8.9 - - - -
65E VAL* 4.1 27.4 - - + +
69E GLY* 6.5 0.2 - - - -
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Residues in contact with ILE 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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23E ALA* 2.8 29.1 + - + +
24E VAL* 3.9 8.5 - - + +
26E ALA* 1.3 72.1 - - + +
28E ARG* 1.3 61.2 + - - +
30E LEU* 3.8 16.0 + - - +
31E LEU* 3.5 17.5 + - + +
65E VAL 5.5 0.2 - - - +
68E GLY* 3.8 32.3 - - - +
69E GLY* 4.1 2.4 - - - +
72E PHE* 3.7 36.9 - - + -
100E PHE* 3.7 21.1 - - + -
101E LEU* 3.2 32.1 - - + -
104E ILE* 5.3 3.1 - - + -
233E PHE* 6.1 2.0 - - + -
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Residues in contact with ARG 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E TYR* 4.8 6.1 + - - +
13E GLN* 2.9 37.6 + - + +
20E MSE 3.8 27.5 - - - +
24E VAL* 2.8 25.4 + - - +
25E ALA* 3.5 3.6 - - - +
26E ALA 2.8 0.2 - - - -
27E ILE* 1.3 80.3 - - - +
29E THR* 1.3 64.5 + - - +
30E LEU 3.1 1.6 - - - -
31E LEU* 3.1 20.8 + - + +
32E GLU* 3.2 11.6 + - - +
101E LEU* 3.4 36.4 - - + +
105E SER* 6.3 1.4 - - - -
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Residues in contact with THR 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1E MSE 4.7 2.3 - - - +
6E LEU* 3.3 43.5 - - + +
9E TYR* 3.2 32.8 - - + -
10E PHE* 3.3 16.8 - - + -
13E GLN* 4.3 0.3 - - - +
25E ALA 2.7 21.9 + - - -
26E ALA* 2.9 9.7 + - - -
28E ARG* 1.3 76.3 - - - +
30E LEU* 1.3 56.3 + - - +
32E GLU* 3.4 3.1 + - - +
33E PHE* 3.1 23.4 + - - +
57E CYS* 5.5 3.6 - - - -
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Residues in contact with LEU 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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6E LEU* 5.0 1.1 - - + -
26E ALA 3.1 18.7 + - - +
27E ILE* 3.8 8.3 - - - +
29E THR* 1.3 74.4 - - - +
31E LEU* 1.3 61.7 + - - +
32E GLU 3.0 2.0 - - - -
33E PHE* 3.0 5.7 + - - +
34E LEU* 2.8 31.5 + - - +
50E THR* 4.3 9.7 - - + +
53E ILE* 3.5 33.9 - - + -
54E GLU* 3.6 41.5 - - + +
57E CYS* 4.8 8.5 - - - -
69E GLY* 4.4 5.8 - - - -
72E PHE* 3.7 33.0 - - + -
73E LEU* 5.9 0.2 - - + -
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Residues in contact with LEU 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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27E ILE* 3.5 12.5 + - + +
28E ARG* 3.1 16.2 + - + +
30E LEU* 1.3 79.4 - - - +
32E GLU* 1.3 61.8 + - + +
34E LEU* 3.8 5.6 + - + +
35E LYS* 3.2 51.1 + - + +
72E PHE* 4.2 12.8 - - + -
94E ILE* 3.9 38.1 - - + +
97E GLY* 4.3 18.4 - - - +
98E GLU* 3.7 9.6 - - + +
101E LEU* 5.5 10.3 - - + -
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Residues in contact with GLU 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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1E MSE 4.4 4.0 - - + -
9E TYR* 3.6 40.6 + - + +
28E ARG 3.2 5.4 + - - +
29E THR 3.6 9.2 - - - +
30E LEU 3.0 0.4 - - - -
31E LEU* 1.3 80.3 - - + +
33E PHE* 1.3 59.6 + - - +
34E LEU 3.2 0.7 - - - -
35E LYS* 3.6 16.9 + - - +
36E ARG* 2.5 78.3 + - - +
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Residues in contact with PHE 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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1E MSE 3.4 55.5 - - + +
2E ASP 5.7 0.2 - - - -
3E ASP* 5.9 0.4 - - - -
6E LEU* 4.2 7.6 - - + -
29E THR 3.1 15.6 + - - +
30E LEU 3.0 5.3 + - - +
32E GLU* 1.3 75.2 - - - +
34E LEU* 1.3 61.5 + - - +
36E ARG* 3.9 0.9 - - - +
37E ASP* 3.0 41.7 + - - +
46E ARG* 4.4 4.9 - - - -
49E LEU* 3.6 29.2 - - + -
50E THR* 3.9 22.9 - - + -
53E ILE* 3.3 44.6 - - + -
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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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30E LEU 2.8 15.6 + - - +
31E LEU* 3.8 11.9 - - + +
33E PHE* 1.3 81.8 - - + +
35E LYS* 1.3 65.4 + - - +
37E ASP 3.2 20.6 + - - +
46E ARG* 4.7 16.6 + - - +
50E THR* 5.2 7.6 - - + -
72E PHE* 5.1 4.5 - - + -
76E ILE* 4.0 26.7 - - + -
91E LYS* 3.6 23.1 - - + +
93E MSE 4.1 18.8 - - + +
94E ILE* 3.3 34.1 - - + +
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Residues in contact with LYS 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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31E LEU* 3.2 35.7 + - + +
32E GLU* 3.9 17.7 + - - +
34E LEU* 1.3 73.3 - - - +
36E ARG* 1.3 58.7 + - + +
37E ASP 2.9 14.0 + - - +
91E LYS* 5.4 1.4 - - - -
94E ILE* 3.5 35.6 - - + +
98E GLU* 2.8 32.1 + - - -
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Residues in contact with ARG 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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1E MSE 3.0 53.1 + - + +
5E GLU* 5.2 8.6 + - - -
9E TYR* 4.5 8.1 - - - -
32E GLU* 2.5 47.9 + - - +
33E PHE* 4.4 3.1 - - - +
34E LEU 3.4 0.2 - - - -
35E LYS* 1.3 77.0 - - - +
37E ASP* 1.3 63.8 + - - +
40E GLU* 4.8 0.7 - - - +
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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