Contacts of the helix formed by residues 18 - 35 (chain E) in PDB entry 5XVO
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 18 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E THR 3.6 0.2 - - - +
17E ASP* 1.3 78.7 - - - +
19E ALA* 1.3 66.3 + - + +
20E SER* 2.8 33.4 - - - +
21E ASP* 2.8 30.6 + - - +
22E ARG* 3.0 22.2 + - - -
69E ARG* 5.4 0.2 - - - +
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Residues in contact with ALA 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E THR* 1.3 76.8 - - + +
20E SER* 1.3 57.8 + - - +
22E ARG* 3.3 23.7 + - - +
23E LYS* 3.1 26.7 + - - +
26E ARG* 4.5 2.8 + - - -
9G T 6.0 1.8 - - - +
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Residues in contact with SER 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E THR* 2.8 24.3 - - - +
19E ALA* 1.3 80.2 - - - +
21E ASP* 1.3 59.0 + - - +
23E LYS* 3.5 10.2 + - - +
24E ALA* 2.9 26.9 + - - +
69E ARG* 3.6 23.1 + - - -
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Residues in contact with ASP 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E MET* 5.4 1.0 - - - +
15E PRO* 3.7 36.2 - - + +
16E THR 3.6 0.9 - - - -
17E ASP* 3.6 8.0 + - - +
18E THR* 2.8 48.5 + - - +
20E SER* 1.3 79.6 + - - +
22E ARG* 1.3 63.3 + - - +
24E ALA* 3.6 2.1 - - - +
25E TYR* 3.2 21.7 + - - +
69E ARG* 3.2 36.8 + - - +
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Residues in contact with ARG 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E PRO 5.0 0.9 - - - -
16E THR* 3.0 31.6 + - + +
17E ASP 3.2 20.4 + - - -
18E THR 3.0 20.8 + - - -
19E ALA* 3.3 21.6 - - - +
20E SER 3.3 0.2 - - - -
21E ASP* 1.3 79.6 + - - +
23E LYS* 1.3 66.2 + - - +
25E TYR* 3.2 12.2 + - + +
26E ARG* 3.0 45.8 + - - +
9G T 4.4 14.6 + - - -
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Residues in contact with LYS 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E ALA 3.1 15.7 + - - +
20E SER* 3.6 9.6 - - - +
22E ARG* 1.3 78.9 - - - +
24E ALA* 1.3 62.5 + - - +
26E ARG* 3.3 19.5 + - - +
27E LYS* 3.0 32.4 + - + +
7G G 4.3 22.0 + - - -
8G C 3.6 32.9 + - - +
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Residues in contact with ALA 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E MET* 4.4 3.1 - - + -
20E SER 2.9 13.4 + - - +
21E ASP 3.6 6.1 - - - +
22E ARG 3.2 0.2 - - - -
23E LYS* 1.3 76.8 - - - +
25E TYR* 1.3 61.6 - - - +
27E LYS* 3.7 6.9 + - - +
28E PHE* 3.2 22.0 + - - +
67E PRO* 4.0 17.0 - - + +
69E ARG* 3.2 37.5 - - - +
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Residues in contact with TYR 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E PHE* 3.9 25.1 - + - -
14E MET* 3.8 29.3 - - + +
15E PRO 5.0 2.5 - - - +
16E THR* 6.1 5.2 - - + -
21E ASP 3.2 11.7 + - - +
22E ARG* 3.4 12.8 - - + +
23E LYS 3.2 0.2 - - - -
24E ALA* 1.3 77.3 - - - +
26E ARG* 1.3 96.4 + - + +
28E PHE* 2.8 4.0 + + - +
29E ARG* 2.8 42.4 + - + +
-8R C 3.5 8.0 - + + +
-7R T 2.5 68.5 + - + +
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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
----------------------------------------------------------
19E ALA 4.5 2.6 + - - -
22E ARG* 3.0 37.4 + - - +
23E LYS* 3.3 28.5 + - - +
25E TYR* 1.3 95.4 - - + +
27E LYS* 1.3 56.7 + - - +
29E ARG* 4.0 4.0 - - - +
30E LYS* 3.0 30.9 + - - +
8G C 3.3 47.0 + - - +
9G T 3.6 39.2 + - - +
-7R T 6.1 0.2 - - + -
-6R C 5.8 4.3 - - - +
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Residues in contact with LYS 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E LYS* 3.0 25.6 + - + +
24E ALA* 3.7 7.9 - - - +
26E ARG* 1.3 77.8 - - - +
28E PHE* 1.3 56.6 + - - +
30E LYS* 3.3 7.6 + - - +
31E PHE* 3.0 26.8 + - + +
65E ASN* 5.7 7.5 + - - +
7G G 5.8 5.4 - - - +
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Residues in contact with PHE 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E LEU* 4.1 15.5 - - + -
12E PHE* 4.5 7.2 - + - -
14E MET* 3.8 20.6 - - + -
24E ALA 3.2 10.8 + - - +
25E TYR* 2.8 8.1 + + - +
27E LYS* 1.3 77.2 - - - +
29E ARG* 1.3 68.6 + - - +
31E PHE* 3.1 17.6 + + + +
32E LEU* 3.0 50.2 + - + +
62E LEU* 4.1 15.5 - - + -
65E ASN 3.7 13.2 - - - -
67E PRO* 3.7 29.6 - - + -
72E ILE* 4.1 27.1 - - + -
88F LEU* 4.2 7.0 - - + -
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Residues in contact with ARG 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E PHE* 5.2 2.5 - - + -
25E TYR* 2.8 45.3 + - + +
26E ARG* 4.0 5.2 - - - +
28E PHE* 1.3 77.6 - - - +
30E LYS* 1.3 66.8 + - - +
32E LEU* 3.0 12.9 + - + +
33E ILE* 2.9 46.5 + - + +
39E MET* 3.2 20.9 - - - +
45E TYR* 2.8 25.2 + - + +
-7R T 3.5 18.0 + - - +
-6R C 2.9 29.9 + - - -
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Residues in contact with LYS 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ASN* 4.8 8.3 - - - +
26E ARG 3.0 19.4 + - - +
27E LYS* 3.5 8.3 - - - +
29E ARG* 1.3 76.4 - - - +
31E PHE* 1.3 62.6 + - - +
33E ILE* 3.2 8.2 + - + +
34E ASN* 3.0 44.8 + - - +
6G A 2.6 69.5 + - - +
7G G 4.0 10.3 + - - -
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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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27E LYS 3.0 13.6 + - - +
28E PHE* 3.2 19.3 - + + +
30E LYS* 1.3 77.3 - - - +
32E LEU* 1.3 70.2 + - + +
34E ASN* 3.3 7.5 + - + +
35E GLU* 2.9 67.3 + - + +
58E MET* 3.8 13.5 - - + -
61E ARG* 3.8 21.8 - - + -
62E LEU* 3.7 25.1 - - + -
65E ASN* 3.5 40.8 - - + +
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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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10E LEU* 3.8 36.3 - - + -
12E PHE* 4.2 7.6 - - + -
28E PHE* 3.0 43.0 + - + +
29E ARG* 3.4 11.9 - - + +
31E PHE* 1.3 87.4 - - + +
33E ILE* 1.3 63.2 + - + +
35E GLU 3.2 6.2 + - - -
36E GLY 3.2 0.2 + - - -
37E PHE* 3.1 54.8 + - + +
45E TYR* 4.2 27.6 - - + -
62E LEU* 4.4 2.0 - - + -
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Residues in contact with ILE 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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18A ASN* 3.9 32.1 - - + +
20A HIS* 3.2 27.9 + - + +
29E ARG* 2.9 68.5 + - + +
30E LYS* 3.8 6.3 - - - +
32E LEU* 1.3 75.5 - - - +
34E ASN* 1.3 59.1 + - - +
36E GLY* 2.9 16.8 + - - -
37E PHE 4.3 10.8 - - - +
45E TYR* 5.2 9.4 - - + +
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Residues in contact with ASN 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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18A ASN* 3.3 40.8 + - - +
19A ASN* 3.1 28.2 + - - +
33A HIS* 2.9 18.6 + - - -
30E LYS* 3.0 45.1 + - - +
31E PHE* 3.7 7.3 - - + +
33E ILE* 1.3 77.9 - - - +
35E GLU* 1.3 62.4 + - + +
36E GLY 3.2 0.2 - - - -
6G A 5.2 2.2 + - - -
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Residues in contact with GLU 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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19A ASN* 5.8 0.7 + - - -
33A HIS* 3.3 8.1 + - - -
31E PHE* 2.9 55.1 + - + +
32E LEU 3.6 5.2 - - - +
33E ILE 3.2 0.2 - - - -
34E ASN* 1.3 82.0 - - + +
36E GLY* 1.3 58.2 + - - +
37E PHE* 3.5 13.7 - - + -
47E LYS* 3.0 26.2 + - - -
58E MET* 3.4 9.0 - - + +
61E ARG* 2.2 43.4 + - - -
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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