Contacts of the helix formed by residues 18 - 35 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16F THR 3.6 0.3 - - - +
17F ASP* 1.3 81.0 - - + +
19F ALA* 1.3 62.8 + - - +
20F SER* 3.1 15.1 + - - -
21F ASP* 2.8 31.9 + - - +
22F ARG* 2.8 34.9 + - - +
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Residues in contact with ALA 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F THR* 1.3 74.7 - - - +
20F SER* 1.3 59.0 + - - +
22F ARG* 3.6 23.3 + - - +
23F LYS* 3.1 27.4 + - - +
26F ARG* 4.4 3.3 + - - -
-14R T 5.8 2.7 - - - +
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Residues in contact with SER 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F THR* 3.1 12.0 + - - -
19F ALA* 1.3 78.4 - - - +
21F ASP* 1.3 57.3 + - - +
22F ARG 3.3 0.2 - - - -
23F LYS* 3.5 9.1 + - - +
24F ALA* 2.9 32.6 + - - +
69F ARG* 3.1 23.2 + - - -
127J GLN* 6.3 0.9 - - - -
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Residues in contact with ASP 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F MET* 5.8 0.5 - - - +
15F PRO* 3.4 44.1 - - + +
16F THR* 4.2 1.1 - - - +
17F ASP* 3.6 6.2 + - - +
18F THR* 2.8 42.2 + - - +
20F SER* 1.3 80.0 + - - +
22F ARG* 1.3 65.7 + - - +
24F ALA* 3.5 2.6 + - - +
25F TYR* 3.1 21.8 + - - +
69F ARG* 2.9 29.1 + - - +
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Residues in contact with ARG 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F PRO 5.0 0.9 - - - -
16F THR* 2.7 54.4 + - + +
17F ASP 2.9 12.9 + - - -
18F THR 2.8 18.6 + - - +
19F ALA* 3.6 28.0 - - - +
20F SER 3.3 0.4 - - - -
21F ASP* 1.3 80.1 - - - +
23F LYS* 1.3 65.1 + - - +
25F TYR* 3.2 11.6 + - + +
26F ARG* 3.0 44.0 + - - +
-14R T 5.0 13.5 + - - -
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Residues in contact with LYS 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F ALA 3.1 18.5 + - - +
20F SER* 3.6 9.0 - - - +
22F ARG* 1.3 76.0 - - - +
24F ALA* 1.3 65.0 + - - +
26F ARG* 3.2 18.2 + - - +
27F LYS* 3.0 32.4 + - + +
-16R G 4.9 11.1 + - - -
-15R C 3.5 31.8 + - - +
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Residues in contact with ALA 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F MET* 5.3 0.9 - - - -
20F SER 2.9 19.2 + - - +
21F ASP 3.6 7.2 - - - +
22F ARG 3.2 0.2 - - - -
23F LYS* 1.3 77.5 - - - +
25F TYR* 1.3 61.7 + - - +
27F LYS* 3.7 6.7 + - - +
28F PHE* 3.2 21.8 + - - +
67F PRO* 4.0 18.1 - - + +
69F ARG* 3.6 31.0 - - + +
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Residues in contact with TYR 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F PHE* 3.9 15.5 - + - -
14F MET* 3.9 37.4 - - + -
15F PRO 5.0 2.5 - - - +
16F THR* 6.0 1.8 - - - +
21F ASP 3.1 11.5 + - - +
22F ARG* 3.3 15.9 - - + +
24F ALA* 1.3 77.6 - - - +
26F ARG* 1.3 91.8 + - + +
28F PHE* 2.9 4.3 + - - +
29F ARG* 2.8 42.2 + - + +
15G C 3.6 5.9 - + + +
16G T 2.6 67.3 + - + +
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Residues in contact with ARG 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F ALA 4.4 3.0 + - - -
22F ARG* 3.0 28.4 + - - +
23F LYS* 3.4 30.2 + - - +
25F TYR* 1.3 94.0 - - + +
27F LYS* 1.3 57.8 + - - +
29F ARG* 3.5 3.4 + - - +
30F LYS* 3.0 31.2 + - - +
17G C 5.8 3.8 - - - +
-16R G 4.9 0.4 - - - +
-15R C 2.5 54.3 + - - +
-14R T 3.4 39.5 + - - +
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Residues in contact with LYS 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F LYS* 3.0 25.0 + - + +
24F ALA* 3.7 7.4 - - - +
26F ARG* 1.3 74.4 - - - +
28F PHE* 1.3 64.7 + - - +
30F LYS* 3.3 7.1 + - - +
31F PHE* 3.0 22.4 + - + +
65F ASN* 5.3 12.3 + - - +
-16R G 5.1 18.6 - - - +
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Residues in contact with PHE 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E LEU* 4.2 15.3 - - + -
10F LEU* 4.1 23.3 - - + -
12F PHE* 4.5 0.7 - + - -
14F MET* 3.4 31.2 - - + -
24F ALA 3.2 11.5 + - - +
25F TYR 2.9 8.4 + - - +
27F LYS* 1.3 77.6 - - - +
29F ARG* 1.3 67.4 + - - +
31F PHE* 3.2 13.5 + + + +
32F LEU* 3.0 43.4 + - + +
62F LEU* 4.1 16.6 - - + -
65F ASN* 3.7 21.8 - - - +
67F PRO* 3.7 20.9 - - + -
72F ILE* 4.1 16.4 - - + -
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Residues in contact with ARG 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F PHE* 5.2 3.1 - - + -
25F TYR* 2.8 45.9 + - + +
26F ARG* 3.9 4.7 - - - +
28F PHE* 1.3 75.1 - - - +
30F LYS* 1.3 67.9 + - - +
32F LEU* 3.0 12.5 + - + +
33F ILE* 2.9 45.9 + - + +
39F MET* 3.2 20.9 - - - +
45F TYR* 2.8 25.3 + - + +
16G T 3.6 17.4 + - - +
17G C 3.0 30.1 + - - -
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Residues in contact with LYS 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ASN* 4.5 9.0 - - - +
26F ARG 3.0 19.9 + - - +
27F LYS* 3.4 7.9 - - - +
29F ARG* 1.3 78.8 - - - +
31F PHE* 1.3 63.1 + - - +
33F ILE* 3.3 9.3 + - + +
34F ASN* 3.0 41.1 + - - +
-17R A 2.6 75.7 + - - +
-16R G 3.9 14.2 + - - +
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Residues in contact with PHE 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F LYS* 3.0 14.0 + - + +
28F PHE* 3.4 16.4 - + - +
29F ARG 3.1 0.2 - - - -
30F LYS* 1.3 77.6 - - - +
32F LEU* 1.3 73.3 + - + +
34F ASN* 3.3 6.5 + - - +
35F GLU* 2.9 61.5 + - + +
58F MET* 3.7 20.6 - - + -
61F ARG* 3.8 20.4 - - + -
62F LEU* 3.8 16.6 - - + -
65F ASN* 3.1 45.5 - - + +
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Residues in contact with LEU 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F LEU* 3.8 35.7 - - + -
12F PHE* 4.3 7.6 - - + -
28F PHE* 3.0 43.5 + - + +
29F ARG* 3.0 11.9 + - + +
31F PHE* 1.3 84.3 - - + +
33F ILE* 1.3 65.2 + - + +
35F GLU 3.2 5.5 + - - -
36F GLY 3.3 0.2 + - - -
37F PHE* 3.1 55.5 + - + +
45F TYR* 4.2 26.5 - - + -
62F LEU* 4.4 2.5 - - + -
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Residues in contact with ILE 33 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D ASN* 4.0 24.7 - - + +
20D HIS* 3.0 33.4 + - + +
31D LEU* 6.6 0.2 - - + -
29F ARG* 2.9 65.2 + - + +
30F LYS* 3.8 8.1 - - + +
32F LEU* 1.3 77.2 - - - +
34F ASN* 1.3 59.2 + - - +
36F GLY* 3.0 17.2 + - - -
37F PHE 4.3 10.0 - - - +
45F TYR* 5.2 9.2 - - + -
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Residues in contact with ASN 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ASN* 3.4 42.0 + - - +
19D ASN* 3.4 23.0 + - - +
33D HIS* 2.8 25.7 + - - -
30F LYS* 3.0 44.9 + - - +
31F PHE* 3.8 7.1 - - - +
33F ILE* 1.3 78.7 - - - +
35F GLU* 1.3 55.4 + - + +
36F GLY 3.2 0.4 - - - -
-17R A 4.6 6.3 + - - -
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Residues in contact with GLU 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D HIS* 3.5 8.7 + - - -
31F PHE* 2.9 56.5 + - + +
32F LEU 3.7 4.7 - - - +
33F ILE 3.2 0.2 - - - -
34F ASN* 1.3 79.4 - - - +
36F GLY* 1.3 56.7 + - - +
37F PHE* 4.0 13.0 - - + -
47F LYS* 3.0 26.0 + - - -
58F MET* 3.5 8.4 - - + +
61F ARG* 2.3 43.9 + - - -
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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