Contacts of the helix formed by residues 18 - 35 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17M ASP* 1.3 84.1 - - + +
19M ALA* 1.3 62.7 + - - +
20M SER* 3.1 18.5 + - - -
21M ASP* 2.8 44.7 + - - +
22M ARG* 3.1 21.3 + - - +
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Residues in contact with ALA 19 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M THR* 1.3 72.8 - - - +
20M SER* 1.3 60.8 + - - +
21M ASP 3.3 0.2 - - - -
22M ARG* 2.8 21.4 + - - +
23M LYS* 3.0 26.5 + - - +
26M ARG* 4.5 2.9 + - - -
9O T 6.0 1.8 - - - +
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Residues in contact with SER 20 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M THR* 3.1 12.5 + - - -
19M ALA* 1.3 79.3 - - - +
21M ASP* 1.3 61.0 + - - +
23M LYS* 3.6 9.7 + - - +
24M ALA* 2.9 27.2 + - - +
69M ARG* 3.5 14.9 + - - -
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Residues in contact with ASP 21 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14M MET* 5.4 1.6 - - - +
15M PRO* 3.7 38.0 - - + +
16M THR 3.7 0.7 - - - -
17M ASP* 3.6 9.4 + - - +
18M THR* 2.8 51.0 + - - +
20M SER* 1.3 80.5 + - - +
22M ARG* 1.3 58.4 + - - +
24M ALA* 3.6 3.3 - - - +
25M TYR* 3.2 25.1 + - - +
69M ARG* 3.4 31.7 - - + +
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Residues in contact with ARG 22 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15M PRO 4.9 0.9 - - - -
16M THR* 3.3 28.8 + - + +
17M ASP 3.2 20.6 + - - -
18M THR 3.3 10.3 + - - +
19M ALA* 2.8 40.7 - - - +
21M ASP* 1.3 80.0 + - - +
23M LYS* 1.3 64.8 + - - +
25M TYR* 3.2 10.5 + - + +
26M ARG* 3.0 46.7 + - - +
9O T 5.0 10.1 + - - -
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Residues in contact with LYS 23 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19M ALA 3.0 18.3 + - - +
20M SER* 3.6 9.2 - - - +
22M ARG* 1.3 75.8 - - - +
24M ALA* 1.3 65.2 + - - +
26M ARG* 3.2 19.0 + - - +
27M LYS* 3.0 35.1 + - + +
7O G 4.5 20.8 + - - -
8O C 3.5 32.8 + - - +
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Residues in contact with ALA 24 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14M MET* 4.4 2.9 - - + -
20M SER 2.9 19.5 + - - +
21M ASP* 3.6 11.7 - - - +
22M ARG 3.2 0.4 - - - -
23M LYS* 1.3 77.7 - - - +
25M TYR* 1.3 61.2 + - - +
27M LYS* 3.7 6.9 - - - +
28M PHE* 3.2 22.3 + - - +
67M PRO* 4.0 13.7 - - + +
69M ARG* 3.9 26.5 - - + +
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Residues in contact with TYR 25 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12M PHE* 3.9 25.4 - + - -
14M MET* 3.8 28.7 - - + +
15M PRO 5.0 2.9 - - - +
16M THR* 6.2 4.7 - - + -
21M ASP 3.2 11.0 + - - +
22M ARG* 3.3 11.7 - - + +
23M LYS 3.1 0.2 - - - -
24M ALA* 1.3 76.8 - - - +
26M ARG* 1.3 95.7 + - + +
28M PHE* 2.8 5.1 + + - +
29M ARG* 2.8 42.6 + - + +
15P C 3.6 6.1 - + + +
16P T 2.6 68.0 + - + +
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Residues in contact with ARG 26 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19M ALA 4.5 2.6 + - - -
22M ARG* 3.0 41.8 + - - +
23M LYS* 3.4 21.0 - - - +
25M TYR* 1.3 97.5 - - + +
27M LYS* 1.3 57.8 + - - +
29M ARG* 3.5 3.7 + - - +
30M LYS* 3.0 30.1 + - - +
8O C 3.0 53.6 + - - +
9O T 3.6 38.8 + - - +
16P T 6.1 0.4 - - + -
17P C 5.8 4.3 - - - +
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Residues in contact with LYS 27 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23M LYS* 3.0 28.5 + - + +
24M ALA* 3.7 7.0 - - - +
26M ARG* 1.3 78.3 - - - +
28M PHE* 1.3 57.6 + - - +
30M LYS* 3.3 6.9 + - + +
31M PHE* 3.0 26.9 + - - +
65M ASN* 5.5 7.5 + - - +
7O G 5.1 17.5 - - - +
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Residues in contact with PHE 28 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10M LEU* 4.1 24.7 - - + -
12M PHE* 4.5 6.7 - + - -
14M MET* 3.8 22.2 - - + -
24M ALA 3.2 11.3 + - - +
25M TYR* 2.8 8.3 + + - +
27M LYS* 1.3 77.4 - - - +
29M ARG* 1.3 67.4 + - - +
31M PHE* 3.1 17.7 + + - +
32M LEU* 3.0 40.1 + - + +
62M LEU* 4.1 16.2 - - + -
65M ASN 3.7 14.4 - - - +
67M PRO* 3.7 27.8 - - + -
72M ILE* 4.0 27.4 - - + -
88N LEU* 4.2 8.1 - - + -
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Residues in contact with ARG 29 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12M PHE* 5.2 3.4 - - + -
25M TYR* 2.8 44.4 + - + +
26M ARG* 3.9 4.9 - - - +
28M PHE* 1.3 76.5 - - - +
30M LYS* 1.3 66.7 + - - +
32M LEU* 3.0 13.4 + - + +
33M ILE* 2.9 45.6 + - + +
39M MET* 3.2 20.2 - - - +
45M TYR* 2.8 25.9 + - + +
16P T 3.7 17.7 + - - +
17P C 2.9 30.7 + - - -
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Residues in contact with LYS 30 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18J ASN* 3.8 19.7 - - - +
26M ARG 3.0 19.3 + - - +
27M LYS* 3.5 8.3 - - + +
29M ARG* 1.3 77.9 - - - +
31M PHE* 1.3 62.2 + - - +
33M ILE* 3.3 8.5 + - + +
34M ASN* 3.0 40.2 + - - +
5O T 4.4 1.4 - - - -
6O A 2.5 62.8 + - - +
7O G 5.2 10.8 + - - +
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Residues in contact with PHE 31 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27M LYS* 3.0 13.8 + - + +
28M PHE* 3.2 20.2 - + + +
29M ARG 3.1 0.2 - - - -
30M LYS* 1.3 76.5 - - - +
32M LEU* 1.3 67.8 + - + +
34M ASN* 3.3 7.4 + - + +
35M GLU* 2.9 66.0 + - + +
58M MET* 3.8 11.4 - - + -
61M ARG* 3.7 24.0 - - + -
62M LEU* 3.7 25.1 - - + -
65M ASN* 3.5 39.9 - - + +
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Residues in contact with LEU 32 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10M LEU* 3.8 36.6 - - + -
12M PHE* 4.2 7.4 - - + -
28M PHE* 3.0 38.9 + - + +
29M ARG* 3.4 11.9 - - + +
31M PHE* 1.3 87.7 - - + +
33M ILE* 1.3 63.4 + - + +
35M GLU 3.2 6.4 + - - -
36M GLY 3.2 0.2 + - - -
37M PHE* 3.0 54.9 + - + +
45M TYR* 4.2 26.7 - - + -
62M LEU* 4.4 2.2 - - + -
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Residues in contact with ILE 33 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J ASN* 4.1 25.4 - - + +
20J HIS* 3.4 31.0 - - + +
29M ARG* 2.9 65.5 + - + +
30M LYS* 3.8 8.5 - - + +
32M LEU* 1.3 75.3 - - - +
34M ASN* 1.3 59.4 + - - +
36M GLY* 2.9 16.1 + - - -
37M PHE 4.2 10.8 - - - +
45M TYR* 5.2 9.0 - - + -
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Residues in contact with ASN 34 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J ASN* 3.1 43.2 + - - +
19J ASN* 3.1 25.2 + - - +
33J HIS* 2.8 18.4 + - - -
30M LYS* 3.0 44.7 + - - +
31M PHE* 3.7 7.3 - - + +
32M LEU 3.3 0.2 - - - -
33M ILE* 1.3 77.7 - - - +
35M GLU* 1.3 61.5 + - + +
36M GLY 3.1 0.7 - - - -
6O A 4.8 5.1 + - - -
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Residues in contact with GLU 35 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19J ASN* 5.5 2.3 + - - -
33J HIS* 3.3 10.4 + - - -
31M PHE* 2.9 50.1 + - + +
32M LEU 3.7 4.9 - - - +
33M ILE 3.2 0.2 - - - -
34M ASN* 1.3 78.9 - - - +
36M GLY* 1.3 57.8 + - - +
37M PHE* 3.4 13.9 - - + -
47M LYS* 3.0 26.9 + - - -
58M MET* 3.5 15.0 - - + +
61M ARG* 2.8 39.3 + - - -
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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