Contacts of the helix formed by residues 6 - 21 (chain R) in PDB entry 5OA3
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 6 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13722 U 4.6 2.2 - - - +
13732 C 3.0 9.9 - - - +
13862 A 3.9 22.7 - - + +
13872 G 3.8 32.2 + - - +
4R VAL 3.9 2.5 + - - -
5R ARG* 1.3 74.2 - - - +
7R LYS* 1.3 77.1 + - + +
8R THR* 3.2 19.7 - - - +
9R VAL* 3.2 21.8 + - - +
10R LYS* 3.0 22.7 + - - +
49R LYS* 5.4 4.3 + - - -
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Residues in contact with LYS 7 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13722 U 4.7 5.4 + - - -
13732 C 2.5 48.1 + - - +
13832 A 5.8 3.3 + - - +
13842 C 4.8 7.9 - - - +
13852 G 3.2 25.7 + - - -
13862 A 4.1 18.7 - - - +
6R THR* 1.3 75.5 - - + +
8R THR* 1.3 59.6 + - - +
10R LYS* 4.1 2.9 - - - +
11R LYS* 2.9 68.0 + - - +
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Residues in contact with THR 8 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13872 G 3.1 25.7 + - - -
206D ASP* 3.5 33.2 + - - +
208D VAL* 4.3 17.3 - - + -
6R THR* 3.2 7.6 - - - +
7R LYS* 1.3 76.7 - - - +
9R VAL* 1.3 65.2 + - - +
11R LYS* 4.2 4.9 - - - +
12R ALA* 2.9 30.1 + - - +
46R LEU* 5.1 9.4 - - + -
50R ILE* 5.4 1.6 - - - -
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Residues in contact with VAL 9 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5R ARG* 3.8 20.0 - - + -
6R THR* 3.2 37.0 + - - +
8R THR* 1.3 79.9 - - - +
10R LYS* 1.3 58.2 + - - +
12R ALA* 3.8 1.0 - - - +
13R ALA* 2.9 31.7 + - - +
46R LEU* 5.3 7.2 - - + +
49R LYS* 4.2 46.9 - - + +
50R ILE* 4.3 13.7 - - + +
53R TYR* 4.2 11.0 - - + -
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Residues in contact with LYS 10 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13732 C 3.1 31.6 + - - +
13742 C 3.7 16.2 - - - +
14652 A 3.0 35.0 + - - -
14662 G 3.8 1.3 + - - -
5R ARG* 3.6 37.5 - - + +
6R THR 3.0 15.6 + - - +
7R LYS* 4.1 3.1 - - - +
9R VAL* 1.3 76.9 - - - +
11R LYS* 1.3 61.6 + - + +
13R ALA* 3.8 1.0 - - - +
14R ARG* 2.9 44.4 + - - +
53R TYR* 3.6 38.6 + - + +
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Residues in contact with LYS 11 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13822 A 4.4 31.2 + - - +
13832 A 5.1 5.5 + - - -
7R LYS* 2.9 51.6 + - - +
8R THR* 4.2 3.8 - - - +
10R LYS* 1.3 73.2 - - + +
12R ALA* 1.3 66.6 + - - +
14R ARG* 3.2 16.2 + - - +
15R VAL* 2.9 32.1 + - + +
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Residues in contact with ALA 12 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D VAL* 4.1 21.3 - - + -
210D ILE* 4.4 6.5 - - + +
8R THR 2.9 21.3 + - - +
9R VAL 3.8 1.6 - - - +
11R LYS* 1.3 76.8 - - - +
13R ALA* 1.3 55.6 + - - +
15R VAL* 3.3 5.2 + - - +
16R ILE* 2.9 39.4 + - + +
50R ILE* 4.0 24.2 - - + -
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Residues in contact with ALA 13 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9R VAL 2.9 18.1 + - - +
10R LYS 3.9 0.2 - - - +
12R ALA* 1.3 76.2 - - - +
14R ARG* 1.3 56.7 + - - +
16R ILE* 3.8 0.6 - - - +
17R ILE* 3.0 35.8 + - - +
50R ILE* 3.8 22.1 - - - +
53R TYR* 3.4 29.6 - - + -
54R VAL* 3.9 15.7 - - + +
57R LEU* 4.5 2.2 - - + -
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Residues in contact with ARG 14 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13742 C 3.0 28.7 + - - -
13752 G 4.4 12.9 + - - -
10R LYS* 2.9 35.6 + - - +
11R LYS* 3.3 16.1 - - - +
12R ALA 3.2 0.2 - - - -
13R ALA* 1.3 75.1 - - - +
15R VAL* 1.3 62.1 + - + +
18R GLU* 2.9 31.6 + - - +
53R TYR* 5.2 6.8 + - + -
57R LEU* 4.4 14.3 - - + +
68R GLY* 4.6 26.9 + - - +
69R ILE* 3.5 22.8 - - + +
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Residues in contact with VAL 15 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D ILE* 3.6 26.0 - - + -
11R LYS* 2.9 21.0 + - + +
12R ALA* 3.9 0.7 - - - +
14R ARG* 1.3 76.0 - - + +
16R ILE* 1.3 63.9 + - - +
18R GLU* 3.2 13.7 + - + +
19R LYS* 2.9 42.5 + - + +
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Residues in contact with ILE 16 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D ILE* 3.7 31.2 - - + -
12R ALA* 2.9 23.8 + - + +
13R ALA* 3.8 5.6 - - - +
15R VAL* 1.3 77.0 - - - +
17R ILE* 1.3 64.6 + - - +
19R LYS* 3.8 2.0 - - - +
20R TYR* 2.9 27.3 + - + +
24R LEU* 4.7 13.5 - - + -
35R CYS* 4.0 26.2 - - - -
38R ILE* 3.6 31.4 - - + -
39R ALA* 3.8 11.9 - - + -
50R ILE* 5.2 3.6 - - + -
54R VAL* 4.2 10.8 - - + -
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Residues in contact with ILE 17 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13R ALA 3.0 21.6 + - - +
14R ARG 3.9 2.0 - - - +
16R ILE* 1.3 76.9 - - - +
18R GLU* 1.3 64.0 + - - +
21R TYR* 3.2 28.4 + - + +
24R LEU* 3.6 15.9 - - + -
54R VAL* 3.2 45.3 - - + +
57R LEU* 4.1 15.5 - - + -
58R MET* 3.6 20.0 - - + +
61R ILE* 3.9 6.3 - - + -
69R ILE* 3.7 17.5 - - + -
71R ILE* 3.5 18.2 - - + +
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Residues in contact with GLU 18 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14R ARG* 2.9 19.9 + - - +
15R VAL* 3.3 14.6 - - + +
16R ILE 3.1 0.2 - - - -
17R ILE* 1.3 79.2 - - - +
19R LYS* 1.3 65.3 + - + +
21R TYR* 4.6 0.3 + - - +
68R GLY 5.1 2.3 - - - +
69R ILE* 4.4 10.0 - - + +
70R SER* 3.6 35.4 + - - +
71R ILE* 3.9 22.8 - - - +
72R LYS 5.1 1.4 + - - -
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Residues in contact with LYS 19 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D ILE* 4.6 17.9 + - + +
212D GLU* 3.5 35.8 + - - +
213D PRO* 3.8 29.8 - - + +
15R VAL* 2.9 31.4 + - + +
16R ILE* 5.1 0.4 - - - -
18R GLU* 1.3 83.2 - - + +
20R TYR* 1.3 80.3 + - + +
21R TYR* 3.5 1.8 + - - +
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Residues in contact with TYR 20 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D ILE* 4.7 2.2 - - + -
211D VAL* 2.8 28.9 + - - +
212D GLU 3.6 1.0 + - - -
213D PRO* 3.1 35.7 - - + +
214D LYS 4.6 0.2 + - - -
16R ILE* 2.9 21.3 + - + +
19R LYS* 1.3 88.5 - - + +
21R TYR* 1.3 50.9 + - - +
22R THR* 2.8 4.6 + - - -
23R ARG* 2.6 79.3 + - + +
24R LEU* 3.7 9.7 + - + -
38R ILE* 3.5 48.8 + - + +
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Residues in contact with TYR 21 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17R ILE* 3.2 21.0 + - + +
18R GLU 4.8 0.7 - - - +
19R LYS 3.5 3.8 + - - +
20R TYR* 1.3 74.1 - - - +
22R THR* 1.3 68.7 + - - +
23R ARG 3.3 0.5 + - - -
24R LEU* 3.4 23.6 + - - +
58R MET* 4.4 14.2 - - + +
61R ILE* 3.5 49.4 - - + +
62R GLN* 4.2 12.9 + - - -
71R ILE* 3.5 37.2 - - + -
72R LYS 5.3 4.5 - - - -
74R GLN* 4.9 14.1 + - + -
212g LYS* 4.0 10.8 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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