Contacts of the helix formed by residues 44 - 62 (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 LYS 44 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13892 C 4.5 0.2 + - - -
14502 G 3.2 38.0 + - - -
14512 G 3.5 34.5 + - - +
14532 C 5.0 0.4 - - - +
32R LYS* 5.3 0.2 - - - +
42R PRO 3.6 0.2 + - - -
43R SER* 1.3 88.2 - - - +
45R LYS* 1.3 71.7 + - + +
46R LEU 3.0 1.3 - - - -
47R ARG* 2.6 52.2 + - - +
48R ASN* 2.8 30.0 + - - +
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Residues in contact with LYS 45 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13882 A 4.8 15.3 + - - +
13892 C 3.8 32.6 + - - +
13912 C 6.0 2.2 - - - +
14532 C 3.2 37.0 - - - +
14782 U 4.9 10.5 + - - -
44R LYS* 1.3 79.4 - - + +
46R LEU* 1.3 64.3 + - - +
48R ASN* 3.4 1.3 + - - +
49R LYS* 2.9 37.6 + - + +
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Residues in contact with LEU 46 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13882 A 4.3 26.5 + - - +
13892 C 4.8 0.2 + - - -
205D PRO 3.4 22.4 - - - +
206D ASP* 4.8 2.7 - - - +
208D VAL* 3.8 24.7 - - + -
8R THR* 5.1 14.1 - - - -
9R VAL* 5.3 7.9 - - + -
41R ILE* 3.9 8.1 - - + -
42R PRO* 3.9 25.1 - - + +
43R SER* 5.2 2.0 - - - -
44R LYS 4.4 1.0 - - - +
45R LYS* 1.3 78.8 - - - +
47R ARG* 1.3 63.3 + - - +
49R LYS* 3.3 5.9 + - - +
50R ILE* 2.9 47.3 + - + +
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Residues in contact with ARG 47 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14502 G 4.4 3.4 + - - -
32R LYS* 3.3 55.0 + - + +
33R ARG* 3.6 25.1 - - - +
35R CYS* 5.4 5.3 - - + +
36R GLU* 3.7 19.4 + - - +
41R ILE* 3.5 39.3 - - + -
42R PRO 4.6 0.4 + - - -
43R SER 4.6 3.3 + - - +
44R LYS* 2.6 57.6 + - - +
46R LEU* 1.3 78.3 - - - +
48R ASN* 1.3 62.8 + - - +
50R ILE* 3.2 6.2 + - - +
51R ALA* 2.9 29.0 + - + +
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Residues in contact with ASN 48 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14522 A 4.0 10.6 - - - -
14532 C 2.4 65.1 + - - +
28R PHE* 3.9 7.3 - - + -
32R LYS* 2.7 31.2 + - - +
44R LYS* 2.8 30.3 + - - +
45R LYS 3.8 0.2 - - - +
47R ARG* 1.3 81.5 + - - +
49R LYS* 1.3 55.6 + - - +
51R ALA* 3.6 4.2 + - - -
52R GLY* 2.9 22.7 + - - -
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Residues in contact with LYS 49 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13872 G 4.9 10.5 + - - -
13882 A 5.0 16.3 + - - -
14532 C 3.2 32.4 + - - +
14542 A 3.9 21.3 - - - +
3R ARG* 6.2 0.7 - - - +
4R VAL 5.2 8.4 + - - -
5R ARG* 4.6 5.2 + - - +
6R THR* 5.4 3.4 + - - +
9R VAL* 4.2 28.5 - - + +
45R LYS* 2.9 26.9 + - + +
46R LEU* 3.6 5.4 - - - +
48R ASN* 1.3 75.0 - - - +
50R ILE* 1.3 64.5 + - - +
52R GLY* 3.0 2.9 + - - -
53R TYR* 2.9 23.4 + - - +
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Residues in contact with ILE 50 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D VAL* 4.0 9.9 - - + -
8R THR 5.0 0.7 - - - +
9R VAL* 4.3 24.5 - - + -
12R ALA* 4.0 13.5 - - + +
13R ALA* 3.8 21.8 - - - +
16R ILE* 5.2 2.9 - - + -
35R CYS* 4.4 18.4 - - - -
41R ILE* 3.9 20.0 - - + -
46R LEU* 2.9 45.8 + - + +
47R ARG* 3.5 7.0 - - - +
49R LYS* 1.3 75.3 - - - +
51R ALA* 1.3 57.5 + - - +
53R TYR* 3.2 4.3 + - - +
54R VAL* 2.9 27.6 + - + +
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Residues in contact with ALA 51 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28R PHE* 4.6 6.1 - - + +
31R ASN* 4.1 9.3 - - - +
32R LYS* 3.9 32.8 - - + +
35R CYS* 4.6 7.9 - - + -
47R ARG* 2.9 17.6 + - + +
48R ASN* 3.9 5.4 - - - +
50R ILE* 1.3 76.6 - - - +
52R GLY* 1.3 59.3 + - - +
54R VAL* 3.1 13.5 + - - +
55R THR* 2.9 31.2 + - - -
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Residues in contact with GLY 52 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14532 C 3.1 23.8 - - - -
14552 A 4.1 14.9 + - - +
5R ARG* 4.4 0.4 - - - -
28R PHE* 4.4 9.8 - - - -
48R ASN 2.9 11.2 + - - -
49R LYS 3.0 0.8 + - - -
51R ALA* 1.3 76.2 - - - +
53R TYR* 1.3 58.2 + - - +
55R THR* 3.3 9.1 - - - +
56R HIS* 3.0 26.2 + - - +
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Residues in contact with TYR 53 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13742 C 5.7 1.2 - - - -
14652 A 4.8 13.1 + - - -
14662 G 4.3 4.3 - - - -
5R ARG* 3.5 34.0 - - + +
9R VAL* 4.2 11.7 - - + -
10R LYS* 3.6 52.8 + - + +
13R ALA* 3.4 20.4 - - + -
14R ARG* 5.2 8.4 + - + -
49R LYS 2.9 12.2 + - - +
50R ILE 3.8 6.3 - - - +
52R GLY* 1.3 74.7 - - - +
54R VAL* 1.3 59.8 + - - +
56R HIS* 4.2 12.6 - + + -
57R LEU* 2.9 64.6 + - + +
60R ARG* 5.8 0.9 + - - -
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Residues in contact with VAL 54 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13R ALA* 3.9 20.2 - - + +
16R ILE* 4.2 14.1 - - + -
17R ILE* 3.2 18.6 - - + +
24R LEU* 3.6 39.7 - - + -
31R ASN* 4.5 13.2 - - + -
35R CYS* 4.6 4.7 - - - -
50R ILE* 2.9 26.1 + - + +
51R ALA* 3.1 11.9 + - - +
53R TYR* 1.3 75.7 - - - +
55R THR* 1.3 57.3 + - - +
57R LEU* 4.4 0.4 - - - -
58R MET* 2.9 26.3 + - + +
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Residues in contact with THR 55 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14552 A 4.6 8.3 - - - +
14562 G 3.7 24.2 - - - +
25R GLY 5.1 0.7 - - - -
26R ASN* 4.1 18.8 - - - +
28R PHE* 3.6 18.9 - - + +
31R ASN* 3.0 26.4 + - - +
51R ALA 2.9 12.7 + - - -
52R GLY* 3.3 12.7 - - - +
53R TYR 3.3 0.2 - - - -
54R VAL* 1.3 77.1 - - - +
56R HIS* 1.3 59.5 + - - +
58R MET* 3.1 6.3 + - - +
59R LYS* 2.9 29.3 + - + +
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Residues in contact with HIS 56 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14542 A 5.4 3.4 - - - -
14552 A 2.5 26.4 + - - +
14562 G 4.7 6.5 + - - -
14652 A 4.1 21.7 + - - -
14662 G 5.7 6.2 + - - -
5R ARG* 4.0 12.7 + - - +
52R GLY 3.0 17.4 + - - +
53R TYR* 4.0 15.7 - + + +
55R THR* 1.3 78.0 - - - +
57R LEU* 1.3 63.3 + - - +
59R LYS* 3.2 15.2 + - + +
60R ARG* 3.0 24.4 + - + +
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Residues in contact with LEU 57 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14652 A 5.9 1.6 - - - +
13R ALA 4.4 13.9 - - - +
14R ARG* 4.4 20.9 - - + -
17R ILE* 4.1 10.5 - - + -
53R TYR* 2.9 53.4 + - + +
54R VAL 3.7 3.6 - - - +
56R HIS* 1.3 77.6 - - - +
58R MET* 1.3 58.5 + - - +
60R ARG* 3.2 18.6 + - - +
61R ILE* 2.9 29.4 + - - +
66R VAL* 4.1 22.6 - - + +
69R ILE* 4.5 18.2 - - + -
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Residues in contact with MET 58 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17R ILE* 3.6 11.0 - - + -
21R TYR* 4.4 12.3 - - + +
24R LEU* 3.4 37.9 - - - +
25R GLY* 3.8 22.2 - - - +
26R ASN* 3.3 25.1 - - - +
54R VAL* 2.9 16.0 + - - +
55R THR* 3.6 6.3 - - - +
57R LEU* 1.3 74.1 - - - +
59R LYS* 1.3 64.2 + - - +
60R ARG 3.1 1.1 - - - -
61R ILE* 3.0 31.3 + - + +
62R GLN* 3.1 41.1 + - - +
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Residues in contact with LYS 59 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14562 G 5.8 2.7 - - - +
14572 U 6.2 0.2 - - - -
26R ASN* 4.3 9.3 + - - +
55R THR* 2.9 15.0 + - + +
56R HIS* 3.4 19.3 - - + +
58R MET* 1.3 77.2 - - - +
60R ARG* 1.3 60.3 + - - +
62R GLN* 3.9 10.9 + - + +
63R ARG* 3.9 42.4 + - - +
280g LYS 5.2 7.7 + - - -
281g ALA* 6.1 0.8 - - - +
282g GLU* 4.0 30.3 + - - +
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Residues in contact with ARG 60 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13752 G 5.0 3.4 + - - -
14642 C 3.7 36.0 + - - +
14652 A 3.7 33.9 + - - +
53R TYR* 5.8 0.6 + - - -
56R HIS* 3.0 14.3 + - + +
57R LEU* 3.4 19.6 - - - +
59R LYS* 1.3 77.4 - - - +
61R ILE* 1.3 62.8 + - - +
63R ARG* 3.5 17.0 + - + +
64R GLY 3.6 9.9 + - - +
65R PRO 4.8 4.9 + - - +
66R VAL* 3.4 37.3 - - + +
67R ARG* 3.6 46.1 - - - +
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Residues in contact with ILE 61 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17R ILE* 3.9 21.8 - - + -
21R TYR* 3.5 45.5 - - + +
57R LEU 2.9 21.5 + - - +
58R MET* 3.0 27.0 + - + +
60R ARG* 1.3 78.1 - - - +
62R GLN* 1.3 66.5 + - - +
64R GLY* 2.8 27.1 + - - +
66R VAL* 4.0 13.9 - - + -
69R ILE* 3.9 11.2 - - + -
71R ILE* 4.8 4.3 - - + -
74R GLN* 6.2 1.6 - - - +
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Residues in contact with GLN 62 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21R TYR* 4.2 13.4 + - - -
26R ASN* 4.1 15.7 + - - +
58R MET* 3.1 52.6 + - - +
59R LYS* 3.9 10.1 + - + +
60R ARG 3.4 0.4 - - - -
61R ILE* 1.3 81.3 - - - +
63R ARG* 1.3 61.5 + - + +
282g GLU* 5.6 3.6 - - - +
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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