Contacts of the helix formed by residues 48 - 64 (chain R) in PDB entry 4ADV
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 ALA 48 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834A U 3.3 34.3 - - - +
835A U 3.6 12.1 - - - +
41R SER* 4.7 4.7 + - - -
45R GLY 4.8 0.8 - - - -
46R THR 2.6 11.5 + - - +
47R ARG* 1.3 70.7 - - - +
49R LYS* 1.3 59.9 + - - +
50R TYR 2.9 1.1 - - - -
51R GLN* 2.6 37.9 + - - +
52R ARG* 3.1 11.7 + - - +
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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
----------------------------------------------------------
662A U 3.7 0.8 + - - -
663A A 3.1 38.3 + - - +
835A U 3.1 29.4 + - - +
836A G 2.8 42.8 + - - +
47R ARG* 2.5 12.0 + - + +
48R ALA* 1.3 74.1 - - - +
50R TYR* 1.3 78.9 + - + +
52R ARG* 3.6 14.9 - - - +
53R GLN* 3.5 25.9 + - - +
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Residues in contact with TYR 50 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19R GLU* 3.8 20.7 - - - +
46R THR* 3.2 24.6 + - - +
47R ARG* 3.9 36.6 + - + -
48R ALA 2.9 0.8 - - - -
49R LYS* 1.3 103.4 - - + +
51R GLN* 1.3 54.2 + - - +
52R ARG 3.1 2.0 - - - -
53R GLN* 3.0 16.0 + - - +
54R LEU* 2.7 36.0 + - - +
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Residues in contact with GLN 51 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720A C 3.2 27.2 + - - +
721A G 3.4 23.1 - - - +
38R ILE* 4.3 4.6 - - - +
39R VAL 3.9 12.6 + - - +
40R PRO 3.8 3.5 - - - +
41R SER* 3.1 34.5 + - - +
44R THR* 4.3 2.4 - - - +
46R THR* 3.1 30.1 + - + +
48R ALA* 2.6 21.4 + - - +
50R TYR* 1.3 72.5 - - - +
52R ARG* 1.3 61.1 - - + +
54R LEU* 3.3 16.8 + - - +
55R ALA* 3.1 21.5 + - - +
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Residues in contact with ARG 52 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663A A 4.5 5.6 + - - -
664A G 2.7 57.8 + - - +
665A A 3.4 13.9 + - - -
720A C 5.5 1.1 - - - -
724A G 4.8 13.7 + - - +
725A G 4.9 7.5 + - - -
733A G 5.9 1.4 - - - +
834A U 5.1 1.2 + - - -
835A U 3.4 25.9 + - - -
48R ALA* 3.2 11.4 - - - +
49R LYS* 3.6 12.8 - - - +
51R GLN* 1.3 79.8 - - + +
53R GLN* 1.3 61.7 + - + +
55R ALA* 3.5 4.7 + - - +
56R ARG* 3.0 41.7 + - - +
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Residues in contact with GLN 53 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663A A 4.3 13.7 + - - +
664A G 5.7 1.1 - - - +
19R GLU* 4.6 15.1 + - + +
20R ILE* 3.2 46.3 - - + +
49R LYS* 3.5 26.8 + - - +
50R TYR* 3.0 16.9 + - - +
52R ARG* 1.3 74.4 - - + +
54R LEU* 1.3 66.4 + - - +
56R ARG* 3.2 27.0 + - - +
57R ALA* 3.3 14.4 + - - +
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Residues in contact with LEU 54 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19R GLU* 3.1 32.1 + - + +
27R THR 5.1 3.4 - - - +
28R LEU* 5.5 5.3 - - + +
31R TYR* 3.3 63.5 - - + -
38R ILE* 5.4 1.3 - - + -
39R VAL* 4.8 4.7 - - + +
44R THR* 5.7 0.2 - - + -
46R THR* 5.5 6.1 - - + +
50R TYR 2.7 19.7 + - - +
51R GLN* 3.3 25.3 + - - +
53R GLN* 1.3 74.6 - - - +
55R ALA* 1.3 59.3 + - - +
57R ALA* 3.7 5.8 + - - +
58R ILE* 3.5 27.2 + - + +
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Residues in contact with ALA 55 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720A C 3.3 34.5 - - - +
38R ILE* 3.8 31.6 - - + +
51R GLN 3.1 11.5 + - - +
52R ARG* 3.9 4.5 - - - +
53R GLN 3.2 0.2 - - - -
54R LEU* 1.3 73.1 - - - +
56R ARG* 1.3 67.6 + - - +
57R ALA 3.1 3.2 + - - -
58R ILE* 3.2 12.7 + - - +
59R LYS* 3.2 15.7 + - - +
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Residues in contact with ARG 56 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664A G 2.7 39.4 + - - -
665A A 4.3 7.1 + - - -
735A C 4.5 20.1 + - - +
736A C 5.2 4.7 - - - +
52R ARG* 3.0 43.0 + - - +
53R GLN* 3.2 20.9 + - - +
55R ALA* 1.3 77.9 - - - +
57R ALA* 1.3 61.8 + - - +
59R LYS* 3.4 10.7 + - - +
60R ARG* 3.3 44.4 + - - +
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Residues in contact with ALA 57 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19R GLU 4.1 11.0 - - - +
21R ASP 2.9 30.5 - - - +
22R TYR* 4.7 0.4 - - - -
28R LEU* 4.5 14.6 - - + -
53R GLN 3.3 8.5 + - - +
54R LEU* 3.8 9.9 - - - +
55R ALA 3.1 0.6 - - - -
56R ARG* 1.3 74.6 - - - +
58R ILE* 1.3 58.1 + - - +
59R LYS 3.0 1.5 + - - -
60R ARG* 3.4 6.4 - - - +
61R ALA* 2.7 39.6 + - - +
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Residues in contact with ILE 58 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28R LEU* 3.9 23.5 - - + +
31R TYR* 3.7 32.1 - - + +
32R ILE* 4.0 9.0 - - + -
36R GLY 4.7 7.9 - - - +
38R ILE* 3.7 23.3 - - + -
54R LEU* 3.5 17.7 - - + +
55R ALA 3.2 8.1 + - - +
57R ALA* 1.3 75.3 - - - +
59R LYS* 1.3 58.4 + - - +
61R ALA* 4.2 5.1 - - - +
62R ARG* 2.9 58.5 + - - +
67R LEU* 4.4 13.2 - - + +
68R PRO 5.7 0.4 - - - +
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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
----------------------------------------------------------
718A A 5.7 0.4 - - - -
719A C 4.1 14.1 - - - +
720A C 2.7 33.5 + - - -
721A G 5.0 4.1 + - - -
734A G 3.1 48.9 - - - +
735A C 3.4 22.7 + - - +
38R ILE* 4.0 4.9 - - - +
55R ALA* 3.2 22.3 + - - +
56R ARG* 3.6 7.7 - - - +
57R ALA 3.0 1.6 + - - -
58R ILE* 1.3 74.6 - - - +
60R ARG* 1.3 67.2 + - - +
62R ARG* 2.9 33.8 + - - +
63R TYR* 2.9 17.3 - - + -
69R TYR* 4.8 1.1 - - - -
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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
----------------------------------------------------------
735A C 3.6 21.7 + - - +
736A C 2.6 29.1 + - - -
88F MET* 5.3 9.4 - - + +
90F MET* 3.1 35.4 - - - +
20R ILE* 5.1 3.2 - - - +
21R ASP 3.8 19.7 + - - +
22R TYR* 3.3 29.2 - - + -
53R GLN 5.8 0.2 + - - -
56R ARG* 3.3 31.2 + - - +
57R ALA* 3.4 12.6 - - - +
59R LYS* 1.3 80.2 - - - +
61R ALA* 1.3 66.5 + - - +
63R TYR* 3.1 32.3 + - - +
64R LEU* 3.9 9.5 + - - +
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Residues in contact with ALA 61 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22R TYR* 3.4 35.0 - - + +
28R LEU* 4.6 2.2 - - + -
57R ALA 2.7 26.3 + - - +
58R ILE* 4.2 4.9 - - - +
60R ARG* 1.3 74.0 - - - +
62R ARG* 1.3 62.1 + - - +
63R TYR 3.4 0.5 + - - -
64R LEU* 3.4 5.1 + - - +
66R LEU* 3.3 29.9 + - + +
67R LEU* 3.6 17.0 + - + -
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Residues in contact with ARG 62 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718A A 2.9 31.1 - - - +
719A C 3.1 31.9 + - - +
49F TYR* 2.6 38.0 + - - -
36R GLY 4.6 5.3 + - - -
38R ILE* 3.6 22.0 - - - +
58R ILE* 2.9 33.5 + - + +
59R LYS* 2.9 18.4 + - - +
61R ALA* 1.3 75.8 - - - +
63R TYR* 1.3 52.6 + - - +
65R SER* 3.1 3.2 + - - -
67R LEU* 3.5 18.6 - - + +
68R PRO 3.2 24.2 - - - +
69R TYR* 3.4 43.7 + - + +
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Residues in contact with TYR 63 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672A U 5.0 1.3 - - - -
673A A 3.5 25.4 + - - -
734A G 2.6 49.2 + - - -
735A C 2.9 34.0 + - - -
9F MET* 4.7 1.7 - - - +
49F TYR* 3.0 15.2 + - - -
51F ILE* 3.6 15.2 - - - +
86F ARG* 3.0 32.2 - - - +
88F MET* 5.3 1.6 - - + -
59R LYS* 2.9 31.9 - - - -
60R ARG* 3.1 16.4 + - - +
62R ARG* 1.3 72.7 - - - +
64R LEU* 1.3 61.2 + - + +
65R SER* 2.8 11.1 + - - -
69R TYR* 3.0 23.8 + + - -
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Residues in contact with LEU 64 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F VAL* 3.6 19.7 - - + -
9F MET* 3.3 24.7 - - + -
42F TRP* 6.0 1.3 - - + -
59F TYR* 2.5 29.4 + - + -
86F ARG* 4.7 2.9 - - + +
88F MET* 3.5 37.0 - - + -
22R TYR* 3.5 40.4 - - + -
60R ARG 4.2 8.5 - - - +
61R ALA 3.4 2.0 + - - +
62R ARG 3.3 0.4 - - - -
63R TYR* 1.3 78.2 - - + +
65R SER* 1.3 50.9 + - - +
66R LEU* 2.6 37.2 + - + -
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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