Contacts of the helix formed by residues 52 - 67 (chain R) in PDB entry 5K0Y
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 TRP 52 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1534A U 4.8 1.8 - - - +
1535A G 3.7 44.9 - - - +
1536A G 4.7 1.0 + - - -
34R VAL* 3.4 36.2 - - + +
37R VAL* 5.0 0.2 - - + -
39R LEU* 3.5 34.5 - - + -
47R PRO* 3.4 16.1 - - + +
49R ASP* 3.2 31.9 + - + -
50R GLU* 4.5 0.7 - - - -
51R ASN* 1.4 76.8 - - - +
53R PHE* 1.4 74.8 + + - +
54R TYR 3.3 0.4 - - - -
55R THR* 3.1 13.8 + - - -
56R ARG* 3.0 66.0 + - + +
99R VAL* 4.2 7.4 - - + -
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Residues in contact with PHE 53 (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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28R LEU* 3.8 36.1 - - + -
30R VAL* 4.4 11.2 - - + -
31R PRO* 3.6 38.6 - - + -
34R VAL* 4.9 4.9 - - + -
50R GLU 4.3 11.0 + - - +
51R ASN 2.8 2.8 + - - +
52R TRP* 1.4 102.9 - + + +
54R TYR* 1.4 60.2 + + + +
56R ARG* 3.5 3.8 + - - +
57R ALA* 3.1 28.4 + - - +
99R VAL* 4.2 16.6 - - + -
102R ARG* 4.0 17.9 - - + -
103R VAL* 3.5 30.7 - - + +
106R ALA* 5.0 0.9 - - + -
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Residues in contact with TYR 54 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19R ALA* 3.8 13.2 - - - +
22R LEU* 3.8 8.9 - - + +
23R LYS* 3.5 66.5 + - + +
26R GLY 5.2 2.4 - - - -
27R LYS 4.7 7.5 + - - -
28R LEU* 3.7 41.4 + - + +
30R VAL* 5.1 8.6 - - + +
50R GLU 5.5 1.8 - - - -
51R ASN* 3.2 17.8 + - - +
53R PHE* 1.4 78.3 - + + +
55R THR* 1.4 58.5 + - - +
57R ALA* 3.3 7.1 + - - +
58R ALA* 3.1 27.9 + - - +
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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
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1535A G 3.7 25.1 + - - +
1536A G 3.9 17.3 - - - -
12R GLN* 6.0 1.1 - - - +
15R VAL* 4.7 12.3 - - + +
16R ARG* 5.5 7.0 - - + +
19R ALA* 3.9 15.9 - - + +
23R LYS* 5.3 2.4 + - - -
51R ASN 4.6 2.1 + - - -
52R TRP* 3.1 16.6 + - - -
54R TYR* 1.4 75.4 - - - +
56R ARG* 1.4 57.7 + - - +
58R ALA* 3.4 4.0 + - - +
59R SER* 3.0 32.2 + - - +
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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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1535A G 4.3 7.9 + - - -
1536A G 3.1 37.8 + - - +
39R LEU* 4.0 22.4 - - - +
43R LYS* 5.5 3.4 - - - +
52R TRP* 3.0 42.2 + - + +
53R PHE* 3.7 5.8 - - - +
55R THR* 1.4 73.1 - - - +
57R ALA* 1.4 55.4 + - - +
59R SER* 3.3 3.5 + - - -
60R THR* 2.9 40.8 + - - +
79R TYR* 3.3 46.1 + - + +
96R SER* 5.6 0.4 - - - -
99R VAL* 3.6 28.7 - - - +
100R ALA* 5.5 4.5 - - - +
103R VAL* 4.5 15.7 - - + -
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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
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22R LEU* 3.9 15.7 - - + -
28R LEU* 3.9 21.3 - - + -
53R PHE 3.1 14.6 + - - +
54R TYR 3.5 9.6 - - - +
56R ARG* 1.4 76.1 - - - +
58R ALA* 1.4 56.3 + - - +
60R THR 3.3 1.2 + - - -
61R ALA* 3.0 26.7 + - - +
103R VAL* 3.7 17.7 - - + +
107R LEU* 3.5 18.0 - - + +
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Residues in contact with ALA 58 (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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15R VAL* 3.2 32.3 - - - +
18R LEU* 3.6 23.9 - - + +
19R ALA* 3.7 15.5 - - - +
22R LEU* 3.8 5.3 - - + +
54R TYR 3.1 10.7 + - - +
55R THR 3.5 7.4 - - - +
56R ARG 3.3 0.2 - - - -
57R ALA* 1.4 74.0 - - - +
59R SER* 1.4 61.2 - - - +
61R ALA* 3.2 6.2 + - - +
62R ARG* 3.0 21.1 + - - +
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Residues in contact with SER 59 (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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1536A G 3.1 27.2 + - - -
1537A C 3.7 17.6 + - - -
15R VAL* 3.6 17.8 - - - +
55R THR 3.0 14.9 + - - -
56R ARG* 3.3 6.3 + - - -
58R ALA* 1.4 75.5 - - - +
60R THR* 1.4 54.7 + - - +
62R ARG* 3.4 4.9 + - - +
63R HIS* 3.0 28.9 + - - +
79R TYR* 3.3 19.5 - - - -
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Residues in contact with THR 60 (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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56R ARG* 2.9 20.3 + - - +
57R ALA 3.6 4.7 - - - -
59R SER* 1.4 71.5 - - - +
61R ALA* 1.4 59.8 + - - +
63R HIS* 3.2 6.5 + - - +
64R LEU* 3.0 33.1 + - + +
75R MET* 3.6 23.7 - - + +
79R TYR* 3.2 14.2 + - - -
103R VAL* 3.7 13.0 - - + +
104R LEU* 3.8 25.8 - - + -
107R LEU* 3.7 18.4 - - + -
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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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18R LEU* 4.0 15.9 - - + -
22R LEU* 6.1 0.4 - - + -
57R ALA 3.0 13.2 + - - +
58R ALA* 3.2 9.4 + - - +
60R THR* 1.4 76.8 - - - +
62R ARG* 1.4 56.5 + - - +
64R LEU* 3.6 2.9 + - - +
65R TYR* 3.1 26.3 + - - +
107R LEU* 4.1 17.0 - - + +
112R MET* 5.1 6.7 - - + -
113R VAL* 4.6 16.5 - - + +
123R LEU* 5.8 0.5 - - - +
131R LEU* 4.1 13.2 - - + +
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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
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1537A C 4.3 4.9 + - - -
1538A U 3.3 35.4 + - - +
37H ARG* 4.6 0.6 - - - +
6R VAL* 3.2 32.5 + - + +
7R LYS* 3.6 28.3 - - - +
11R GLN* 3.7 27.2 + - - +
14R PHE* 3.6 36.8 - - + +
15R VAL* 3.9 21.1 - - - -
58R ALA 3.0 12.4 + - - +
59R SER* 3.4 10.5 - - - +
61R ALA* 1.4 73.1 - - - +
63R HIS* 1.4 63.6 + - - +
65R TYR* 3.2 21.4 + - - +
66R LEU* 3.3 16.3 + - + +
131R LEU* 4.4 6.9 - - - +
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Residues in contact with HIS 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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1537A C 5.9 2.5 - - - +
1538A U 5.6 5.8 - - - -
1582A G 6.1 0.2 - - - -
59R SER 3.0 16.4 + - - +
60R THR* 3.2 6.0 + - - +
62R ARG* 1.4 76.5 - - - +
64R LEU* 1.4 63.3 + - - +
66R LEU* 3.5 17.9 + - + +
67R ARG* 3.4 57.2 + - + +
70R ALA* 5.3 0.2 - - - +
74R SER* 3.7 24.6 - - - -
75R MET* 3.5 20.9 - - + +
77R LYS* 4.1 7.2 + - - -
78R ILE* 3.9 34.0 - - + +
79R TYR* 6.0 0.2 - - - +
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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
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60R THR* 3.0 25.3 + - + +
61R ALA 3.9 4.7 - - - +
63R HIS* 1.4 74.4 - - - +
65R TYR* 1.4 57.9 + - - +
67R ARG* 2.9 29.0 + - + +
69R GLY 4.9 0.9 + - - -
70R ALA* 3.3 40.2 - - + +
75R MET* 3.9 14.8 - - + -
104R LEU* 3.8 24.0 - - + -
113R VAL* 3.9 28.5 - - + -
121R ARG* 3.5 26.2 - - + +
122R LYS* 4.7 3.1 - - - -
123R LEU* 4.5 8.5 + - - +
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Residues in contact with TYR 65 (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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1413A C 4.8 0.2 + - - -
1425A G 4.3 3.5 + - - -
1426A C 3.3 47.9 + + - +
1427A G 4.8 3.1 - - - +
4R VAL 3.8 13.2 + - - -
5R THR* 4.4 0.4 - - - -
6R VAL* 3.8 36.5 - - + +
61R ALA 3.1 14.1 + - - +
62R ARG* 3.3 11.7 - - - +
64R LEU* 1.4 75.5 - - - +
66R LEU* 1.4 63.2 + - - +
67R ARG 3.5 2.4 + - - +
123R LEU* 3.5 41.5 - - + +
127R GLY 5.8 0.2 - - - -
128R GLN* 4.1 33.4 + - + +
131R LEU* 3.8 24.5 - - + -
132R ASP* 3.8 15.6 + - - -
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Residues in contact with LEU 66 (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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1426A C 3.7 20.0 + - - +
1427A G 3.0 30.0 - - - +
1538A U 4.7 16.4 - - - +
1580A U 3.5 2.8 - - - +
5R THR* 4.2 1.8 - - - +
6R VAL* 3.7 20.2 - - + -
7R LYS* 3.7 41.1 - - + +
62R ARG* 3.3 16.6 + - + +
63R HIS* 3.5 15.7 - - + +
64R LEU 3.2 0.2 - - - -
65R TYR* 1.4 77.5 - - - +
67R ARG* 1.4 86.3 + - - +
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Residues in contact with ARG 67 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1426A C 5.3 2.6 + - - -
1427A G 3.5 5.1 + - - -
1538A U 5.4 1.6 + - - -
1539A C 4.9 3.8 + - - -
1580A U 3.6 19.6 + - - +
1582A G 3.4 78.0 + - - +
7R LYS* 6.1 1.4 - - - +
63R HIS* 3.4 44.2 + - + +
64R LEU* 2.9 19.6 + - - +
65R TYR 3.8 2.3 - - - +
66R LEU* 1.4 107.0 + - - +
68R GLY* 1.4 61.6 + - - +
69R GLY 3.2 16.2 - - - +
70R ALA* 4.9 6.7 - - + -
74R SER* 5.8 0.7 - - - +
122R LYS* 3.6 12.5 + - - +
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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