Contacts of the helix formed by residues 49 - 70 (chain W) in PDB entry 5A0Q
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 49 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20W ALA* 5.2 2.7 - - + -
31W CYS* 5.4 4.9 - - - -
47W GLY 3.4 3.8 + - - -
48W THR* 1.3 73.0 - - - +
50W ALA* 1.4 56.5 + - - +
52W THR* 2.8 15.8 - - + +
53W ASP* 2.9 19.1 + - - +
300W KNM 3.0 59.8 + - + +
124X ASP* 5.6 0.9 - - - +
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Residues in contact with ALA 50 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48W THR* 3.3 13.1 - - + +
49W ALA* 1.4 75.4 - - - +
51W ASP* 1.3 66.3 + - - +
53W ASP* 3.4 2.8 + - - +
54W MET* 3.1 32.0 + - + +
300W KNM 4.8 0.4 + - - -
95X TYR* 4.1 15.3 - - + -
98X ARG* 5.5 4.7 - - - +
124X ASP* 4.9 17.1 + - + +
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Residues in contact with ASP 51 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48W THR* 3.5 6.4 + - - +
50W ALA* 1.3 75.3 - - - +
52W THR* 1.3 62.6 + - - +
55W THR* 2.9 35.7 + - - -
93W TYR 3.4 2.6 - - - +
94W ILE* 3.8 19.3 - - + +
95W GLY* 3.2 24.4 + - - -
96W ALA* 3.4 19.7 + - + +
95X TYR* 3.6 18.3 + - - -
98X ARG* 2.9 42.5 + - - +
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Residues in contact with THR 52 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35W HIS* 4.6 9.5 + - - +
45W GLY* 3.0 28.4 - - - -
46W ALA 3.8 1.3 + - - -
48W THR 3.2 5.3 + - - +
49W ALA* 2.8 25.6 - - - +
51W ASP* 1.3 81.3 - - - +
53W ASP* 1.3 57.1 + - - +
55W THR* 4.3 1.9 - - - -
56W THR* 2.7 33.6 + - - -
96W ALA* 3.8 12.6 - - - -
98W LEU* 3.3 14.1 - - - +
300W KNM 3.2 32.1 - - + -
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Residues in contact with ASP 53 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35W HIS* 3.1 36.0 + - + -
49W ALA 2.9 18.3 + - - +
50W ALA* 3.9 4.5 - - - +
52W THR* 1.3 77.4 - - - +
54W MET* 1.3 64.0 + - + +
56W THR* 3.3 2.3 + - - -
57W GLN* 3.0 48.3 + - - +
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Residues in contact with MET 54 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50W ALA* 3.1 17.6 + - + +
53W ASP* 1.3 76.4 - - + +
55W THR* 1.3 63.6 + - - +
57W GLN* 3.2 31.9 + - - +
58W LEU* 3.1 20.6 + - - +
91X ALA* 3.5 45.8 - - + +
92X ASN* 4.0 13.0 - - + +
95X TYR* 3.4 46.2 - - + -
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Residues in contact with THR 55 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51W ASP 2.9 20.9 + - - -
52W THR* 4.3 2.5 - - - -
54W MET* 1.3 74.2 - - - +
56W THR* 1.3 61.1 + - - +
58W LEU* 3.2 9.1 + - + +
59W ILE* 3.0 22.2 + - + +
83W LEU* 4.3 7.9 - - + -
86W MET* 4.0 25.7 - - + +
87W LEU* 4.3 8.7 - - + -
90W TYR* 5.8 0.2 - - - -
94W ILE* 3.9 18.6 - - + +
98W LEU* 4.2 20.9 - - + -
95X TYR* 3.9 9.2 + - - -
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Residues in contact with THR 56 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35W HIS* 3.6 33.6 - - + +
36W PHE 5.1 0.9 - - - -
37W ILE* 3.5 29.6 - - + +
43W CYS* 4.5 4.2 - - + -
52W THR* 2.7 24.3 + - - -
53W ASP 3.6 3.8 - - - -
55W THR* 1.3 77.5 - - - +
57W GLN* 1.3 55.2 + - + +
59W ILE* 3.5 4.9 + - - +
60W SER* 2.8 27.1 + - - -
98W LEU* 3.4 24.0 - - - +
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Residues in contact with GLN 57 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98P LEU* 3.9 18.3 - - + +
101P GLN* 3.3 35.2 + - - +
53W ASP* 3.0 43.8 + - - +
54W MET* 3.2 36.8 + - - +
56W THR* 1.3 75.3 - - - +
58W LEU* 1.4 57.1 + - - +
60W SER* 3.5 7.2 - - - -
61W SER* 3.0 28.8 + - - -
87X MET* 6.2 1.6 - - - +
91X ALA* 6.1 0.4 - - - +
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Residues in contact with LEU 58 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98P LEU* 5.2 10.3 - - + -
54W MET 3.1 11.3 + - - +
55W THR* 3.2 12.1 + - - +
57W GLN* 1.4 73.3 - - - +
59W ILE* 1.3 61.7 + - + +
61W SER* 2.9 22.4 + - - +
62W ASN* 3.0 38.9 + - - +
86W MET* 3.6 38.1 - - + -
89W ARG* 5.9 0.2 - - - +
90W TYR* 4.8 6.1 - - - +
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Residues in contact with ILE 59 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37W ILE* 4.0 22.2 - - + -
55W THR* 3.0 18.2 + - + +
56W THR* 4.1 3.1 - - - +
58W LEU* 1.3 73.3 - - + +
60W SER* 1.3 60.4 + - - +
62W ASN* 4.0 14.6 - - - +
63W LEU* 2.8 68.8 + - + +
79W ALA 4.6 1.3 - - - +
82W MET* 3.8 29.2 - - + +
83W LEU* 3.7 24.9 - - + -
86W MET* 4.1 26.7 - - + -
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Residues in contact with SER 60 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97P TYR* 5.0 9.1 - - - -
36W PHE* 3.8 8.5 + - - -
37W ILE* 3.0 24.8 + - - +
56W THR* 2.8 19.6 + - - -
57W GLN* 3.5 9.6 - - - -
58W LEU 3.2 0.2 - - - -
59W ILE* 1.3 75.5 - - - +
61W SER* 1.3 60.2 + - - +
63W LEU* 3.9 0.3 - - - +
64W GLU* 2.2 65.9 + - - +
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Residues in contact with SER 61 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94P GLN* 2.8 46.0 - - - +
97P TYR* 5.6 6.0 - - - -
98P LEU* 3.4 33.1 - - - +
57W GLN 3.0 13.8 + - - -
58W LEU* 2.9 18.2 + - - +
60W SER* 1.3 75.7 + - - +
62W ASN* 1.4 59.6 + - - +
64W GLU* 4.8 0.7 - - - -
65W LEU* 3.1 16.5 + - - +
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Residues in contact with ASN 62 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58W LEU* 3.0 42.1 + - - +
59W ILE* 3.5 22.5 - - - +
60W SER 3.1 0.2 - - - -
61W SER* 1.4 76.1 + - - +
63W LEU* 1.3 66.4 + - - +
65W LEU* 3.4 9.2 + - - +
66W HIS* 3.3 20.8 + - - +
82W MET* 4.0 18.2 - - - +
86W MET* 4.7 6.5 - - - +
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Residues in contact with LEU 63 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37W ILE* 3.4 27.1 - - + +
38W SER* 5.1 2.7 - - - -
41W ILE* 4.6 9.2 - - + -
59W ILE* 2.8 41.4 + - + +
60W SER 4.1 1.6 - - - +
62W ASN* 1.3 73.7 - - - +
64W GLU* 1.3 57.2 + - - +
66W HIS* 3.2 7.2 + - - +
67W SER* 3.1 30.3 + - - -
74W PRO* 4.5 22.3 - - + +
78W THR* 5.6 1.1 - - + -
79W ALA* 3.4 31.0 - - + +
82W MET* 2.8 44.9 - - + -
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Residues in contact with GLU 64 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69P LYS* 4.9 11.8 - - - -
94P GLN* 3.2 23.2 + - - +
97P TYR* 5.1 8.5 - - - -
36W PHE* 3.8 24.2 - - + -
37W ILE 2.9 14.2 - - - +
38W SER* 4.6 11.9 - - - +
39W PRO* 5.4 1.8 - - + -
60W SER* 2.2 42.7 + - - +
63W LEU* 1.3 77.2 - - - +
65W LEU* 1.3 56.7 + - - +
67W SER* 3.6 8.9 + - - +
68W LEU* 2.9 29.1 + - - +
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Residues in contact with LEU 65 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87P HIS 5.5 0.7 - - - +
90P ARG* 3.7 38.1 - - + +
91P LYS* 4.8 9.2 - - + +
94P GLN* 3.1 20.2 + - + +
61W SER 3.1 20.5 + - - +
62W ASN* 3.6 8.7 - - - +
63W LEU 3.2 0.2 - - - -
64W GLU* 1.3 78.2 - - - +
66W HIS* 1.3 58.6 + - - +
67W SER 3.5 0.2 - - - -
68W LEU* 3.5 3.9 - - + +
69W SER* 2.9 36.0 + - - +
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Residues in contact with HIS 66 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101O TRP* 3.4 20.4 - + - -
105O TYR* 3.7 44.4 - + + +
107O TYR* 2.9 28.9 + + - -
113O MET* 4.7 7.4 - - + +
62W ASN 3.3 10.8 + - - +
63W LEU* 3.2 10.6 + - - +
65W LEU* 1.3 75.9 - - - +
67W SER* 1.4 58.1 + - - +
69W SER* 3.3 6.8 + - - -
70W THR* 3.0 32.3 + - + +
72W ARG* 5.2 2.4 + - - -
74W PRO* 5.1 9.7 - - + +
75W ARG 6.3 0.2 - - - -
78W THR* 3.8 18.5 - - + +
82W MET* 5.0 2.5 - - + +
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Residues in contact with SER 67 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38W SER* 5.1 2.6 + - - -
63W LEU 3.1 16.0 + - - -
64W GLU* 3.6 11.8 + - - +
66W HIS* 1.4 73.8 - - - +
68W LEU* 1.3 61.2 + - - +
70W THR* 4.0 0.4 - - - -
71W GLY* 2.9 28.9 + - - -
72W ARG 3.6 22.0 + - - -
73W LEU* 4.2 6.5 - - - +
74W PRO* 3.7 26.2 - - - +
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Residues in contact with LEU 68 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66P PRO* 3.7 38.1 - - + +
67P ILE 3.4 24.2 - - - +
68P THR* 4.6 6.1 - - - +
90P ARG* 3.3 39.8 + - + +
94P GLN* 4.8 10.8 - - + -
64W GLU 2.9 23.2 + - - +
65W LEU* 3.5 12.1 - - + +
66W HIS 3.3 0.2 - - - -
67W SER* 1.3 77.9 + - - +
69W SER* 1.3 58.8 + - - +
71W GLY* 4.2 4.7 + - - -
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Residues in contact with SER 69 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112O ASP* 5.7 0.2 - - - +
113O MET* 4.4 15.9 - - - +
116O LYS* 5.1 11.9 - - - +
65P GLU* 5.7 1.4 - - - +
87P HIS* 5.5 2.7 - - - -
90P ARG* 3.4 31.3 + - - +
65W LEU* 2.9 22.6 + - - +
66W HIS* 3.3 12.3 - - - -
68W LEU* 1.3 75.5 - - - +
70W THR* 1.3 61.6 + - - +
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Residues in contact with THR 70 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110O PRO* 5.2 4.2 - - - +
112O ASP* 4.7 6.9 + - - +
113O MET* 3.7 32.2 - - - +
66W HIS* 3.0 29.0 + - + +
67W SER* 3.9 1.1 - - - +
69W SER* 1.3 74.0 - - - +
71W GLY* 1.3 59.8 + - - +
72W ARG* 2.8 55.4 + - + +
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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
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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