Contacts of the helix formed by residues 51 - 67 (chain T) in PDB entry 5A2Q
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 ASN 51 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19T ALA* 5.3 9.2 + - + +
23T LYS* 2.8 40.1 + - - +
49T ASP* 3.1 24.9 + - - +
50T GLU* 1.3 80.3 - - - +
52T TRP* 1.3 63.1 + - - +
53T PHE 3.1 3.1 - - - -
54T TYR* 2.9 20.8 + - + -
55T THR* 3.0 17.0 + - + +
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Residues in contact with TRP 52 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15402 G 5.2 5.1 - - - +
46S ARG* 4.0 16.3 - - - +
33T TRP* 5.3 2.0 - - - -
34T VAL* 2.9 64.9 + - + +
37T VAL* 4.9 11.4 - - + -
39T LEU* 3.5 36.3 - - + -
47T PRO* 3.5 29.9 - - + +
49T ASP* 3.5 23.5 + - + +
50T GLU 3.3 1.7 - - - -
51T ASN* 1.3 75.5 - - - +
53T PHE* 1.3 61.6 + + - +
55T THR* 3.4 11.4 - - + +
56T ARG* 2.9 62.6 + - - +
99T VAL* 3.7 16.4 - - + -
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Residues in contact with PHE 53 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28T LEU* 3.4 37.5 - - + -
29T LYS 4.0 5.4 - - - -
30T VAL* 4.5 5.4 - - + -
31T PRO* 3.5 26.9 - - + -
34T VAL* 3.7 31.0 - - + -
50T GLU 4.9 1.7 + - - +
51T ASN 2.9 1.0 + - - -
52T TRP* 1.3 100.2 - + + +
54T TYR* 1.3 68.6 + + + +
56T ARG* 3.9 2.1 - - - +
57T ALA* 2.9 25.8 + - + +
99T VAL* 4.2 10.3 - - + -
102T ARG* 4.6 7.0 - - + -
103T VAL* 3.6 37.4 - - + +
106T ALA* 5.1 3.1 - - + -
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Residues in contact with TYR 54 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19T ALA* 3.3 24.6 - - + +
22T LEU* 3.3 49.3 - - + +
23T LYS* 3.5 37.5 - - + -
28T LEU* 3.5 33.4 + - + +
30T VAL* 3.1 34.1 - - + +
50T GLU 5.4 1.8 - - - -
51T ASN* 2.9 12.1 + - + +
53T PHE* 1.3 80.8 - - + +
55T THR* 1.3 60.3 + - - +
57T ALA* 3.6 0.4 + - - -
58T ALA* 3.0 25.1 + - - +
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Residues in contact with THR 55 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15402 G 4.2 26.4 + - - +
15412 G 4.1 1.7 + - - -
15T VAL* 3.3 24.9 + - - +
16T ARG* 5.4 0.5 - - - -
19T ALA* 3.5 20.3 - - - +
49T ASP* 5.6 4.9 - - + +
51T ASN* 3.0 20.3 + - + +
52T TRP* 3.4 15.9 - - + +
54T TYR* 1.3 75.1 - - - +
56T ARG* 1.3 62.1 + - - +
58T ALA* 3.3 4.7 - - - +
59T SER* 2.9 24.1 + - - -
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Residues in contact with ARG 56 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15402 G 4.8 0.9 - - - +
15412 G 3.1 12.8 - - - +
39T LEU* 4.2 29.6 + - + +
52T TRP* 2.9 51.7 + - - +
53T PHE* 4.1 2.6 - - - +
55T THR* 1.3 75.5 - - + +
57T ALA* 1.3 56.1 + - - +
58T ALA 3.2 0.4 - - - -
59T SER* 3.8 0.7 - - - -
60T THR* 2.5 44.9 + - - -
79T TYR* 3.1 41.6 + - + +
96T SER* 3.6 10.7 + - - -
99T VAL* 3.2 41.1 - - - +
100T ALA* 4.8 6.2 - - - +
103T VAL* 4.1 13.9 - - - +
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Residues in contact with ALA 57 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22T LEU* 3.6 24.6 - - + +
28T LEU* 4.8 2.7 - - + -
53T PHE* 2.9 25.8 + - + +
54T TYR 3.8 0.2 - - - +
55T THR 3.3 0.2 - - - -
56T ARG* 1.3 74.7 - - - +
58T ALA* 1.3 60.9 + - - +
60T THR* 3.8 0.7 - - - -
61T ALA* 2.9 29.6 + - - +
103T VAL* 3.9 26.0 - - + +
107T LEU* 4.4 10.4 - - + +
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Residues in contact with ALA 58 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14T PHE* 5.3 0.2 - - - -
15T VAL* 3.8 21.5 - - + +
18T LEU* 3.5 40.8 - - + +
19T ALA 3.8 0.9 - - - +
54T TYR 3.0 16.4 + - - +
55T THR 3.3 11.4 - - - +
57T ALA* 1.3 73.7 - - - +
59T SER* 1.3 60.6 + - - +
61T ALA* 3.2 3.3 + - - +
62T ARG* 3.0 29.5 + - - +
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Residues in contact with SER 59 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15412 G 3.7 24.7 + - - -
15422 C 3.2 34.3 + - - -
15T VAL* 4.2 4.6 - - - +
55T THR 2.9 16.9 + - - -
56T ARG 3.6 3.1 + - - -
58T ALA* 1.3 75.1 - - - +
60T THR* 1.3 61.8 + - - +
62T ARG* 3.2 2.7 + - - +
63T HIS* 2.9 33.0 + - - +
79T TYR* 3.6 11.3 + - - -
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Residues in contact with THR 60 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56T ARG* 2.5 34.4 + - - -
57T ALA 3.8 0.9 - - - -
59T SER* 1.3 75.7 - - - +
61T ALA* 1.3 57.8 + - - +
63T HIS* 3.4 5.9 + - - +
64T LEU* 3.0 29.5 + - - +
75T MET* 3.5 24.0 - - - +
79T TYR* 4.6 5.5 + - - -
100T ALA* 4.8 3.5 - - - +
103T VAL* 3.6 23.3 - - + +
104T LEU* 3.4 31.6 - - + -
107T LEU* 4.7 0.9 - - + -
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Residues in contact with ALA 61 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18T LEU* 3.9 17.3 - - + -
57T ALA 2.9 20.0 + - - +
58T ALA 3.2 5.8 + - - +
60T THR* 1.3 77.6 - - - +
62T ARG* 1.3 56.9 + - - +
64T LEU* 3.5 5.0 + - - +
65T TYR* 2.9 24.9 + - - +
107T LEU* 4.6 19.5 - - + +
112T MET* 5.9 3.4 - - + -
113T VAL* 6.4 0.7 - - - -
123T LEU* 4.9 9.1 - - + +
131T LEU* 3.9 13.0 - - + +
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Residues in contact with ARG 62 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15422 C 2.4 62.3 + - - -
15432 U 3.5 5.1 + - - -
6T VAL* 3.8 24.2 - - + -
11T GLN* 3.0 31.6 + - - +
14T PHE* 4.1 21.8 - - + -
15T VAL* 3.3 20.4 - - + +
18T LEU* 5.2 0.2 - - - +
58T ALA 3.0 14.7 + - - +
59T SER 3.2 1.5 + - - +
61T ALA* 1.3 75.8 - - - +
63T HIS* 1.3 79.1 + - - +
65T TYR* 3.2 11.0 - - + +
66T LEU* 2.9 42.1 + - + +
131T LEU* 4.4 2.2 - - + +
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Residues in contact with HIS 63 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15422 C 4.1 18.8 + - - -
15432 U 5.1 19.7 + + - -
15872 G 5.4 3.2 + + + -
59T SER* 2.9 22.7 + - - +
60T THR* 3.9 6.5 - - - +
62T ARG* 1.3 100.4 + - - +
64T LEU* 1.3 58.2 + - - +
66T LEU* 3.9 7.8 - - + +
67T ARG* 3.0 29.3 + - - +
70T ALA* 5.4 1.5 - - - +
75T MET* 4.8 8.9 - - + +
78T ILE* 3.5 46.8 - - + +
79T TYR* 5.8 0.6 - - - -
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Residues in contact with LEU 64 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60T THR 3.0 18.0 + - - +
61T ALA* 3.7 5.6 - - - +
63T HIS* 1.3 74.1 - - - +
65T TYR* 1.3 64.1 + - - +
67T ARG 3.0 28.8 - - - +
68T GLY* 4.1 3.3 + - - -
70T ALA* 3.5 36.6 - - + +
75T MET* 4.8 5.8 - - + -
104T LEU* 3.5 30.5 - - + -
107T LEU* 6.0 0.2 - - + -
113T VAL* 4.5 13.2 - - + -
121T ARG* 3.3 38.5 - - + +
122T LYS* 4.9 1.4 - - - -
123T LEU* 4.7 16.6 + - + +
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Residues in contact with TYR 65 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14262 U 4.7 6.3 + - - -
14272 C 4.8 8.6 + - - -
5T THR* 3.1 31.5 - - - +
6T VAL* 3.3 38.8 + - + +
7T LYS* 4.7 3.0 + - + -
61T ALA 2.9 16.2 + - - +
62T ARG* 3.1 9.8 + - + +
64T LEU* 1.3 80.8 - - - +
66T LEU* 1.3 87.5 + - + +
67T ARG* 4.7 0.3 - - - -
123T LEU* 4.4 14.1 - - + -
128T GLN* 4.5 19.7 + - + -
131T LEU* 3.5 29.8 - - + -
132T ASP* 4.2 5.8 + - - -
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Residues in contact with LEU 66 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14272 C 4.5 15.1 + - - +
14282 G 4.4 17.9 + - - +
15432 U 3.9 17.0 - - - +
15872 G 5.2 4.8 + - - +
6T VAL* 5.5 0.4 - - + -
7T LYS* 3.5 45.1 - - + +
11T GLN* 5.0 2.0 - - - +
62T ARG* 2.9 41.7 + - - +
63T HIS* 4.3 8.1 - - + +
65T TYR* 1.3 101.1 - - + +
67T ARG* 1.3 60.6 + - - +
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Residues in contact with ARG 67 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14282 G 3.3 28.9 + - - -
15842 G 5.2 4.9 - - - -
15852 U 3.1 67.6 + - - +
15872 G 3.0 73.5 + - + +
63T HIS 3.0 12.6 + - - +
64T LEU* 3.0 34.5 - - - +
65T TYR 3.4 0.6 - - - -
66T LEU* 1.3 81.2 - - - +
68T GLY* 1.3 73.3 + - - +
70T ALA* 4.6 1.6 - - + -
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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) + - + + + + + -
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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