Contacts of the helix formed by residues 47 - 58 (chain f) in PDB entry 5T0J
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 ASP 47 (chain f).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4f SER* 3.2 35.1 + - - +
13f GLU* 3.5 11.3 + - - +
32f ILE* 3.4 32.4 - - - +
35f TYR* 4.4 6.4 - - + +
36f ASN* 3.6 21.8 - - - +
43f HIS 3.9 11.4 + - - +
44f GLU 3.9 1.0 + - - -
45f ALA 3.3 0.8 - - - -
46f CYS* 1.3 76.1 - - - +
48f LEU* 1.3 65.2 + - - +
49f LEU 3.2 0.2 - - - -
50f MET* 3.3 17.3 + - - +
51f GLU* 3.1 16.9 + - - +
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Residues in contact with LEU 48 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36f ASN* 3.6 28.9 - - + +
44f GLU 4.0 1.1 - - - +
45f ALA* 3.4 33.9 - - + +
46f CYS 3.2 0.4 - - - -
47f ASP* 1.3 76.2 - - - +
49f LEU* 1.3 61.4 + - + +
51f GLU* 3.5 6.5 - - + -
52f ILE* 2.9 31.2 + - - +
66f ALA 4.9 2.5 - - - +
67f TYR* 3.5 62.9 - - + +
70f VAL* 4.6 10.5 - - + -
71f CYS* 4.7 0.8 - - - -
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Residues in contact with LEU 49 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11f TRP* 5.4 7.0 - - + -
14f LEU* 3.7 45.9 - - + +
15f ASP 5.5 1.4 + - - -
45f ALA 3.5 18.8 - - - +
46f CYS* 3.6 17.0 - - - +
47f ASP 3.2 1.0 - - - -
48f LEU* 1.3 78.3 - - - +
50f MET* 1.3 56.8 + - - +
52f ILE* 3.1 21.4 - - - +
53f GLU* 4.6 2.6 + - - +
70f VAL* 4.9 8.1 - - + -
71f CYS* 3.7 25.8 - - + -
74f LEU* 4.1 26.1 - - + +
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Residues in contact with MET 50 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1f MET* 3.8 24.5 - - + +
4f SER* 3.3 24.2 - - - +
13f GLU* 3.9 16.0 + - + +
14f LEU* 5.6 0.7 - - - +
15f ASP 5.9 0.9 - - - +
16f ASP* 3.3 32.5 - - - +
17f ALA* 4.3 15.7 - - + +
32f ILE* 4.0 20.2 - - + -
46f CYS 4.3 1.0 + - - -
47f ASP* 3.3 17.7 + - - +
48f LEU 3.3 0.4 - - - -
49f LEU* 1.3 78.1 - - - +
51f GLU* 1.3 66.2 + - - +
52f ILE 3.3 0.8 + - - -
53f GLU* 3.6 13.5 + - - +
54f GLN* 3.7 29.9 + - - +
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Residues in contact with GLU 51 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29f VAL* 3.3 24.5 - - - +
32f ILE* 3.3 33.4 - - + +
36f ASN* 5.5 0.2 - - - +
47f ASP 3.1 15.4 + - - +
48f LEU* 3.2 13.2 + - + +
50f MET* 1.3 77.0 - - + +
52f ILE* 1.3 65.3 + - - +
54f GLN* 2.9 36.4 + - - +
55f VAL* 3.1 29.3 + - + +
67f TYR* 3.6 28.5 - - + -
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Residues in contact with ILE 52 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48f LEU 2.9 13.6 + - - +
49f LEU* 3.1 26.5 - - - +
51f GLU* 1.3 76.6 - - - +
53f GLU* 1.3 62.5 + - + +
55f VAL* 3.4 9.0 - - - +
56f ASP* 3.1 24.6 + - + +
64f GLU* 3.4 32.5 - - + +
67f TYR* 5.0 11.0 - - + +
68f ALA* 3.6 20.2 - - + -
71f CYS* 4.8 8.7 - - - -
74f LEU* 5.4 5.6 - - + -
75f THR* 4.0 20.4 - - + +
78f VAL* 5.2 15.3 - - + -
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Residues in contact with GLU 53 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17f ALA* 5.2 15.0 - - + -
21f GLN* 4.7 10.7 + - + +
49f LEU 5.1 2.0 - - - +
50f MET* 3.6 10.4 + - - +
51f GLU 3.2 0.8 - - - -
52f ILE* 1.3 82.7 - - + +
54f GLN* 1.3 64.8 + - + +
56f ASP* 3.9 7.8 - - - +
57f MET* 3.3 42.6 + - - +
78f VAL* 3.3 15.7 - - + +
79f ASN* 3.0 55.6 - - - +
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Residues in contact with GLN 54 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1f MET* 6.1 0.6 - - - +
17f ALA* 5.8 5.3 - - + +
24f PRO* 5.2 14.1 + - - +
25f LEU* 5.7 8.1 - - + -
27f THR* 5.6 2.8 + - - -
28f LEU 5.3 3.3 - - - +
29f VAL* 5.3 6.2 - - + +
32f ILE* 4.2 9.9 - - - +
50f MET* 3.7 36.2 - - + +
51f GLU* 2.9 34.5 + - - +
53f GLU* 1.3 80.2 - - + +
55f VAL* 1.3 61.0 + - + +
57f MET* 3.6 7.1 - - - +
58f LEU* 3.3 35.6 + - + +
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Residues in contact with VAL 55 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29f VAL* 5.4 0.4 - - + -
51f GLU* 3.1 39.4 + - + +
52f ILE* 3.4 10.8 - - - +
54f GLN* 1.3 76.8 - - + +
56f ASP* 1.3 65.1 + - - +
57f MET 3.6 0.2 - - - -
58f LEU 4.0 0.9 - - - -
59f GLU 3.7 0.7 + - - -
60f LYS* 3.1 59.4 + - - +
63f ASP* 4.4 17.9 - - + -
64f GLU* 3.6 29.4 - - + +
67f TYR* 4.6 5.4 - - + -
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Residues in contact with ASP 56 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52f ILE* 3.1 20.1 + - + +
53f GLU* 3.9 12.1 - - - +
54f GLN 3.3 0.4 - - - -
55f VAL* 1.3 78.0 - - - +
57f MET* 1.3 63.2 + - - +
59f GLU* 3.3 13.3 + - - -
60f LYS 5.1 0.9 - - - -
64f GLU* 4.5 17.1 - - + +
78f VAL* 4.7 16.1 - - + +
79f ASN 4.8 4.2 - - - +
85f GLU* 5.4 2.9 - - - +
88f ALA* 3.9 22.9 - - - +
89f LEU* 5.9 0.3 - - - -
92f CYS* 5.1 9.7 - - - +
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Residues in contact with MET 57 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21f GLN* 4.6 17.5 - - - +
25f LEU* 3.7 44.6 - - + -
53f GLU* 3.3 32.6 + - - +
54f GLN* 3.6 10.8 - - - +
56f ASP* 1.3 79.7 - - - +
58f LEU* 1.3 69.8 + - + +
59f GLU* 3.2 7.6 + - - +
88f ALA* 5.0 7.8 - - - +
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Residues in contact with LEU 58 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25f LEU* 5.1 8.1 - - + -
28f LEU* 6.0 7.0 - - + -
29f VAL* 5.5 4.9 - - + -
54f GLN* 3.3 25.3 + - + +
55f VAL 4.3 1.8 - - - +
56f ASP 3.2 1.0 - - - -
57f MET* 1.3 95.2 - - + +
59f GLU* 1.3 64.0 + - - +
60f LYS* 3.0 46.6 + - + +
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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
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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