Contacts of the helix formed by residues 43 - 55 (chain A) in PDB entry 1BX4
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 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A GLU* 1.3 75.7 - - - +
44A LYS* 1.3 58.6 + - - +
45A HIS 3.1 5.8 + - - -
46A LYS* 3.2 49.8 + - - +
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Residues in contact with LYS 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A TYR* 4.6 20.3 + - - +
32A SER* 5.3 7.3 - - - -
42A GLU* 3.5 37.2 + - + +
43A ASP* 1.3 79.0 + - - +
45A HIS* 1.3 78.9 + - - +
46A LYS 3.4 1.2 + - - -
47A GLU* 4.5 7.9 + - - +
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Residues in contact with HIS 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A TYR* 4.5 18.0 + + - -
33A LEU* 4.7 1.5 - - + +
39A ILE* 3.9 26.9 - - + +
40A LEU 4.1 2.2 - - - -
41A ALA* 3.6 12.8 - - + -
42A GLU* 2.9 57.7 + - + +
43A ASP 3.1 1.6 - - - -
44A LYS* 1.3 94.7 + - - +
46A LYS* 1.3 64.5 + - - +
47A GLU 3.1 3.4 - - - -
48A LEU* 3.1 44.0 + - + +
49A PHE* 3.5 12.2 - - + -
135A ILE* 4.4 6.5 - - + -
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Residues in contact with LYS 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A GLU 4.1 4.7 - - - +
43A ASP* 3.2 52.2 + - - +
44A LYS 3.4 0.8 - - - -
45A HIS* 1.3 78.2 - - - +
47A GLU* 1.3 69.0 + - + +
48A LEU 3.5 0.3 + - - -
49A PHE* 3.8 12.7 + - - +
50A ASP* 3.8 17.0 + - - +
137A ASN* 5.0 13.7 - - - +
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Residues in contact with GLU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LYS* 6.0 0.9 - - - -
31A TYR* 3.3 24.8 + - + +
44A LYS 4.5 6.7 + - - +
45A HIS 3.1 0.2 - - - -
46A LYS* 1.3 87.5 - - + +
48A LEU* 1.3 61.5 + - - +
50A ASP* 3.3 10.8 + - - +
51A GLU* 3.0 21.1 + - - +
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Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A PHE* 4.1 21.6 - - + -
31A TYR* 3.4 42.9 + - + -
33A LEU* 4.1 5.6 - - + -
45A HIS* 3.1 33.6 + - + +
47A GLU* 1.3 78.0 - - - +
49A PHE* 1.3 70.6 + - + +
51A GLU* 3.3 1.4 + - - +
52A LEU* 3.0 24.3 + - + +
124A ALA* 4.1 25.4 - - + -
126A CYS* 4.5 4.7 - - - -
135A ILE* 4.0 22.0 - - + -
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Residues in contact with PHE 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ILE* 4.7 12.8 - - + -
41A ALA* 4.1 13.2 - - + -
45A HIS* 3.5 17.9 + - + -
46A LYS* 4.3 7.4 - - - +
47A GLU 3.5 0.4 - - - -
48A LEU* 1.3 87.7 - - + +
50A ASP* 1.3 64.2 + - - +
52A LEU* 3.7 5.6 + - + +
53A VAL* 3.5 28.9 + - - +
122A THR* 3.7 22.7 - - - -
123A CYS 4.3 1.3 - - - -
124A ALA* 3.7 30.3 - - + -
135A ILE* 3.4 29.6 - - + -
137A ASN* 3.7 26.5 - - + -
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Residues in contact with ASP 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LYS 3.8 12.5 + - - +
47A GLU* 3.3 13.7 + - - +
49A PHE* 1.3 76.5 - - - +
51A GLU* 1.3 65.1 + - - +
53A VAL* 3.6 5.0 + - - +
54A LYS* 3.2 25.7 + - - +
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Residues in contact with GLU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A PHE* 4.1 21.0 - - + -
30A LYS* 2.7 38.8 + - - +
31A TYR* 2.8 17.1 + - - +
47A GLU* 3.0 16.2 + - + +
48A LEU 3.9 2.9 - - - +
50A ASP* 1.3 79.3 - - - +
52A LEU* 1.3 55.6 + - - +
54A LYS* 4.6 4.0 - - - -
55A LYS* 2.8 65.6 + - + +
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Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ILE* 3.9 28.0 - - + +
21A ALA* 4.0 15.3 - - + +
23A VAL* 3.6 30.3 - - + -
27A PHE* 4.1 14.1 - - + -
48A LEU* 3.0 18.2 + - + +
49A PHE* 3.9 8.3 - - + +
50A ASP 3.3 0.2 - - - -
51A GLU* 1.3 76.7 - - - +
53A VAL* 1.3 60.9 + - + +
56A PHE* 3.2 34.1 + - + +
58A VAL* 3.8 9.9 - - + +
124A ALA* 3.8 28.7 - - + -
125A ALA 5.0 1.1 - - - +
126A CYS* 4.3 9.6 - - - -
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Residues in contact with VAL 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ILE* 4.3 23.1 - - + -
49A PHE 3.5 18.0 + - - +
50A ASP* 4.1 3.8 - - - +
51A GLU 3.4 0.4 - - - -
52A LEU* 1.3 76.0 - - + +
54A LYS* 1.3 58.1 + - - +
56A PHE 4.0 8.1 - - - +
58A VAL* 4.2 14.3 - - + +
60A TYR* 3.9 24.9 - - - +
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Residues in contact with LYS 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ASP 3.2 18.6 + - - +
51A GLU* 4.0 4.3 - - - +
53A VAL* 1.3 79.3 - - + +
55A LYS* 1.3 93.9 + - + +
56A PHE 3.6 1.3 - - - +
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Residues in contact with LYS 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A GLU* 2.8 51.9 + - + +
54A LYS* 1.3 108.3 - - + +
56A PHE* 1.3 82.5 + - + +
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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