Contacts of the helix formed by residues 48 - 54 (chain I) in PDB entry 1BHC
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 48 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48C ALA* 3.8 4.5 - - + -
49C GLU* 3.7 26.5 - - - +
52C MET* 4.3 8.7 - - - +
21I TYR* 3.5 31.4 - - + -
47I SER* 1.3 71.2 - - - +
49I GLU* 1.3 63.6 + - - +
51I CYS* 3.0 14.3 + - - +
52I MET* 3.1 15.4 + - - +
59I SCN 3.1 21.3 + - - +
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Residues in contact with GLU 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C TYR* 2.6 41.6 + - + +
32C THR* 3.1 14.0 - - - +
48C ALA* 3.6 8.5 - - + +
20D ARG* 2.4 35.5 + - - -
46D LYS* 3.4 15.7 - - + +
47I SER* 3.2 5.8 + - - +
48I ALA* 1.3 79.1 - - - +
50I ASP* 1.3 65.0 + - - +
52I MET* 3.1 25.4 - - + +
53I ARG* 2.6 39.3 + - - +
59I SCN 4.6 0.6 - - - -
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Residues in contact with ASP 50 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D ASN 5.5 0.2 - - - -
45D PHE* 3.7 15.3 - - + +
46D LYS* 2.9 26.9 + - - +
47D SER 3.1 19.9 + - - -
50D ASP* 2.6 36.8 - - + +
45I PHE* 4.0 8.1 - - + -
47I SER* 3.2 10.9 + - - +
49I GLU* 1.3 74.6 - - - +
51I CYS* 1.3 62.0 + - - +
53I ARG* 3.8 11.3 + - - +
54I THR* 2.9 37.1 + - - -
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Residues in contact with CYS 51 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I TYR* 4.1 5.4 - - + -
22I PHE 3.7 20.4 - - - -
23I TYR* 3.7 4.7 - - - -
30I CYS* 2.0 47.1 - - + -
45I PHE* 3.4 40.8 - - + -
47I SER 3.2 3.3 + - - +
48I ALA 3.0 8.6 + - - +
50I ASP* 1.3 79.6 - - - +
52I MET* 1.3 55.8 + - - +
54I THR* 3.8 0.3 - - - -
55I CYS* 2.8 34.5 + - - +
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Residues in contact with MET 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C TYR* 5.3 2.2 - - - -
29C LEU* 3.6 26.2 - - + +
30C CYS* 3.1 56.3 - - + +
48C ALA* 4.6 6.3 - - - -
52C MET* 3.7 34.5 - - + +
23I TYR* 5.9 0.2 - - - -
30I CYS* 3.3 9.3 - - - -
48I ALA 3.1 5.0 + - - +
49I GLU* 3.1 27.4 - - - +
51I CYS* 1.3 79.7 - - - +
53I ARG* 1.3 57.3 + - + +
56I GLY* 2.9 30.1 + - - +
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Residues in contact with ARG 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C LEU* 4.8 5.8 - - + -
32C THR* 4.3 7.1 + - - +
20D ARG* 3.8 3.6 - - - +
35D TYR* 5.0 0.2 + - - -
40D ALA* 3.9 27.6 - - - +
41D LYS 3.3 24.9 - - - +
42D ARG* 3.2 46.4 + - - +
44D ASN* 2.7 42.6 + - - -
45D PHE* 4.6 0.2 - - - +
49I GLU* 2.6 60.4 + - - +
50I ASP* 3.9 10.4 + - - +
52I MET* 1.3 80.4 - - + +
54I THR* 1.3 63.7 + - - +
56I GLY 4.6 0.7 + - - +
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Residues in contact with THR 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D PHE* 4.0 12.1 - - + -
42D ARG* 3.8 14.5 + - - +
45D PHE* 3.8 22.2 - - - -
54D THR* 3.9 14.1 - - + -
2I PRO* 3.1 21.8 - - + +
4I PHE* 3.7 31.6 - - + -
45I PHE* 3.8 16.7 - - + -
50I ASP* 2.9 17.8 + - - -
53I ARG* 1.3 80.5 - - - +
55I CYS* 1.3 57.2 + - - +
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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