Contacts of the helix formed by residues 48 - 54 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A ALA* 3.8 19.1 - - + -
49A GLU* 3.9 12.1 - - - +
52A MET* 4.3 8.1 - - - +
60A SCN 3.6 8.7 - - - -
21F TYR* 3.6 41.3 - - + -
47F SER* 1.3 71.1 + - - +
49F GLU* 1.3 64.6 + - - +
51F CYS* 2.9 14.3 + - - +
52F MET* 3.0 17.4 + - - +
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Residues in contact with GLU 49 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A TYR* 2.6 45.5 + - + +
32A THR* 3.4 10.2 - - + +
48A ALA* 3.8 4.0 - - - +
60A SCN 5.4 0.2 - - - -
20B ARG* 2.4 37.1 + - - -
46B LYS* 3.7 9.6 - - + +
47F SER* 3.2 7.1 + - - +
48F ALA* 1.3 78.2 - - - +
50F ASP* 1.3 64.1 + - - +
52F MET* 3.2 15.1 - - - +
53F ARG* 2.5 53.0 + - - +
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Residues in contact with ASP 50 (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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45B PHE* 3.5 17.3 - - + +
46B LYS* 2.8 28.8 + - - +
47B SER 3.2 18.4 + - - -
50B ASP* 2.4 37.5 - - + +
45F PHE* 3.9 8.5 - - + -
47F SER* 3.1 10.1 + - - +
49F GLU* 1.3 76.2 - - - +
51F CYS* 1.3 62.7 + - - +
53F ARG* 3.9 12.1 + - - +
54F THR* 2.8 31.9 + - - -
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Residues in contact with CYS 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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21F TYR* 4.1 6.1 - - + -
22F PHE* 3.7 19.1 - - - -
23F TYR* 3.7 4.3 - - - -
30F CYS* 2.0 46.2 - - + -
45F PHE* 3.6 41.0 - - + -
47F SER 3.1 6.2 + - - +
48F ALA 2.9 10.0 + - - +
50F ASP* 1.3 77.9 - - - +
52F MET* 1.3 55.1 + - - +
54F THR* 4.0 0.3 - - - -
55F CYS* 2.9 35.2 + - - +
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Residues in contact with MET 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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21A TYR* 5.4 2.0 - - - -
29A LEU* 3.6 21.6 - - + +
30A CYS* 2.8 59.7 - - + +
48A ALA* 4.3 9.2 - - - -
52A MET* 3.6 29.4 - - + +
30F CYS* 3.5 11.8 - - - -
48F ALA 3.0 16.4 + - - +
49F GLU* 3.2 20.6 - - - +
51F CYS* 1.3 74.7 - - - +
53F ARG* 1.3 55.3 - - + +
56F GLY* 2.7 32.2 + - - +
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Residues in contact with ARG 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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29A LEU* 4.9 6.3 - - + -
32A THR* 4.8 4.4 + - - +
20B ARG* 3.9 3.4 - - - +
35B TYR* 4.9 0.6 + - - -
40B ALA* 3.9 25.2 - - - +
41B LYS 3.4 24.8 + - - -
42B ARG* 3.2 48.2 + - - +
44B ASN* 2.5 41.6 + - - -
49F GLU* 2.5 59.2 + - - +
50F ASP* 3.9 11.2 + - - +
52F MET* 1.3 76.6 - - - +
54F THR* 1.3 65.6 + - - +
56F GLY 4.5 0.5 - - - +
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Residues in contact with THR 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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4B PHE* 3.9 13.4 - - + -
42B ARG* 3.7 16.0 + - - +
45B PHE* 3.9 17.5 - - - -
54B THR* 3.8 25.4 - - + -
2F PRO* 3.1 27.5 - - + +
4F PHE* 3.8 19.5 - - + -
45F PHE* 3.8 16.7 - - + -
50F ASP* 2.8 18.2 + - - -
53F ARG* 1.3 79.9 - - - +
55F CYS* 1.3 60.4 + - - +
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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
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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