Contacts of the helix formed by residues 48 - 54 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21C TYR* 3.6 31.5 - - + -
47C SER* 1.3 70.8 + - - +
49C GLU* 1.3 64.8 + - - +
51C CYS* 3.0 13.6 + - - +
52C MET* 3.0 20.4 + - - +
48I ALA* 3.8 2.9 - - + -
49I GLU* 3.6 23.8 - - - +
52I MET* 4.6 7.0 - - - -
59I SCN 3.3 24.3 - - - -
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Residues in contact with GLU 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C SER* 3.3 6.7 + - - +
48C ALA* 1.3 80.8 - - - +
50C ASP* 1.3 66.6 + - - +
52C MET* 3.5 7.6 + - - +
53C ARG* 2.5 56.4 + - - +
59C SCN 4.7 2.2 + - - +
21I TYR* 2.6 43.1 + - + +
32I THR* 3.2 12.0 - - - +
48I ALA* 3.7 9.3 - - + +
59I SCN 4.6 1.3 - - - +
20J ARG* 2.5 28.1 + - - -
46J LYS* 3.4 14.1 - - + +
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Residues in contact with ASP 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C PHE* 4.0 5.2 - - + -
47C SER* 3.2 11.0 + - - +
49C GLU* 1.3 76.7 - - - +
51C CYS* 1.3 57.4 + - - +
53C ARG* 4.0 12.5 + - - +
54C THR* 2.9 36.8 + - - -
45J PHE* 3.6 15.3 - - + +
46J LYS* 2.7 28.9 + - - +
47J SER 3.2 18.7 + - - +
50J ASP* 2.5 41.6 - - + +
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Residues in contact with CYS 51 (chain C).
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* 4.1 4.9 - - + -
22C PHE* 3.7 19.3 - - - -
23C TYR* 3.7 3.4 - - - -
30C CYS* 2.0 45.8 - - + -
45C PHE* 3.5 40.1 - - + -
47C SER 3.2 4.6 + - - +
48C ALA 3.0 10.2 + - - +
50C ASP* 1.3 79.5 - - - +
52C MET* 1.3 59.1 + - - +
54C THR* 4.1 0.2 - - - -
55C CYS* 2.9 35.2 + - - +
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Residues in contact with MET 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C CYS* 4.0 6.1 - - - -
48C ALA 3.0 17.2 + - - +
49C GLU* 3.9 5.6 - - - +
51C CYS* 1.3 76.6 - - - +
53C ARG* 1.3 56.7 + - - +
56C GLY* 2.8 31.7 + - - +
21I TYR* 5.9 1.1 - - - -
29I LEU* 3.6 21.7 - - + +
30I CYS* 3.2 58.1 - - + +
48I ALA* 4.3 16.8 - - - +
52I MET* 3.7 41.7 - - + +
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Residues in contact with ARG 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C GLU* 2.5 51.3 + - - +
50C ASP* 4.0 17.0 + - - +
52C MET* 1.3 77.1 - - - +
54C THR* 1.3 63.0 + - - +
56C GLY 4.6 0.7 - - - +
59C SCN 2.7 30.7 + - - +
29I LEU* 4.7 7.2 - - + -
32I THR* 4.6 0.4 + - - +
20J ARG* 3.9 4.6 - - - +
40J ALA* 4.0 13.4 + - - +
41J LYS 3.5 21.8 - - - -
42J ARG* 3.1 47.9 + - + +
44J ASN* 2.4 48.9 + - - -
45J PHE* 4.4 0.2 - - - +
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Residues in contact with THR 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C ARG* 4.5 0.2 - - - +
2C PRO* 3.1 28.2 - - + +
4C PHE* 3.7 30.7 - - + -
45C PHE* 3.7 18.4 - - + -
50C ASP* 2.9 18.1 + - - -
53C ARG* 1.3 77.8 - - - +
55C CYS* 1.3 60.1 + - - +
4J PHE* 4.1 12.0 - - + -
42J ARG* 3.9 15.8 + - - +
45J PHE* 3.8 19.2 - - - -
54J THR* 3.8 14.8 - - + -
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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