Contacts of the helix formed by residues 48 - 54 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B ALA* 3.9 10.1 - - + -
49B GLU 3.9 4.5 - - - +
52B MET* 4.2 9.9 - - - +
60B SCN 3.0 34.1 - - - +
21J TYR* 3.6 31.1 - - + -
47J SER* 1.3 72.8 - - - +
49J GLU* 1.3 60.6 + - - +
51J CYS* 3.2 5.5 + - - +
52J MET* 2.9 30.4 + - - +
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Residues in contact with GLU 49 (chain J).
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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21B TYR* 2.8 38.7 + - + +
32B THR* 3.1 13.5 - - - +
48B ALA* 3.9 7.0 - - + +
59B SCN 4.8 3.4 + - - +
60B SCN 4.7 0.6 - - - -
20C ARG* 2.5 38.3 + - - -
46C LYS* 3.6 12.1 - - + +
47J SER* 3.2 7.1 + - - +
48J ALA* 1.3 80.3 - - - +
50J ASP* 1.3 64.2 + - - +
52J MET* 3.5 10.3 - - - +
53J ARG* 2.6 51.5 + - - +
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Residues in contact with ASP 50 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C ASN 4.0 3.2 - - - +
45C PHE* 3.4 16.9 - - + -
46C LYS* 2.8 25.8 + - - +
47C SER 3.2 21.0 + - - +
50C ASP* 2.5 37.7 - - + +
45J PHE* 4.0 8.7 - - + -
47J SER* 3.2 11.5 + - - +
49J GLU* 1.3 76.7 - - - +
51J CYS* 1.3 64.7 + - - +
53J ARG* 3.8 8.5 + - - +
54J THR* 2.9 31.3 + - - -
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Residues in contact with CYS 51 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21J TYR* 4.1 4.5 - - + -
22J PHE 3.8 17.5 - - - -
23J TYR* 3.9 2.9 - - - -
30J CYS* 2.0 47.1 - - + -
45J PHE* 3.5 39.0 - - + -
47J SER 3.2 4.8 + - - +
48J ALA 3.2 10.3 + - - +
49J GLU 3.2 0.4 - - - -
50J ASP* 1.3 80.1 - - - +
52J MET* 1.3 58.2 + - - +
54J THR* 3.9 0.7 - - - -
55J CYS* 2.9 32.7 + - - +
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Residues in contact with MET 52 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B TYR* 5.6 1.8 - - + -
29B LEU* 3.9 22.6 - - + +
30B CYS* 3.0 54.7 - - + +
48B ALA* 4.3 11.4 - - + -
52B MET* 3.1 37.0 - - + +
59B SCN 6.1 0.4 - - - +
30J CYS* 3.4 11.2 - - - -
48J ALA 2.9 17.9 - - - +
49J GLU* 3.5 9.9 - - - +
51J CYS* 1.3 75.7 - - - +
53J ARG* 1.3 56.2 + - - +
56J GLY* 2.8 32.3 + - - +
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Residues in contact with ARG 53 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B LEU* 5.0 5.8 - - - -
32B THR* 4.6 0.4 - - - +
59B SCN 2.9 33.1 + - - +
20C ARG* 4.0 3.6 - - - +
40C ALA* 3.9 15.6 + - - +
41C LYS 3.5 22.9 + - - -
42C ARG* 3.2 49.1 + - - +
44C ASN* 2.5 45.1 + - - -
45C PHE* 4.5 0.2 - - - +
49J GLU* 2.6 57.5 + - - +
50J ASP* 3.8 9.5 + - - +
52J MET* 1.3 78.9 - - - +
54J THR* 1.3 64.2 + - - +
56J GLY 4.5 0.7 + - - +
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Residues in contact with THR 54 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C PHE* 3.9 17.2 - - + -
42C ARG* 3.7 11.9 + - - +
45C PHE* 3.8 21.8 - - - -
54C THR* 3.8 15.5 - - + -
1J ARG* 4.5 0.2 - - - +
2J PRO* 3.2 26.3 - - + +
4J PHE* 3.8 29.2 - - + -
45J PHE* 3.9 14.5 - - + -
50J ASP* 2.9 17.4 + - - -
53J ARG* 1.3 81.9 - - - +
55J CYS* 1.3 58.7 + - - +
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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