Contacts of the helix formed by residues 48 - 54 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48D ALA* 4.0 6.1 - - + -
49D GLU* 4.0 24.0 - - - +
52D MET* 4.6 9.2 - - + +
21H TYR* 3.7 44.0 - - + -
30H CYS* 4.9 0.3 - - - -
47H SER* 1.3 72.1 + - - +
49H GLU* 1.3 64.8 + - - +
51H CYS* 2.9 14.8 + - - +
52H MET* 3.1 17.4 + - - +
59H SCN 5.1 0.4 + - - -
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Residues in contact with GLU 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D TYR* 2.7 41.9 + - + +
32D THR* 3.2 16.3 - - - +
48D ALA* 3.9 6.8 - - + +
20E ARG* 2.5 39.7 + - - -
46E LYS* 3.8 8.3 - - + +
47H SER* 3.1 6.7 + - - +
48H ALA* 1.3 79.5 - - - +
50H ASP* 1.3 63.8 + - - +
52H MET* 3.2 13.5 - - + +
53H ARG* 2.6 50.4 + - - +
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Residues in contact with ASP 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E ASN 5.5 0.2 - - - -
45E PHE* 3.5 17.7 - - + +
46E LYS* 2.9 26.6 + - - +
47E SER 3.3 18.5 + - - -
50E ASP* 2.5 36.8 - - + +
45H PHE* 4.0 9.0 - - + -
47H SER* 3.1 11.9 + - - +
49H GLU* 1.3 78.1 - - - +
51H CYS* 1.3 64.3 + - - +
53H ARG* 4.0 11.6 + - - +
54H THR* 2.9 30.9 + - - -
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Residues in contact with CYS 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H TYR* 4.1 4.9 - - + -
22H PHE* 3.6 20.0 - - - -
23H TYR* 3.6 4.0 - - - -
30H CYS* 2.0 47.3 - - + -
45H PHE* 3.4 40.8 - - + -
47H SER 3.2 3.1 + - - +
48H ALA 2.9 9.0 + - - +
50H ASP* 1.3 79.6 - - - +
52H MET* 1.3 56.7 + - - +
54H THR* 3.9 0.5 - - - -
55H CYS* 2.8 34.1 + - - +
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Residues in contact with MET 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D TYR* 5.7 2.0 - - + -
29D LEU* 3.5 26.0 - - + +
30D CYS* 2.8 57.4 - - + +
48D ALA* 4.6 8.7 - - - -
52D MET* 3.8 28.7 - - + +
30H CYS* 3.5 10.9 - - - +
48H ALA 3.1 8.0 + - - +
49H GLU* 3.2 24.5 - - + +
51H CYS* 1.3 77.2 - - - +
53H ARG* 1.3 59.1 + - + +
56H GLY* 2.8 33.4 + - - +
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Residues in contact with ARG 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D LEU* 5.2 4.0 - - - -
32D THR* 4.8 3.8 + - - +
20E ARG* 3.9 4.0 - - - +
40E ALA* 3.9 28.2 + - - +
41E LYS 3.4 22.0 - - - -
42E ARG* 3.2 48.5 + - - +
44E ASN* 2.5 41.7 + - - -
49H GLU* 2.6 53.2 + - - +
50H ASP* 4.0 15.8 + - - +
52H MET* 1.3 80.3 - - + +
54H THR* 1.3 65.3 + - - +
56H GLY 4.4 0.5 - - - +
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Residues in contact with THR 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E PHE* 3.9 22.6 - - + -
42E ARG* 3.7 16.4 + - - +
45E PHE* 3.7 22.2 - - - -
54E THR* 3.9 5.4 - - + -
2H PRO* 3.1 27.6 - - + +
4H PHE* 3.7 30.5 - - + -
45H PHE* 3.9 14.5 - - + -
50H ASP 2.9 17.6 + - - -
53H ARG* 1.3 79.5 - - - +
55H CYS* 1.3 58.6 + - - +
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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