Contacts of the helix formed by residues 47 - 53 (chain T) in PDB entry 1BGX
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 PHE 47 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7T LEU* 4.2 14.9 - - + +
8T PHE* 5.6 9.6 - + - -
44T VAL 4.0 5.0 + - - +
45T TYR 3.2 2.0 + - - -
46T GLY* 1.3 74.5 - - - +
48T ALA* 1.3 68.4 + - + +
49T LYS 3.3 4.8 + - - -
51T LEU* 3.6 39.9 + - + +
99T ILE* 3.9 38.1 - - + -
102T LEU* 3.8 52.9 - - + -
103T VAL* 4.8 4.7 - - + -
106T LEU* 3.8 29.6 - - + -
108T LEU* 4.6 11.0 - - + -
269T LEU* 5.5 0.9 - - + -
273T LEU* 6.0 1.3 - - + -
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Residues in contact with ALA 48 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45T TYR 4.2 4.4 + - - +
47T PHE* 1.3 84.0 - - + +
49T LYS* 1.3 57.0 + - - +
51T LEU* 5.7 0.2 - - - -
52T LEU* 3.4 27.0 - - - +
273T LEU* 4.8 20.2 - - + -
281T LEU* 3.9 30.1 - - + +
282T LEU* 5.3 7.4 - - + -
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Residues in contact with LYS 49 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4T MET* 5.7 4.2 - - - +
5T LEU* 3.2 36.8 - - + +
45T TYR* 4.6 20.8 + - + +
46T GLY* 4.3 2.7 + - - +
47T PHE 3.3 1.0 - - - +
48T ALA* 1.3 79.9 - - - +
50T SER* 1.3 63.7 + - - +
51T LEU 3.5 0.4 - - - -
52T LEU* 3.4 12.5 - - + +
53T LYS* 3.2 33.5 + - - +
159T GLU 5.6 3.6 + - - -
281T LEU* 6.3 3.1 - - + -
422T GLY* 3.4 25.6 - - - +
423T GLU* 2.9 32.0 + - - +
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Residues in contact with SER 50 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5T LEU* 3.9 17.2 + - - +
6T PRO 3.2 15.0 + - - -
7T LEU* 3.3 20.7 - - - +
46T GLY 3.5 8.2 + - - -
49T LYS* 1.3 80.2 - - - +
51T LEU* 1.3 60.9 + - - +
52T LEU 3.0 5.6 + - - -
53T LYS* 3.2 9.6 + - - -
54T ALA 3.4 5.5 + - - -
158T PRO* 3.3 48.7 + - - +
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Residues in contact with LEU 51 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7T LEU* 3.0 32.4 - - + +
8T PHE 5.3 0.4 - - - +
15T LEU* 4.9 13.2 - - + -
47T PHE* 3.6 24.4 + - + +
48T ALA* 5.7 0.2 - - - -
49T LYS 3.5 0.2 - - - -
50T SER* 1.3 78.9 - - - +
52T LEU* 1.3 57.4 + - - +
54T ALA* 4.1 5.2 - - + +
55T LEU* 3.5 35.4 + - + +
62T VAL* 4.8 22.0 - - + -
106T LEU* 3.9 28.7 - - + -
108T LEU* 4.2 22.7 - - + -
158T PRO* 5.0 0.2 - - - -
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Residues in contact with LEU 52 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48T ALA 3.4 27.5 + - - +
49T LYS* 3.4 15.0 - - + +
51T LEU* 1.3 77.2 - - - +
53T LYS* 1.3 63.8 + - - +
54T ALA 3.2 1.6 - - - -
55T LEU* 3.2 21.0 + - + +
56T LYS* 3.9 12.7 + - + +
281T LEU 5.0 3.8 - - - +
284T GLU* 3.7 45.3 - - + +
285T PHE* 3.8 38.6 - - + -
419T ARG* 5.6 4.0 - - - +
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Residues in contact with LYS 53 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49T LYS* 3.2 21.2 + - - +
50T SER* 3.2 2.9 + - - +
52T LEU* 1.3 79.1 - - - +
54T ALA* 1.3 56.4 + - - +
56T LYS* 3.6 34.6 - - - +
57T GLU* 3.3 31.0 + - - +
157T HIS 5.7 2.1 + - - +
158T PRO 3.5 24.9 - - - +
159T GLU 4.6 10.6 + - - +
160T GLY* 5.6 6.6 - - - -
161T TYR* 5.6 2.6 - - - +
419T ARG* 5.9 2.2 - - - +
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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