Contacts of the helix formed by residues 296 - 307 (chain B) in PDB entry 1B43
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 GLU 296 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294B PRO* 2.9 19.2 + - + +
295B ASP* 1.3 69.6 + - - +
297B GLU* 1.3 71.9 + - - +
299B ILE* 3.7 2.7 - - - +
300B LEU* 2.9 41.9 + - + +
318B LEU* 3.5 31.6 - - + +
319B GLU* 3.5 15.6 - - - +
322B LYS* 2.8 44.4 + - + +
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Residues in contact with GLU 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B ASP* 3.2 13.6 - - - +
296B GLU* 1.3 86.8 + - + +
298B GLY* 1.3 66.9 + - - +
300B LEU* 3.5 8.6 + - + +
301B LYS* 3.0 25.3 + - - +
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Residues in contact with GLY 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B LEU* 3.4 12.6 - - - +
295B ASP* 3.0 26.2 + - - -
297B GLU* 1.3 78.4 - - - +
299B ILE* 1.3 57.1 + - - +
301B LYS* 3.6 7.1 - - - +
302B PHE* 2.9 31.7 + - - +
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Residues in contact with ILE 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B PHE* 3.9 22.0 - - + -
137B LEU* 5.0 2.7 - - + -
140B LEU* 3.5 44.6 - - + +
141B MET* 3.9 14.4 - - + +
294B PRO* 3.6 12.6 - - + -
295B ASP 2.8 16.3 + - - +
296B GLU 3.7 3.6 - - - +
298B GLY* 1.3 74.4 - - - +
300B LEU* 1.3 58.4 + - - +
301B LYS 3.1 0.2 + - - -
302B PHE* 3.2 1.6 + - - -
303B LEU* 2.8 42.6 + - + +
314B VAL* 4.0 11.0 - - + -
318B LEU* 3.5 28.7 - - + -
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Residues in contact with LEU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B GLU* 2.9 33.1 + - + +
297B GLU* 3.9 8.1 - - + +
299B ILE* 1.3 76.7 - - - +
301B LYS* 1.3 58.0 + - - +
304B CYS* 3.0 48.2 + - + +
305B ASP* 3.4 4.5 + - - +
311B GLU* 4.2 10.3 - - + -
314B VAL* 3.7 19.5 - - + -
315B LYS* 3.7 36.3 - - + +
318B LEU* 4.0 11.7 - - + -
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Residues in contact with LYS 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B GLU 3.0 18.2 + - - +
298B GLY* 3.6 7.6 - - - +
300B LEU* 1.3 74.0 - - - +
302B PHE* 1.3 58.4 + - + +
305B ASP* 2.8 44.4 + - - +
306B GLU* 2.6 30.4 - - - +
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Residues in contact with PHE 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B LEU* 3.7 28.0 - - + -
133B ASP* 3.9 29.4 - - - -
136B LYS* 3.7 42.8 - - + -
137B LEU* 4.1 23.8 - - + -
140B LEU* 4.2 8.7 - - + -
298B GLY 2.9 14.9 + - - +
299B ILE* 3.9 1.8 - - - +
301B LYS* 1.3 80.0 - - - +
303B LEU* 1.3 61.6 + - + +
306B GLU* 3.3 24.0 - - - +
307B HIS* 3.0 52.0 + + - -
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Residues in contact with LEU 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B LEU* 4.3 9.6 - - + -
61B PHE* 3.6 48.5 - - + -
137B LEU* 3.8 32.1 - - + -
299B ILE* 2.8 26.1 + - + +
302B PHE* 1.3 83.3 - - + +
304B CYS* 1.3 57.7 + - - +
307B HIS* 3.3 8.7 + - - +
308B ASP 3.1 11.3 + - - -
309B PHE* 3.0 55.2 + - + -
314B VAL* 4.5 6.1 - - + -
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Residues in contact with CYS 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B LEU* 3.0 27.1 + - + +
303B LEU* 1.3 74.7 - - - +
305B ASP* 1.3 67.6 + - - +
308B ASP* 3.2 21.8 - - - +
309B PHE 3.4 24.9 - - - +
311B GLU* 3.5 37.9 - - + +
314B VAL* 3.6 25.8 - - - -
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Residues in contact with ASP 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B LEU 3.6 7.8 - - - +
301B LYS* 2.8 46.7 + - + +
304B CYS* 1.3 76.3 - - - +
306B GLU* 1.3 62.8 + - - +
308B ASP* 4.1 8.5 - - - +
311B GLU* 5.3 2.9 - - - +
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Residues in contact with GLU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ASP* 3.1 4.3 - - - +
49B SER* 5.4 1.6 + - - -
52B ARG* 2.4 41.4 + - - +
136B LYS* 4.5 6.9 + - - -
301B LYS* 2.6 38.9 + - - +
302B PHE* 3.3 32.3 - - + +
305B ASP* 1.3 81.1 - - - +
307B HIS* 1.3 71.8 + - + +
308B ASP* 3.6 4.5 - - - +
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Residues in contact with HIS 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B MET 4.5 2.6 - - - +
48B ASP* 3.3 41.6 - - - +
52B ARG* 3.5 20.2 + - + +
53B ILE 5.3 1.1 + - - -
54B THR* 3.6 24.6 + - + +
57B LEU* 4.1 14.0 - - + +
133B ASP* 5.0 5.8 + - - -
302B PHE* 3.0 50.6 + + - +
303B LEU* 3.3 15.0 + - + +
306B GLU* 1.3 86.8 - - + +
308B ASP* 1.3 68.4 + - - +
309B PHE* 3.5 16.4 + - + -
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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