Contacts of the helix formed by residues 349 - 357 (chain C) in PDB entry 4BPU
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 THR 349 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C PHE* 4.6 8.5 - - + -
327C THR 3.7 20.2 - - - +
328C GLY* 3.2 14.8 - - - -
329C ARG* 4.2 18.6 - - - +
330C ILE* 4.5 1.3 - - - -
347C VAL 3.4 2.2 + - - +
348C PRO* 1.3 77.5 - - - +
350C ILE* 1.3 64.7 + - - +
351C SER* 3.2 11.8 + - - -
352C PHE* 3.2 27.5 + - - +
353C ILE* 3.1 24.2 + - - +
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Residues in contact with ILE 350 (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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4C PHE* 3.8 21.8 - - + -
9C LEU* 4.2 4.9 - - + -
12C LEU* 3.6 27.8 - - + +
13C LEU* 3.8 20.6 - - + -
16C TYR* 3.5 41.5 - - + -
323C VAL* 3.9 19.7 - - + -
328C GLY 3.0 13.7 + - - +
330C ILE* 4.3 4.8 - - + +
349C THR* 1.3 72.1 - - - +
351C SER* 1.3 60.4 + - - +
353C ILE* 3.3 9.8 - - + +
354C CYS* 2.8 37.7 + - - +
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Residues in contact with SER 351 (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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4C PHE* 3.9 21.8 - - - +
8C GLU* 4.5 8.7 - - - -
12C LEU* 3.7 30.4 - - - +
349C THR* 3.2 10.4 + - - -
350C ILE* 1.3 81.6 - - - +
352C PHE* 1.3 63.3 + - - +
354C CYS* 4.0 0.6 - - - +
355C ARG* 3.2 23.6 + - - +
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Residues in contact with PHE 352 (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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348C PRO* 5.4 4.5 - - + -
349C THR* 3.2 25.9 + - - +
350C ILE 3.1 0.2 - - - -
351C SER* 1.3 84.0 + - - +
353C ILE* 1.3 66.0 + - + +
355C ARG* 3.4 34.6 - - - +
356C GLU* 3.4 44.9 + - + +
387C SER* 4.5 9.0 - - - -
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Residues in contact with ILE 353 (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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16C TYR* 3.7 26.0 - - + -
20C LEU* 3.6 33.8 - - + +
330C ILE* 4.1 12.1 - - + -
348C PRO* 3.5 25.4 - - + -
349C THR 3.1 11.4 + - - +
350C ILE* 3.3 20.4 - - + +
352C PHE* 1.3 77.8 - - + +
354C CYS* 1.3 61.9 + - - +
356C GLU* 3.9 18.2 + - - +
357C LEU* 3.6 15.2 + - - +
386C THR* 4.4 6.8 - - - +
387C SER* 4.8 2.7 - - - -
388C LEU* 4.4 23.8 - - + +
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Residues in contact with CYS 354 (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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12C LEU* 3.4 47.3 - - + -
15C LEU* 3.9 29.7 - - + +
16C TYR 4.2 2.0 - - - -
20C LEU* 4.1 15.5 - - - -
350C ILE* 2.8 30.3 + - - +
351C SER 4.3 0.2 - - - +
353C ILE* 1.3 76.5 - - - +
355C ARG* 1.3 63.9 + - - +
357C LEU* 3.2 18.9 + - - +
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Residues in contact with ARG 355 (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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12C LEU* 5.5 0.2 - - - +
351C SER 3.2 18.9 + - - +
352C PHE* 3.4 38.3 - - - +
354C CYS* 1.3 80.1 - - - +
356C GLU* 1.3 65.8 + - + +
357C LEU 3.3 4.2 + - - -
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Residues in contact with GLU 356 (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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352C PHE* 3.4 29.3 + - + +
353C ILE* 4.0 12.2 - - - +
354C CYS 3.3 0.4 - - - -
355C ARG* 1.3 80.8 - - + +
357C LEU* 1.3 65.4 + - - +
386C THR* 3.6 15.6 - - + -
387C SER* 2.8 48.6 + - - -
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Residues in contact with LEU 357 (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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15C LEU* 3.8 34.1 - - + -
19C ARG* 3.3 63.9 + - + +
20C LEU* 4.6 21.8 - - + -
353C ILE 3.6 12.3 + - - +
354C CYS* 3.2 15.8 + - - +
355C ARG 3.2 5.2 - - - -
356C GLU* 1.3 83.9 - - - +
386C THR* 4.8 10.3 - - + -
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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