Contacts of the helix formed by residues 296 - 300 (chain I) in PDB entry 3PB1
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 296 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57I GLN* 3.3 9.0 + - - -
291I GLU* 3.8 40.4 - - + +
294I GLY* 3.2 7.5 + - - -
295I MET* 1.3 75.8 - - - +
297I ASP* 1.3 75.7 + - - +
298I MET 3.3 0.9 - - - -
299I PHE* 3.4 15.1 + - - +
300I ARG* 3.8 14.4 + - - +
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Residues in contact with ASP 297 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53I GLU* 2.9 35.9 - - - +
54I THR* 3.5 17.2 + - - +
57I GLN* 3.1 28.3 + - - +
296I THR* 1.3 82.3 + - - +
298I MET* 1.3 57.4 + - - +
300I ARG* 2.9 25.2 + - - +
303I GLN* 4.3 26.0 + - - +
304I ALA* 3.3 17.8 + - - +
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Residues in contact with MET 298 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I LEU* 5.0 3.4 - - + -
46I LEU* 4.2 15.0 - - - -
54I THR* 3.8 24.7 - - + +
57I GLN* 4.5 1.0 + - - -
58I ILE* 4.2 18.6 - - + -
165I LEU* 6.2 0.7 - - + -
290I LEU* 3.5 23.8 - - + -
295I MET* 3.7 33.2 - - + +
297I ASP* 1.3 78.3 - - - +
299I PHE* 1.3 98.8 + - + +
300I ARG 3.5 0.2 - - - -
304I ALA* 4.1 0.7 - - - -
306I PHE* 3.7 16.9 - - + -
316I HIS* 3.6 6.4 - - - +
317I VAL* 3.0 28.5 + - + +
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Residues in contact with PHE 299 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287I ARG* 3.5 83.9 + - + +
290I LEU* 4.2 8.5 - - + -
291I GLU* 3.9 6.3 - - + +
295I MET 3.6 16.8 - - - -
296I THR 3.4 6.3 + - - +
297I ASP 3.0 1.0 - - - -
298I MET* 1.3 110.9 - - + +
300I ARG* 1.3 62.3 + - - +
301I GLN 3.7 0.5 + - - -
316I HIS* 3.4 16.4 + - - -
317I VAL* 3.7 39.3 - - + +
318I ALA 5.6 2.2 - - - -
319I LEU* 5.8 0.2 - - - -
320I ALA* 4.1 12.8 - - + -
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Residues in contact with ARG 300 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287I ARG* 5.2 9.6 - - - +
291I GLU* 6.2 0.2 - - - +
296I THR* 3.8 12.3 + - - +
297I ASP* 2.9 13.1 + - - +
298I MET 3.5 0.2 - - - -
299I PHE* 1.3 77.6 - - - +
301I GLN* 1.3 92.7 + - - +
302I PHE* 3.3 29.6 - - - +
303I GLN* 2.6 49.1 + - + +
304I ALA* 2.9 28.6 + - - +
316I HIS* 4.0 1.8 - - - -
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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