Contacts of the strand formed by residues 345 - 349 (chain B) in PDB entry 2P28
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 VAL 345 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A PHE* 3.5 57.4 - - + -
342B SER* 4.3 7.2 - - - +
344B ARG* 1.3 76.7 - - - +
346B PHE* 1.3 61.6 + - - +
347B LEU* 3.8 2.2 + - + -
376B GLY 3.7 0.5 - - - +
377B ASP* 3.6 3.5 - - - -
378B CYS 3.0 32.0 + - - +
381B VAL* 3.6 22.0 - - + -
387B ILE* 4.1 5.4 - - + -
389B PHE* 3.8 20.4 - - + -
408B ALA* 4.2 10.8 - - + -
411B PHE* 4.9 3.6 - - + -
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Residues in contact with PHE 346 (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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344B ARG* 3.1 58.4 + - + -
345B VAL* 1.3 72.2 - - - +
347B LEU* 1.3 60.3 + - - +
348B ASP 3.9 0.5 + - - -
375B ARG* 3.0 50.0 - - - +
376B GLY 3.2 11.4 - - - -
377B ASP* 3.2 28.0 - - + -
407B ARG 3.6 1.0 - - - +
408B ALA* 3.1 6.2 - - - -
409B LEU* 3.1 49.1 + - + +
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Residues in contact with LEU 347 (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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76A LEU* 4.2 18.6 - - + -
95A VAL* 4.4 14.6 - - + -
345B VAL* 3.8 1.4 + - + -
346B PHE* 1.3 71.6 - - - +
348B ASP* 1.3 59.8 + - - +
360B TYR* 3.7 17.8 - - + -
375B ARG* 3.1 10.6 - - - +
376B GLY* 2.8 46.3 + - - +
389B PHE* 3.8 41.3 - - + -
391B VAL* 4.6 0.9 - - + -
406B ILE* 3.6 26.7 - - + -
407B ARG 3.4 22.2 - - - +
408B ALA* 3.7 8.3 - - + +
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Residues in contact with ASP 348 (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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346B PHE 3.9 0.6 + - - +
347B LEU* 1.3 75.0 - - - +
349B HIS* 1.3 84.9 + - - +
360B TYR* 3.5 9.6 - - - -
374B PRO 4.5 1.9 - - - +
375B ARG* 3.7 33.4 + - - +
406B ILE* 3.3 6.2 - - - +
407B ARG* 3.0 46.6 + - - +
409B LEU* 4.4 12.4 - - + +
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Residues in contact with HIS 349 (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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348B ASP* 1.3 90.2 + - - +
350B ASN* 1.3 82.6 - - - +
351B ALA* 5.1 0.9 - - - -
352B LEU* 3.5 20.7 + - + +
358B VAL* 3.4 28.0 - - + +
360B TYR* 3.2 21.3 + - - +
374B PRO 4.2 16.4 - - - -
404B PHE* 4.0 16.2 - - + -
405B VAL 3.2 14.4 - - - +
406B ILE* 4.3 1.1 - - + -
407B ARG* 3.2 16.1 + - - -
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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