Contacts of the strand formed by residues 331 - 338 (chain B) in PDB entry 3BRW
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 LEU 331 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321B GLN 3.7 1.0 - - - +
323B GLU* 3.2 34.6 + - + +
325B GLY* 3.4 36.6 - - - +
328B ASP 4.9 0.9 - - - +
329B GLY 3.7 2.7 - - - +
330B PRO* 1.3 69.6 - - - +
332B TYR* 1.3 62.0 + - - +
333B LYS* 3.8 2.4 + - - +
354B VAL* 3.8 16.5 - - + +
355B PHE 3.4 5.2 - - - +
356B ARG* 3.6 33.7 - - + +
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Residues in contact with TYR 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B ALA 4.3 2.1 + - - -
222B GLU* 3.9 19.1 + - - -
223B PHE* 4.0 25.3 - + - +
226B PHE* 5.2 2.2 - + - -
297B PHE* 4.2 11.9 - + - -
320B VAL* 3.7 24.0 - - + -
321B GLN 3.1 15.0 - - - +
322B ALA* 3.8 24.2 - - + -
330B PRO* 3.3 29.7 - - + +
331B LEU* 1.3 69.9 - - - +
333B LYS* 1.3 60.3 + - - +
334B VAL* 3.5 10.4 + - + +
354B VAL* 3.2 9.0 - - - +
355B PHE 2.8 38.5 + - - +
357B LYS* 4.1 27.3 - - + +
361B PHE* 4.0 22.7 - + + -
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Residues in contact with LYS 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B ASN* 4.6 6.1 - - - +
319B VAL* 3.4 5.9 - - - +
321B GLN* 2.8 64.2 + - + +
323B GLU* 3.5 28.3 - - - -
331B LEU 4.8 5.2 - - - +
332B TYR* 1.3 68.9 - - - +
334B VAL* 1.3 59.3 + - - +
335B SER* 4.0 1.1 + - - -
353B ALA 4.2 0.4 - - - -
354B VAL* 3.8 23.5 - - + +
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Residues in contact with VAL 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B VAL* 4.1 20.9 - - + -
319B VAL 3.2 7.9 - - - +
320B VAL* 4.1 11.9 - - + -
332B TYR* 3.5 14.8 + - + +
333B LYS* 1.3 75.0 - - - +
335B SER* 1.3 64.3 + - - +
336B VAL* 5.2 2.2 - - + -
349B LEU* 3.4 32.2 - - + +
353B ALA* 3.5 16.7 + - - +
355B PHE* 4.3 9.0 - - + -
361B PHE* 3.9 32.5 - - + -
364B PHE* 5.0 11.9 - - + -
365B LEU* 5.3 1.1 - - + -
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Residues in contact with SER 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B VAL* 4.0 0.2 - - - -
319B VAL* 2.9 50.8 + - - +
333B LYS 4.0 1.1 + - - -
334B VAL* 1.3 77.0 - - - +
336B VAL* 1.3 68.3 + - - +
337B THR* 6.1 0.2 - - - +
349B LEU* 4.7 5.8 - - - -
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Residues in contact with VAL 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B TYR 3.8 4.0 - - - +
318B VAL* 3.9 29.4 - - + -
334B VAL* 5.2 3.6 - - + -
335B SER* 1.3 81.9 - - - +
337B THR* 1.3 61.4 + - - +
345B PHE* 4.9 12.1 - - + -
349B LEU* 4.1 18.3 - - + +
368B LYS* 3.7 38.6 - - + +
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Residues in contact with THR 337 (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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304B PHE* 4.2 26.8 + - + +
305B VAL* 5.4 1.6 - - - +
306B PRO* 3.3 28.8 - - + +
316B ALA* 4.4 0.2 - - - +
317B TYR* 2.9 42.4 + - + +
319B VAL* 4.4 11.4 - - + -
335B SER* 6.1 0.2 - - - +
336B VAL* 1.3 74.8 - - - +
338B ALA* 1.3 64.2 + - - +
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Residues in contact with ALA 338 (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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306B PRO* 3.9 18.4 - - - +
315B HIS 3.4 17.3 - - - +
316B ALA* 3.7 10.5 - - + +
317B TYR* 5.5 0.4 - - - -
337B THR* 1.3 78.8 + - - +
339B ARG* 1.3 67.6 + - - +
340B ASP* 5.1 1.6 - - - +
342B VAL* 3.4 23.3 - - + -
345B PHE* 5.3 5.6 - - + -
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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