Contacts of the strand formed by residues 344 - 349 (chain A) in PDB entry 3BRF
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 ASN 344 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289A TYR 3.7 0.7 - - - +
290A ILE* 3.4 4.1 - - - -
291A GLY 3.1 32.9 + - - +
293A GLY* 5.6 6.5 - - - +
299A ARG* 5.0 7.1 + - - -
342A ASP* 4.0 4.2 + - - +
343A LEU* 1.3 74.7 - - - +
345A ALA* 1.3 60.4 + - - +
346A GLN* 3.8 22.7 + - - +
357A GLY* 3.9 7.7 - - - -
358A PHE 3.3 26.3 + - - +
359A VAL* 3.7 17.9 - - + +
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Residues in contact with ALA 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A ILE* 4.6 6.9 - - + +
242A ILE* 3.6 31.2 - - + -
289A TYR 3.1 9.2 - - - +
290A ILE* 4.1 11.4 - - + +
302A LEU* 4.7 1.3 - - + -
343A LEU 4.2 0.4 - - - -
344A ASN* 1.3 73.4 - - - +
346A GLN* 1.3 59.6 + - - +
347A PHE* 3.9 10.8 - - + -
356A GLY 3.9 0.7 - - - +
357A GLY* 3.2 1.4 - - - -
358A PHE* 2.8 39.5 + - - +
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Residues in contact with GLN 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A VAL 4.0 0.3 - - - +
288A ALA* 3.1 5.7 - - - +
289A TYR 2.9 30.9 + - - -
299A ARG* 3.4 27.8 + - - +
344A ASN* 3.8 20.0 + - - +
345A ALA* 1.3 77.1 - - - +
347A PHE* 1.3 63.0 + - - +
348A PHE* 3.7 21.3 - - + -
354A GLU* 2.9 27.1 + - - +
356A GLY 3.3 3.6 - - - +
357A GLY* 4.0 12.7 - - - +
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Residues in contact with PHE 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ILE* 3.3 32.3 - - + -
219A ILE* 5.9 0.2 - - + -
242A ILE* 3.7 24.9 - - + -
244A LEU* 4.3 11.9 - - + -
249A TRP* 6.0 3.4 - + - -
286A LEU* 4.9 12.8 - - + -
287A VAL 3.6 3.4 - - - -
288A ALA* 3.5 20.2 - - + -
304A PHE* 4.3 15.7 - + - -
325A CYS* 5.3 0.2 - - - -
345A ALA* 3.9 20.9 - - + -
346A GLN* 1.3 77.2 - - - +
348A PHE* 1.3 66.8 + - - +
354A GLU* 3.8 2.6 - - - +
355A ILE* 2.9 47.5 + - + -
356A GLY 2.9 11.8 + - - +
358A PHE* 3.8 22.0 - + + -
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Residues in contact with PHE 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A LEU* 3.2 5.7 - - - +
287A VAL* 2.8 40.9 + - + +
289A TYR* 4.0 31.2 - + - -
299A ARG* 4.6 7.9 - - - -
346A GLN* 3.7 36.3 - - + -
347A PHE* 1.3 74.1 - - - +
349A TYR* 1.3 70.7 + - - +
352A GLY* 4.2 11.2 - - - -
353A MET 3.7 5.2 - - - +
354A GLU* 3.7 36.1 - - + -
355A ILE* 4.3 5.4 - - - +
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Residues in contact with TYR 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A TRP* 4.7 7.3 + - - -
252A LYS* 3.7 37.7 - - - +
253A LYS* 4.1 18.0 + - + -
256A VAL* 3.7 34.5 - - + -
284A THR 4.1 19.1 - - - +
285A GLU 3.9 1.3 - - - -
286A LEU* 3.7 27.1 - - + +
287A VAL* 4.9 1.9 - - - +
322A TYR* 6.0 0.7 - - - -
348A PHE* 1.3 80.1 - - - +
350A GLY* 1.3 57.1 + - - +
351A CYS* 3.1 19.7 - - - +
352A GLY* 2.8 24.1 + - - -
353A MET* 3.2 24.3 + - + +
355A ILE* 3.6 25.4 - - + +
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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