Contacts of the strand formed by residues 377 - 388 (chain A) in PDB entry 3RBH
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 377 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332A ARG* 3.3 3.1 - - - +
333A GLY 2.9 29.9 + - - +
366A PHE* 5.1 7.2 - - + -
370A PHE* 4.1 22.0 - - + -
372A GLY* 4.2 5.4 - - - -
373A GLU 3.0 28.0 - - - +
374A LEU* 4.0 11.1 - - + +
375A SER 3.0 13.9 - - - +
376A ASN* 1.3 78.6 - - - +
378A GLN* 1.3 78.7 + - - +
379A ALA* 4.9 0.7 - - + +
401A PHE* 4.1 18.4 - - + -
402A TRP 3.4 10.5 - - - +
404A VAL* 4.0 2.7 - - - -
410A ILE* 5.1 4.3 - - + +
426A ILE* 3.6 20.2 - - + -
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Residues in contact with GLN 378 (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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330A TYR* 2.7 45.1 + - + +
331A ALA 3.6 2.5 - - - +
332A ARG* 4.4 12.7 - - + +
377A LEU* 1.3 78.2 - - - +
379A ALA* 1.3 59.6 + - - +
401A PHE* 3.4 3.6 - - - -
402A TRP* 2.7 68.7 + - + +
403A ARG 4.7 4.2 - - - +
404A VAL* 4.2 11.7 - - + +
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Residues in contact with ALA 379 (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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329A GLY 4.6 0.2 - - - -
330A TYR* 3.4 10.0 - - - -
331A ALA* 3.0 31.1 + - + +
365A ARG* 5.2 0.6 + - - +
366A PHE* 4.0 25.1 - - + -
374A LEU* 6.0 0.2 - - + -
377A LEU* 5.0 4.0 - - + -
378A GLN* 1.3 77.0 - - - +
380A ALA* 1.3 60.5 + - - +
381A THR* 4.6 5.9 + - - +
399A HIS* 5.4 0.7 - - - +
400A LYS 3.4 4.7 - - - -
401A PHE* 3.7 26.9 - - + -
402A TRP* 4.1 2.5 - - - -
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Residues in contact with ALA 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A GLY 3.6 6.1 - - - +
330A TYR* 4.7 7.0 - - + +
379A ALA* 1.3 72.4 - - - +
381A THR* 1.3 63.1 + - - +
382A LEU* 5.8 1.6 - - + -
398A TYR* 3.8 2.0 - - - +
399A HIS* 3.3 6.9 + - - +
400A LYS* 3.0 33.5 + - + +
402A TRP* 3.6 25.2 - - + -
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Residues in contact with THR 381 (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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328A VAL* 3.2 2.8 - - - +
329A GLY* 2.8 41.9 + - - +
356A PHE* 4.4 9.9 - - + -
365A ARG* 3.1 27.5 + - - +
379A ALA* 4.6 3.5 + - - +
380A ALA* 1.3 78.2 + - - +
382A LEU* 1.3 78.7 + - - +
383A PHE* 4.6 4.3 - - + -
397A VAL* 3.7 13.7 - - + -
398A TYR* 3.4 5.6 - - - +
399A HIS* 3.3 30.4 + - + +
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Residues in contact with LEU 382 (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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327A GLY 3.7 3.1 - - - +
328A VAL* 3.9 20.0 - - + -
380A ALA* 5.8 1.3 - - + -
381A THR* 1.3 87.5 - - - +
383A PHE* 1.3 64.5 + - - +
397A VAL* 3.4 1.7 - - - +
398A TYR* 2.7 61.9 + - + +
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Residues in contact with PHE 383 (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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275A TRP* 4.3 9.9 - + - -
316A LEU 4.0 6.7 - - - -
317A ARG* 3.9 18.8 - - + -
326A ALA* 3.2 9.2 - - - +
327A GLY* 3.0 75.7 + - - +
328A VAL* 3.7 4.9 - - - -
356A PHE* 3.5 36.3 - + - -
357A THR* 3.6 32.3 - - + -
381A THR* 4.6 6.5 - - + -
382A LEU* 1.3 79.2 - - - +
384A GLY* 1.3 64.9 + - - +
385A SER* 4.9 0.7 - - - -
396A LEU 3.2 12.3 - - - +
397A VAL* 3.9 17.0 - - + -
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Residues in contact with GLY 384 (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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325A LYS 3.3 11.7 - - - -
326A ALA* 4.3 2.5 - - - -
383A PHE* 1.3 79.3 - - - +
385A SER* 1.3 60.6 + - - -
395A SER* 3.4 1.7 - - - -
396A LEU* 2.7 43.7 + - - +
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Residues in contact with SER 385 (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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323A GLN 4.3 0.7 - - - -
324A TRP* 3.7 11.0 - - - -
325A LYS* 3.0 44.7 + - - +
357A THR* 2.7 30.5 + - - -
359A THR* 3.7 8.9 - - - +
383A PHE* 5.1 0.6 - - - -
384A GLY* 1.3 76.7 - - - -
386A TRP* 1.3 62.2 + - - +
394A ALA 3.1 13.0 - - - -
395A SER* 3.5 12.1 - - - +
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Residues in contact with TRP 386 (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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323A GLN* 3.2 33.1 + - + -
324A TRP* 3.5 49.3 - + + +
359A THR* 4.1 2.4 - - - +
385A SER* 1.3 77.3 - - - +
387A GLN* 1.3 75.6 + - - +
388A LEU* 3.7 37.2 - - + -
392A TYR* 3.7 28.3 - + + -
393A ASP* 3.3 2.4 - - - +
394A ALA* 2.8 48.7 + - + +
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Residues in contact with GLN 387 (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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266A TYR* 3.7 30.8 + - - +
267A ARG* 5.6 0.6 - - - +
322A GLU 4.1 13.7 + - - +
323A GLN* 3.0 40.0 + - - +
325A LYS* 3.5 10.2 + - - +
358A GLY 3.1 25.1 - - - +
359A THR* 3.8 10.6 - - + +
360A ARG* 5.5 1.1 - - - +
386A TRP* 1.3 86.8 + - - +
388A LEU* 1.3 62.8 + - - +
389A ARG* 4.1 18.0 + - - +
392A TYR 3.5 14.6 - - - +
393A ASP* 3.9 7.2 - - + -
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Residues in contact with LEU 388 (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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323A GLN* 4.1 26.5 - - - +
386A TRP* 3.7 28.0 - - + -
387A GLN* 1.3 75.4 - - - +
389A ARG* 1.3 107.2 + - + +
391A ASP* 2.9 19.8 + - - +
392A TYR* 3.2 28.9 + - + -
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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