Contacts of the strand formed by residues 329 - 345 (chain A) in PDB entry 4QDR
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 329 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A ILE* 4.1 4.9 - - + -
294A SER 3.5 15.5 - - - +
295A ALA* 4.2 1.1 - - + -
306A PRO* 4.1 12.1 - - + +
309A SER* 3.4 33.4 - - - +
318A TRP* 3.8 38.4 - - + -
328A TYR* 1.3 74.4 - - - +
330A GLN* 1.3 63.1 + - - +
331A VAL* 5.0 3.1 - - + +
407A VAL 3.7 0.7 - - - +
408A ARG* 3.4 2.6 - - - -
409A ILE* 2.9 34.2 + - + +
420A LEU* 4.2 20.9 - - + -
422A LEU* 3.9 26.7 - - + -
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Residues in contact with GLN 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A GLN 3.6 1.2 + - - +
293A ILE* 3.6 4.7 - - - +
294A SER* 2.8 56.3 + - - +
328A TYR* 4.1 10.4 + - + -
329A LEU* 1.3 75.0 - - - +
331A VAL* 1.3 71.7 + - - +
332A ASP* 5.2 3.4 - - - +
369A GLY* 6.0 0.4 - - - -
372A TRP* 3.8 6.3 - - + -
406A PHE* 3.5 30.1 - - + -
407A VAL 3.2 10.8 - - - +
408A ARG* 3.0 41.9 + - + -
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Residues in contact with VAL 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A MET* 4.1 14.6 - - + -
288A ILE* 3.9 28.7 - - + -
292A GLN 3.4 3.6 - - - +
293A ILE* 4.8 5.4 - - + -
329A LEU* 5.0 5.6 - - + +
330A GLN* 1.3 80.8 - - - +
332A ASP* 1.3 62.9 + - - +
333A LEU* 3.7 22.5 + - + -
405A ARG 3.7 0.3 - - - +
406A PHE* 3.4 4.2 - - - +
407A VAL* 2.8 39.6 + - + +
422A LEU* 4.0 26.7 - - + -
424A LEU* 4.0 14.6 - - + -
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Residues in contact with ASP 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A GLN* 2.8 47.7 + - + +
330A GLN* 4.9 3.1 - - - +
331A VAL* 1.3 74.6 - - - +
333A LEU* 1.3 60.1 + - - +
334A ARG* 2.8 37.8 + - - +
405A ARG* 2.6 49.0 + - - +
406A PHE* 3.3 24.8 - - + -
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Residues in contact with LEU 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A LEU* 4.1 22.2 - - + -
288A ILE* 3.8 30.1 - - + -
292A GLN* 4.0 6.6 + - - +
331A VAL* 3.9 12.6 - - + +
332A ASP* 1.3 71.2 - - - +
334A ARG* 1.3 61.9 + - - +
335A PHE* 2.9 27.7 + - - +
337A THR* 3.8 27.4 + - - +
339A LEU* 5.6 4.3 - - + -
404A THR* 4.2 10.3 - - + +
405A ARG 2.6 22.6 + - - +
407A VAL* 4.3 17.9 - - + -
424A LEU* 4.0 8.7 - - + -
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Residues in contact with ARG 334 (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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291A GLU* 3.3 33.1 + - - +
292A GLN* 3.7 35.1 - - - +
332A ASP* 2.8 37.6 + - - +
333A LEU* 1.3 74.9 - - - +
335A PHE* 1.3 80.4 + - + +
405A ARG* 3.7 30.8 + - - +
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Residues in contact with PHE 335 (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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333A LEU* 2.9 20.2 + - - +
334A ARG* 1.3 94.5 - - + +
336A LEU* 1.3 62.3 + - - +
337A THR* 2.6 26.4 + - - +
404A THR 3.8 1.9 - - - +
405A ARG* 4.2 5.6 - - - -
428A ARG* 3.4 38.4 - - - +
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Residues in contact with LEU 336 (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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335A PHE* 1.3 78.2 - - - +
337A THR* 1.3 59.6 + - - +
367A THR* 5.3 3.8 - - + +
403A LEU* 4.6 26.2 - - + -
404A THR* 3.6 12.1 - - - +
405A ARG* 4.7 9.6 - - + +
428A ARG* 5.0 11.6 + - - +
429A VAL* 5.2 9.6 - - + +
437A MET* 4.9 10.8 - - + -
441A LEU* 3.9 17.5 - - + -
467A LEU* 3.7 23.3 - - + -
468A VAL* 3.5 43.3 - - + -
502A ILE* 5.0 1.6 - - + -
558A PRO* 4.8 4.0 - - + -
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Residues in contact with THR 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A LEU* 3.8 31.2 - - + -
333A LEU* 3.8 22.7 + - + +
335A PHE* 2.6 23.1 + - - +
336A LEU* 1.3 73.9 + - - +
338A MET* 1.3 73.5 + - - +
339A LEU 3.7 0.5 + - - -
402A LEU 3.5 0.3 - - - +
403A LEU* 3.4 7.9 - - - +
404A THR* 2.9 31.3 + - - +
427A CYS 3.3 17.0 - - - +
428A ARG* 4.5 7.9 + - + +
429A VAL 5.5 0.2 - - - +
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Residues in contact with MET 338 (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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277A CYS* 3.9 20.2 - - - -
281A LEU* 4.6 0.3 - - - +
337A THR* 1.3 78.0 - - - +
339A LEU* 1.3 60.0 + - - +
340A THR* 4.3 1.8 - - + -
401A PRO* 3.7 28.3 - - + +
402A LEU 3.3 24.0 - - - +
403A LEU* 3.7 26.7 - - + +
425A PHE 4.5 0.2 - - - -
426A GLY* 3.0 5.4 - - - -
427A CYS* 2.7 43.4 + - - +
429A VAL* 4.5 8.7 - - + +
560A ILE* 3.7 27.6 - - + -
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Residues in contact with LEU 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A LEU* 4.6 6.1 - - + -
333A LEU* 5.6 2.7 - - + -
337A THR 3.7 0.6 + - - +
338A MET* 1.3 73.6 - - - +
340A THR* 1.3 60.6 + - - +
341A ALA 3.6 17.7 - - - +
342A ILE* 4.6 2.9 - - + -
363A LEU* 4.1 20.4 - - + -
365A VAL* 4.5 3.4 - - + -
398A LEU* 3.5 24.4 - - + +
401A PRO* 3.4 6.6 - - - +
402A LEU* 2.7 37.5 + - + +
404A THR* 4.5 14.4 - - + -
407A VAL* 4.2 23.8 - - + -
424A LEU* 4.1 24.2 - - + -
425A PHE 3.5 15.5 - - - +
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Residues in contact with THR 340 (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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277A CYS* 2.6 50.7 + - + +
278A ASN* 4.1 2.5 - - - +
338A MET* 4.3 1.8 - - + -
339A LEU* 1.3 77.2 - - - +
341A ALA* 1.3 64.4 + - - +
397A LYS* 3.6 13.9 - - - -
398A LEU* 2.9 30.8 + - - +
401A PRO* 4.1 22.4 - - + -
425A PHE* 2.7 21.8 + - - +
426A GLY* 4.2 0.2 - - - -
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Residues in contact with ALA 341 (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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278A ASN* 6.3 0.9 - - + -
339A LEU* 3.6 9.5 - - - +
340A THR* 1.3 84.7 + - - +
342A ILE* 1.3 63.8 + - - +
395A LEU* 4.1 7.9 - - + -
396A ASN 3.3 13.9 - - - +
397A LYS* 3.8 20.2 - - + -
398A LEU* 4.2 4.9 - - - +
424A LEU* 3.6 0.5 - - - -
425A PHE* 2.8 50.6 + - + -
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Residues in contact with ILE 342 (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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339A LEU* 4.6 5.4 - - + -
341A ALA* 1.3 80.2 - - - +
343A ALA* 1.3 61.3 + - - +
344A THR* 4.1 3.8 - - + -
361A TYR* 3.5 38.0 + - + +
363A LEU* 4.0 37.9 - - + -
384A PHE* 4.7 4.9 - - + -
394A VAL 3.7 1.2 - - - +
395A LEU* 3.7 3.5 - - - -
396A ASN* 2.9 33.6 + - - +
398A LEU* 4.2 12.8 - - + -
409A ILE* 4.1 7.9 - - + -
422A LEU* 3.6 27.1 - - + -
423A GLU 3.5 4.9 - - - +
424A LEU* 4.3 9.4 - - + -
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Residues in contact with ALA 343 (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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311A LEU* 4.2 4.9 - - + -
342A ILE* 1.3 72.6 - - - +
344A THR* 1.3 66.6 + - - +
393A VAL* 3.8 21.5 - - + -
394A VAL 3.2 5.8 - - - +
395A LEU* 4.0 7.9 - - + -
422A LEU* 3.3 5.0 - - - +
423A GLU* 2.8 38.5 + - + +
425A PHE* 3.5 25.7 - - + -
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Residues in contact with THR 344 (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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311A LEU* 4.3 2.0 - - - -
342A ILE* 4.1 4.9 - - + -
343A ALA* 1.3 79.5 - - - +
345A GLN* 1.3 58.0 + - - +
361A TYR* 4.0 23.3 + - + +
386A ALA* 3.9 14.6 - - - +
387A ASN* 2.8 40.5 + - - -
393A VAL* 3.4 2.9 - - - -
394A VAL* 2.9 32.9 + - - +
409A ILE* 5.3 2.0 - - + -
420A LEU* 4.1 20.2 - - + -
421A ARG 3.2 5.8 - - - +
422A LEU* 3.8 18.8 - - + -
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Residues in contact with GLN 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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311A LEU* 3.7 8.1 - - + +
312A HIS* 2.9 40.9 + - - -
344A THR* 1.3 78.1 - - - +
346A GLY* 1.3 69.8 + - - +
358A VAL 5.8 0.2 - - - -
387A ASN* 3.4 14.2 - - - +
390A ALA 4.7 1.1 - - - +
391A THR 2.9 24.1 + - - +
392A GLU 3.7 8.1 - - - +
393A VAL* 3.7 27.6 - - + +
419A ALA 3.6 1.4 - - - +
420A LEU* 3.5 9.2 - - - +
421A ARG* 2.8 52.9 + - + +
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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