Contacts of the strand formed by residues 394 - 415 (chain B) in PDB entry 4QDQ
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 394 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342B ILE 3.7 1.0 - - - +
343B ALA* 3.3 2.3 - - - -
344B THR* 2.9 36.3 + - - +
361B TYR* 5.6 0.3 + - - -
385B GLN 4.0 21.1 - - - +
386B ALA* 4.0 13.9 - - - +
387B ASN* 4.0 27.8 - - - +
388B ASN* 4.2 14.1 - - - +
392B GLU* 4.6 4.5 - - + +
393B VAL* 1.3 80.3 - - - +
395B LEU* 1.3 65.1 + - - +
396B ASN* 4.3 8.0 + - - +
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Residues in contact with LEU 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B ALA* 3.9 14.1 - - + -
342B ILE 3.4 9.6 - - - +
343B ALA* 4.1 4.9 - - + +
393B VAL* 4.2 3.9 + - + -
394B VAL* 1.3 77.5 - - - +
396B ASN* 1.3 66.4 + - - +
397B LYS* 3.5 36.2 + - + +
425B PHE* 3.7 33.9 - - + -
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Residues in contact with ASN 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B ALA* 3.3 3.1 - - - -
342B ILE* 2.8 37.3 + - + +
344B THR* 5.7 0.2 + - - -
361B TYR* 3.5 24.3 + - - +
384B PHE* 3.8 34.0 - - + +
385B GLN* 2.8 31.5 + - - +
394B VAL* 4.3 8.4 + - - +
395B LEU* 1.3 77.2 - - - +
397B LYS* 1.3 61.5 + - - +
398B LEU* 3.8 3.1 + - - +
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Residues in contact with LYS 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ASN* 6.4 4.0 - - + -
340B THR 3.5 7.4 - - - +
341B ALA* 4.1 13.2 - - + -
384B PHE* 5.0 3.6 - - - -
395B LEU* 3.5 31.4 - - + +
396B ASN* 1.3 74.1 - - - +
398B LEU* 1.3 68.4 + - - +
399B HIS* 3.5 2.3 + - - -
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Residues in contact with LEU 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B LEU* 3.5 34.1 - - + +
340B THR 2.7 25.5 + - - +
341B ALA 4.3 0.4 - - - +
342B ILE* 4.3 11.7 - - + -
363B LEU* 4.1 9.4 - - + -
375B TYR* 3.7 12.1 - - + +
384B PHE* 3.7 32.8 - - + -
396B ASN 4.6 4.0 - - - +
397B LYS* 1.3 76.6 - - - +
399B HIS* 1.3 65.2 + - - +
400B ALA* 3.3 10.0 + - - +
401B PRO* 4.2 5.6 - - - +
402B LEU* 3.9 31.9 - - + +
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Residues in contact with HIS 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B TYR* 3.3 32.1 + + - -
376B ARG 2.9 27.3 + - - -
377B HIS* 3.7 36.4 + + + +
378B GLY 5.3 1.1 - - - -
382B LYS* 5.0 7.9 - - + -
384B PHE* 5.9 1.0 - + - -
397B LYS 3.5 4.0 + - - -
398B LEU* 1.3 73.1 - - - +
400B ALA* 1.3 68.1 + - + +
401B PRO* 4.4 2.2 - - - +
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Residues in contact with ALA 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B TYR* 2.8 34.7 + - + +
398B LEU* 3.8 3.5 - - - +
399B HIS* 1.3 92.1 - - + +
401B PRO* 1.3 76.3 - - + +
402B LEU* 3.6 1.0 + - - +
553B MET* 5.8 8.3 - - + -
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Residues in contact with PRO 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B MET* 3.5 25.1 - - + +
339B LEU 3.4 11.7 - - - +
340B THR* 3.9 15.7 - - + -
398B LEU* 4.2 11.4 - - + +
399B HIS 4.4 2.9 - - - +
400B ALA* 1.3 92.2 - - + +
402B LEU* 1.3 59.1 + - - +
403B LEU 4.4 0.2 + - - -
559B ASP* 5.7 1.2 - - - +
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Residues in contact with LEU 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B THR 3.4 1.6 - - - +
338B MET* 3.3 6.9 - - - -
339B LEU* 2.6 49.1 + - + +
363B LEU* 3.9 5.8 - - + -
365B VAL* 3.8 29.8 - - + -
373B MET* 3.6 15.9 - - + -
375B TYR* 3.6 33.2 - - + -
398B LEU* 3.9 14.1 - - + +
400B ALA 4.9 0.2 - - - +
401B PRO* 1.3 74.6 - - - +
403B LEU* 1.3 59.7 + - - +
404B THR* 3.8 2.6 + - + -
557B THR* 3.6 29.6 - - + -
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Residues in contact with LEU 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B LEU* 4.4 14.8 - - + -
337B THR 3.5 19.7 - - - +
338B MET* 3.8 15.1 - - - -
367B THR* 4.8 0.3 - - - +
401B PRO 4.4 0.4 + - - -
402B LEU* 1.3 71.5 - - - +
404B THR* 1.3 64.6 + - - +
429B VAL* 3.6 27.6 - - + -
502B ILE* 3.7 35.4 - - + -
557B THR* 3.8 9.5 - - - +
558B PRO* 3.5 38.0 + - + +
559B ASP* 4.4 2.0 - - - -
560B ILE* 4.0 28.3 - - + +
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Residues in contact with THR 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B LEU* 4.3 4.5 - - + +
335B PHE 3.6 1.2 - - - +
336B LEU* 3.9 11.3 - - - +
337B THR* 2.9 39.2 + - - +
339B LEU* 4.5 13.9 - - + -
365B VAL* 3.3 18.3 - - + +
366B SER 3.0 30.8 + - - -
367B THR* 5.0 1.3 - - - -
402B LEU* 4.7 2.2 - - + +
403B LEU* 1.3 78.7 - - - +
405B ARG* 1.3 66.7 + - - +
406B PHE 3.2 3.0 + - - +
407B VAL* 3.8 27.8 - - + -
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Residues in contact with ARG 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A GLY 2.9 26.7 + - - -
444A LEU* 2.8 27.6 + - - +
446A ALA* 4.4 7.5 - - - +
449A GLN* 5.1 0.6 + - - -
331B VAL 3.7 0.2 - - - +
332B ASP* 2.7 36.4 + - - +
333B LEU* 2.8 38.3 + - - +
334B ARG* 3.4 36.1 + - - +
335B PHE* 4.0 9.4 - - - +
336B LEU* 4.7 4.7 - - + +
366B SER 3.1 8.7 + - - +
367B THR* 3.8 19.7 + - - +
368B ASN* 5.6 1.6 - - - +
404B THR* 1.3 80.4 + - - +
406B PHE* 1.3 81.3 + - + +
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Residues in contact with PHE 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A ALA* 4.0 17.3 - - + -
330B GLN* 3.6 27.8 - - - +
331B VAL 3.4 4.7 - - - +
332B ASP* 3.5 28.7 - - + -
365B VAL* 3.4 5.5 - - - +
366B SER* 2.8 36.4 + - - +
368B ASN* 3.6 8.1 - - - -
369B GLY* 3.4 34.5 - - - -
372B TRP* 3.6 19.5 - - + -
404B THR* 3.2 6.2 + - - -
405B ARG* 1.3 115.6 - - + +
407B VAL* 1.3 61.3 + - - +
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Residues in contact with VAL 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B LEU 3.6 1.2 - - - +
330B GLN* 3.3 4.9 - - - +
331B VAL* 2.8 42.9 + - + +
333B LEU* 4.2 16.8 - - + -
339B LEU* 4.0 15.0 - - + -
363B LEU* 3.7 20.9 - - + -
364B GLU 3.8 2.5 - - - -
365B VAL* 4.5 1.6 - - + -
404B THR* 3.8 20.4 - - + -
406B PHE* 1.3 78.6 - - - +
408B ARG* 1.3 64.0 + - - +
409B ILE* 4.3 10.1 - - + -
422B LEU* 5.8 0.2 - - + -
424B LEU* 4.0 34.1 - - + -
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Residues in contact with ARG 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B TYR* 3.3 57.0 + - + -
329B LEU 3.3 3.1 - - - +
330B GLN* 2.6 32.3 + - + +
362B LYS 3.8 0.3 - - - +
363B LEU* 3.4 8.8 - - - +
364B GLU* 2.7 69.9 + - + +
369B GLY 4.8 2.4 + - - -
372B TRP* 3.3 48.1 - - + +
406B PHE 4.3 0.2 - - - -
407B VAL* 1.3 76.3 - - - +
409B ILE* 1.3 63.1 + - - +
410B ARG* 3.9 5.4 + - + +
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Residues in contact with ILE 409 (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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328B TYR* 3.2 5.2 - - - -
329B LEU* 3.0 30.9 + - + +
342B ILE* 4.0 37.7 - - + -
344B THR* 5.2 0.7 - - + -
358B VAL* 5.9 0.4 - - + -
361B TYR* 3.7 35.9 - - + -
362B LYS 3.7 1.6 - - - -
363B LEU* 4.2 7.6 - - + -
407B VAL* 4.3 9.0 - - + -
408B ARG* 1.3 77.9 - - - +
410B ARG* 1.3 61.7 + - - +
411B PRO* 3.3 7.1 - - + +
420B LEU* 3.9 28.7 - - + +
422B LEU* 3.9 27.1 - - + -
424B LEU* 4.8 0.2 - - + -
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Residues in contact with ARG 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B ASN 4.3 5.6 + - - +
326B LYS* 3.0 36.2 + - - +
327B GLU 3.7 5.8 + - - +
328B TYR* 3.7 29.4 - - + -
361B TYR* 3.9 1.3 - - - -
362B LYS* 2.8 49.5 + - + +
364B GLU* 2.8 48.2 + - + +
374B VAL* 5.5 4.7 - - - -
408B ARG* 4.2 13.7 - - + +
409B ILE* 1.3 75.2 - - - +
411B PRO* 1.4 62.7 - - - +
412B GLN* 2.9 18.5 + - - +
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Residues in contact with PRO 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B TRP* 4.4 8.1 - - + -
325B ASN* 3.3 24.8 - - - +
327B GLU 3.5 15.7 - - - +
328B TYR* 4.5 1.3 - - - -
358B VAL* 3.8 31.6 - - + -
360B SER 3.6 7.0 - - - +
361B TYR* 3.9 3.8 - - + -
409B ILE* 3.3 14.1 - - + +
410B ARG* 1.4 83.9 - - - +
412B GLN* 1.3 61.3 + - - +
414B TRP* 4.1 4.3 - - + -
418B ILE* 3.9 32.8 - - + -
420B LEU* 4.5 6.1 - - + -
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Residues in contact with GLN 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B ASN* 4.0 27.3 + - - +
360B SER* 2.8 23.0 + - - +
361B TYR* 4.0 4.0 - - - +
362B LYS* 3.6 48.2 + - + +
383B VAL* 4.8 7.2 - - + -
410B ARG* 2.9 32.5 + - - +
411B PRO* 1.3 81.6 + - - +
413B THR* 1.3 66.8 + - + +
414B TRP* 3.2 17.1 - - - -
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Residues in contact with THR 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B VAL* 3.6 4.3 - - - +
359B LYS* 2.8 37.0 + - - +
360B SER* 2.6 35.0 + - - +
412B GLN* 1.3 83.6 - - + +
414B TRP* 1.3 71.1 + - - +
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Residues in contact with TRP 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ASP* 3.3 30.7 - - + +
324B SER* 3.6 34.1 - - - -
325B ASN* 3.6 4.7 - - + -
357B TYR 3.2 13.7 - - - +
358B VAL* 4.1 4.9 - - - -
359B LYS* 3.7 19.1 + - - +
411B PRO* 4.1 5.8 - - + -
412B GLN 3.2 23.1 - - - -
413B THR* 1.3 98.1 - - - +
415B HIS* 1.3 58.9 + - - +
416B SER 3.8 4.1 + - - -
417B GLY* 3.5 36.6 - - - +
418B ILE* 3.7 19.5 - - + +
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Residues in contact with HIS 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B GLY 3.7 15.5 - - - -
356B TYR* 3.6 1.7 - - - -
357B TYR* 2.7 68.3 + + + +
359B LYS* 3.9 11.2 + - + +
414B TRP* 1.3 69.9 - - - +
416B SER* 1.3 63.0 + - - +
417B GLY 2.7 22.4 + - - +
701B GOL 3.4 35.5 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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