Contacts of the strand formed by residues 329 - 345 (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 LEU 329 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B ILE* 4.0 12.8 - - + -
294B SER 3.5 16.2 - - - +
295B ALA* 4.3 1.3 - - + -
306B PRO* 4.1 5.8 - - + -
309B SER* 3.5 33.4 - - - +
318B TRP* 3.9 34.7 - - + -
328B TYR* 1.3 73.7 - - - +
330B GLN* 1.3 61.3 + - - +
331B VAL* 5.2 1.5 - - + +
407B VAL 3.6 1.2 - - - +
408B ARG* 3.3 5.0 - - - -
409B ILE* 3.0 33.7 + - + +
420B LEU* 4.1 22.9 - - + -
422B LEU* 3.9 28.7 - - + +
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Residues in contact with GLN 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B GLN 3.7 0.9 - - - +
293B ILE* 3.5 5.5 - - - +
294B SER* 2.8 56.1 + - - +
328B TYR* 3.8 10.6 + - + -
329B LEU* 1.3 73.4 - - - +
331B VAL* 1.3 72.4 + - - +
332B ASP* 4.2 1.8 - - - +
369B GLY* 5.8 0.8 - - - -
372B TRP* 3.6 10.6 - - + -
406B PHE* 3.6 25.3 - - + -
407B VAL 3.3 8.7 - - - +
408B ARG* 2.6 46.9 + - + +
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Residues in contact with VAL 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B MET* 4.0 21.8 - - + -
288B ILE* 4.1 23.8 - - + -
292B GLN 3.5 2.9 - - - +
293B ILE* 4.8 7.2 - - + -
329B LEU* 5.2 2.7 - - + +
330B GLN* 1.3 80.6 - - - +
332B ASP* 1.3 63.1 + - - +
333B LEU* 3.7 27.0 + - + -
405B ARG 3.7 0.3 - - - +
406B PHE* 3.4 3.8 - - - +
407B VAL* 2.8 42.7 + - + +
422B LEU* 4.0 21.1 - - + -
424B LEU* 3.9 17.0 - - + -
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Residues in contact with ASP 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A GLN* 5.4 2.3 - - - +
292B GLN* 2.7 56.9 + - - +
330B GLN* 4.2 2.1 - - - +
331B VAL* 1.3 74.5 - - - +
333B LEU* 1.3 52.3 + - - +
334B ARG* 2.8 29.2 + - - +
405B ARG* 2.7 45.8 + - - +
406B PHE* 3.5 26.4 - - + -
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Residues in contact with LEU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B LEU* 4.1 26.5 - - + -
288B ILE* 4.0 19.5 - - + -
292B GLN* 4.0 6.9 + - - +
331B VAL* 3.9 22.9 - - + +
332B ASP* 1.3 72.1 - - - +
334B ARG* 1.3 59.8 + - - +
335B PHE* 2.8 23.9 + - - +
337B THR* 3.9 32.8 + - + +
339B LEU* 5.5 3.4 - - + -
404B THR* 4.3 9.4 - - + +
405B ARG 2.8 22.1 + - - +
407B VAL* 4.2 19.3 - - + -
424B LEU* 4.4 4.7 - - + -
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Residues in contact with ARG 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A LEU* 3.5 42.7 + - + +
496A LYS* 5.7 5.5 - - - +
289B ALA* 5.1 1.2 - - - +
291B GLU* 3.4 35.0 + - - +
292B GLN* 3.5 36.6 + - - +
332B ASP* 2.8 28.8 + - - +
333B LEU* 1.3 76.7 - - - +
335B PHE* 1.3 80.3 + - + +
405B ARG* 3.4 26.8 + - - +
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Residues in contact with PHE 335 (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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444A LEU* 5.0 11.9 - - + -
333B LEU* 2.8 16.9 + - - +
334B ARG* 1.3 100.8 - - + +
336B LEU* 1.3 61.6 + - - +
337B THR* 2.7 25.2 + - - +
404B THR 3.6 5.2 - - - +
405B ARG* 4.0 6.2 - - - +
428B ARG* 5.7 12.6 - - + -
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Residues in contact with LEU 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B PHE* 1.3 76.7 - - - +
337B THR* 1.3 59.1 + - - +
367B THR* 4.1 24.2 - - + +
403B LEU* 4.4 21.5 - - + -
404B THR* 3.5 27.1 - - - +
405B ARG* 4.3 5.8 - - + +
428B ARG* 4.8 4.0 - - - +
429B VAL* 4.1 13.3 + - - +
437B MET* 3.8 25.5 - - + +
441B LEU* 4.1 7.6 - - + -
467B LEU* 3.7 20.2 - - + -
468B VAL* 3.6 26.7 - - + -
502B ILE* 5.2 0.9 - - + -
558B PRO* 4.6 3.1 - - + -
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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
----------------------------------------------------------
281B LEU* 3.8 26.0 - - + -
333B LEU* 3.9 20.0 + - + +
335B PHE* 2.7 24.4 + - - +
336B LEU* 1.3 73.4 + - - +
338B MET* 1.3 70.4 + - - +
339B LEU 3.6 0.3 + - - -
402B LEU 3.4 1.0 - - - +
403B LEU* 3.5 7.1 - - - +
404B THR* 2.9 34.8 + - - +
427B CYS 3.3 24.2 - - - +
428B ARG* 4.3 10.5 - - + +
429B VAL 5.1 0.4 - - - +
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Residues in contact with MET 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B CYS* 3.6 16.4 - - - -
281B LEU* 4.3 1.0 - - - +
337B THR* 1.3 79.2 - - - +
339B LEU* 1.3 59.0 + - - +
340B THR* 4.9 1.3 - - + -
401B PRO* 3.5 47.1 - - + +
402B LEU 3.3 8.7 - - - +
403B LEU* 3.8 27.5 - - + +
425B PHE 4.0 0.2 - - - +
426B GLY* 3.2 5.0 - - - -
427B CYS* 2.8 42.6 + - - +
428B ARG* 4.9 0.2 - - - +
429B VAL* 5.0 9.6 - - + +
560B ILE* 4.1 22.2 - - + -
562B ARG* 6.1 2.5 - - - +
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Residues in contact with LEU 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B LEU* 4.4 6.3 - - + -
333B LEU* 5.5 1.8 - - + -
337B THR 3.6 0.2 + - - -
338B MET* 1.3 73.0 - - - +
340B THR* 1.3 60.2 + - - +
341B ALA 3.6 17.3 - - - +
342B ILE* 4.6 4.9 - - + -
363B LEU* 4.3 20.9 - - + -
365B VAL* 4.7 2.0 - - + -
398B LEU* 3.5 20.0 - - + +
401B PRO* 3.4 4.2 - - - +
402B LEU* 2.6 48.5 + - + +
404B THR* 4.5 9.0 - - + -
407B VAL* 4.0 24.7 - - + -
424B LEU* 3.8 25.6 - - + -
425B PHE 3.5 15.3 - - - +
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Residues in contact with THR 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B CYS* 2.6 50.2 + - + +
278B ASN* 4.0 5.4 - - - +
338B MET* 4.9 1.3 - - + -
339B LEU* 1.3 78.5 - - - +
341B ALA* 1.3 62.1 + - - +
397B LYS* 3.5 4.5 - - - +
398B LEU* 2.7 38.5 + - - +
401B PRO* 3.9 19.5 - - + -
425B PHE* 2.8 17.8 + - - +
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Residues in contact with ALA 341 (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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278B ASN* 6.3 1.1 - - + -
339B LEU* 3.6 6.3 - - - +
340B THR* 1.3 82.7 + - - +
342B ILE* 1.3 70.8 + - - +
395B LEU* 3.9 13.0 - - + -
396B ASN 3.3 11.9 - - - +
397B LYS* 4.1 15.7 - - + -
398B LEU* 4.3 2.6 - - - +
424B LEU* 3.7 0.5 - - - -
425B PHE* 3.0 45.8 + - + -
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Residues in contact with ILE 342 (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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339B LEU* 4.6 6.5 - - + -
341B ALA* 1.3 82.1 - - - +
343B ALA* 1.3 62.3 + - - +
344B THR* 4.1 3.1 - - + -
361B TYR* 3.4 31.7 + - + +
363B LEU* 3.9 39.5 - - + -
384B PHE* 5.0 2.2 - - + -
394B VAL 3.7 1.2 - - - +
395B LEU* 3.4 4.1 - - - -
396B ASN* 2.8 36.3 + - - +
398B LEU* 4.3 10.5 - - + -
409B ILE* 4.0 13.5 - - + -
422B LEU* 3.5 28.7 - - + -
423B GLU 3.6 3.8 - - - +
424B LEU* 3.9 10.5 - - + -
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Residues in contact with ALA 343 (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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311B LEU* 4.3 5.4 - - + -
342B ILE* 1.3 73.9 - - - +
344B THR* 1.3 65.0 + - - +
393B VAL* 3.7 22.9 - - + -
394B VAL 3.3 5.2 - - - +
395B LEU* 4.1 6.7 - - + -
422B LEU* 3.2 6.2 - - - +
423B GLU* 2.9 38.0 + - + +
425B PHE* 3.5 25.5 - - + -
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Residues in contact with THR 344 (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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311B LEU* 4.3 2.2 - - - -
342B ILE* 4.1 4.3 - - + -
343B ALA* 1.3 79.9 - - - +
345B GLN* 1.3 62.3 + - - +
358B VAL* 6.2 0.2 - - - -
361B TYR* 3.8 25.6 - - + +
386B ALA* 3.9 15.1 - - - +
387B ASN* 3.1 20.7 + - - +
393B VAL* 3.4 4.2 - - - -
394B VAL* 2.9 39.4 + - - +
396B ASN* 5.7 0.2 + - - -
409B ILE* 5.2 1.1 - - + -
420B LEU* 3.8 23.3 - - + -
421B ARG 3.2 6.3 - - - -
422B LEU* 4.1 12.8 - - + -
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Residues in contact with GLN 345 (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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311B LEU* 3.4 11.6 - - + +
312B HIS* 2.8 52.4 + - - -
344B THR* 1.3 77.8 - - - +
346B GLY* 1.3 69.0 + - - +
387B ASN* 3.0 15.9 + - - +
390B ALA 4.4 1.6 - - - +
391B THR 3.0 24.2 + - - +
392B GLU 3.8 3.8 - - - +
393B VAL* 3.8 14.8 - - + +
419B ALA 3.7 0.7 - - - +
420B LEU* 3.5 7.8 - - - +
421B ARG* 2.8 54.7 + - + +
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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
------------------------------------------------------------
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