Contacts of the strand formed by residues 380 - 389 (chain X) in PDB entry 2QW0
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 TRP 380 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331X GLU* 3.7 38.4 - - + -
333X ARG* 3.3 59.3 - - + +
341X VAL* 3.6 28.4 - - + +
342X ASP* 5.2 0.2 + - - -
354X ILE* 3.7 28.7 - - + -
355X VAL 3.5 6.5 - - - +
356X ALA* 3.4 33.0 - - + -
357X ALA* 3.9 3.6 - - - -
375X LYS 3.5 0.5 - - - +
376X LEU* 3.3 8.5 - - - +
377X GLN 2.8 31.1 + - - +
378X ASP 3.2 18.7 + - - -
379X GLY* 1.3 80.4 - - - +
381X TYR* 1.3 61.3 + - - +
382X ARG* 5.2 0.9 - - + -
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Residues in contact with TYR 381 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306X THR* 3.9 17.6 - - + +
308X GLU* 3.1 48.0 + - + -
309X ALA* 4.3 11.0 - - + -
354X ILE* 3.3 4.3 - - - -
355X VAL* 2.6 60.7 + - + +
357X ALA* 3.9 7.2 - - + +
361X ALA* 5.6 1.3 - - + -
362X PHE* 3.7 18.8 - + + -
375X LYS* 3.2 39.8 + - + -
376X LEU* 4.4 7.6 - - + -
380X TRP* 1.3 72.9 - - - +
382X ARG* 1.3 81.1 + - - +
383X THR* 3.6 15.8 + - + -
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Residues in contact with ARG 382 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335X VAL* 3.5 20.7 - - - +
336X ARG 4.3 2.0 + - - -
338X GLY* 4.6 4.6 - - - +
339X GLY 2.9 37.3 + - - +
341X VAL* 4.2 15.6 - - + +
352X GLU* 2.8 37.1 + - - +
354X ILE* 4.0 14.3 - - + +
374X GLU 3.6 17.7 - - - +
375X LYS* 2.9 49.5 + - + +
377X GLN* 2.8 47.7 - - + +
380X TRP 5.0 2.7 - - - +
381X TYR* 1.3 77.1 - - - +
383X THR* 1.3 58.9 + - - +
384X SER* 3.3 1.1 + - - +
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Residues in contact with THR 383 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304X TYR* 3.2 27.6 - - + +
306X THR* 4.5 7.2 - - + +
352X GLU* 3.8 0.2 + - - -
353X LEU* 2.4 43.5 + - + +
355X VAL* 4.2 17.3 - - + -
375X LYS* 3.3 7.4 + - - -
381X TYR* 3.8 22.1 + - + +
382X ARG* 1.3 72.4 - - - +
384X SER* 1.3 66.5 + - - +
385X ASP* 3.1 25.6 + - - +
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Residues in contact with SER 384 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352X GLU* 2.9 21.3 + - - -
375X LYS* 2.9 23.9 + - - +
382X ARG* 3.3 0.7 + - - +
383X THR* 1.3 77.2 + - - +
385X ASP* 1.3 58.6 + - - +
400X ARG* 3.6 4.3 - - - +
401X VAL* 2.7 43.6 + - - -
402X ASP* 5.8 2.2 - - - -
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Residues in contact with ASP 385 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304X TYR* 2.7 35.2 + - + +
306X THR* 5.5 1.0 - - - +
352X GLU* 3.4 4.2 - - - -
353X LEU* 2.9 30.5 + - + +
383X THR* 3.1 16.5 + - - +
384X SER* 1.3 81.6 - - - +
386X VAL* 1.3 66.1 + - - +
397X ILE* 4.9 11.4 - - + +
399X GLY 3.6 4.8 - - - +
400X ARG* 3.5 28.1 + - - +
401X VAL* 4.2 0.9 - - - -
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Residues in contact with VAL 386 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337X ILE* 4.3 11.2 - - + -
350X GLU* 4.0 13.5 - - + -
351X GLY 3.2 12.6 - - - +
385X ASP* 1.3 73.6 - - - +
387X ALA* 1.3 60.6 - - - +
397X ILE* 3.6 4.2 - - - +
398X LEU* 2.7 42.7 + - + -
399X GLY 2.7 19.0 + - - +
400X ARG 4.3 0.4 - - - +
401X VAL* 3.7 30.1 - - + -
404X MET* 4.2 11.4 - - - -
413X HIS* 3.6 32.3 - - + +
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Residues in contact with ALA 387 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334X ILE* 3.5 16.1 - - + +
350X GLU* 3.4 3.5 - - - -
351X GLY 2.8 32.0 + - - +
353X LEU* 4.3 15.7 - - + -
385X ASP 3.8 0.4 + - - -
386X VAL* 1.3 75.8 - - - +
388X VAL* 1.3 61.3 + - - +
395X VAL* 3.7 22.7 - - + -
396X ARG 3.1 14.8 - - - +
397X ILE* 4.3 3.8 - - + -
398X LEU* 4.0 5.8 - - - -
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Residues in contact with VAL 388 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334X ILE* 3.9 6.7 - - - -
348X GLY* 3.4 38.8 - - - +
349X GLU 3.7 11.0 - - - +
350X GLU* 4.2 8.3 - - + +
387X ALA* 1.3 74.2 - - - +
389X TRP* 1.3 65.8 + - - +
390X THR 3.5 0.5 + - - -
395X VAL* 3.7 1.2 - - - -
396X ARG* 2.8 73.6 + - + +
398X LEU* 4.2 17.5 - - + -
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Residues in contact with TRP 389 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326X PRO* 4.6 11.7 - - + -
332X VAL* 4.1 26.7 - - + -
333X ARG* 5.0 1.0 - - - +
334X ILE* 3.5 35.1 - - + +
344X ILE* 5.8 5.0 - - + +
345X VAL* 5.2 8.7 - - + -
347X ASN* 3.6 36.8 + - - +
348X GLY* 4.0 12.1 + - - +
349X GLU 5.0 1.2 + - - -
388X VAL* 1.3 78.4 - - - +
390X THR* 1.3 64.9 + - - +
391X PRO* 3.8 2.1 - - - +
393X GLY* 3.4 30.7 - - - -
394X THR* 3.4 21.3 - - - -
395X VAL* 3.5 29.4 - - + -
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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