Contacts of the strand formed by residues 378 - 384 (chain D) in PDB entry 1ZQ1
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 ALA 378 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314D ILE 3.6 0.7 - - - +
315D LYS* 3.8 2.4 - - - -
316D LEU* 3.0 32.8 + - - +
319D PHE* 3.7 27.6 - - + +
320D ARG* 4.1 2.2 - - - +
323D ILE* 3.9 12.1 - - + -
351D ILE* 3.1 27.6 - - + -
373D LEU* 3.9 6.2 - - - +
376D GLU 3.7 0.2 + - - -
377D ASP* 1.3 75.1 - - - +
379D PHE* 1.3 64.4 + - - +
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Residues in contact with PHE 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314D ILE 3.0 17.7 - - - +
316D LEU* 4.8 2.5 - - - +
323D ILE* 4.5 2.4 - - - +
350D HIS* 3.4 5.9 - - - +
351D ILE* 3.3 58.9 + - + +
354D LEU* 4.5 13.0 - - + -
364D VAL* 4.4 14.8 - - + -
367D VAL* 4.2 25.6 - - + -
368D ILE* 4.4 2.2 - - + -
371D LEU* 4.1 13.0 - - + -
373D LEU* 3.4 24.0 - - + -
378D ALA* 1.3 76.2 - - - +
380D VAL* 1.3 75.6 + - - +
381D LEU* 3.5 39.5 - - + -
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Residues in contact with VAL 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312D LEU 3.5 0.7 - - - +
313D ALA* 3.1 23.4 - - - -
314D ILE* 3.1 13.8 + - + -
316D LEU* 4.0 22.2 - - + -
323D ILE* 4.7 0.9 - - + -
337D PHE* 4.4 7.2 - - + -
348D ILE* 4.2 17.7 - - + -
349D PHE 3.2 9.2 - - - +
350D HIS* 4.3 11.9 - - + -
379D PHE* 1.3 83.5 - - - +
381D LEU* 1.3 69.2 + - - +
382D VAL* 4.3 1.1 - - + -
393D LEU* 3.7 21.5 - - + +
396D VAL* 4.2 23.8 - - + -
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Residues in contact with LEU 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289D VAL* 5.3 1.6 - - + -
293D PHE* 3.5 36.3 - - + -
301D ILE* 5.6 2.2 - - + -
311D VAL* 4.4 10.5 - - + -
312D LEU 3.2 5.8 - - - +
313D ALA* 3.4 31.0 - - + -
348D ILE* 3.7 1.7 - - - +
349D PHE* 2.7 53.7 + - + +
354D LEU* 4.9 7.2 - - + -
359D ILE* 5.2 2.0 - - + -
367D VAL* 4.4 7.9 - - + -
379D PHE* 3.5 37.0 - - + -
380D VAL* 1.3 71.0 - - - +
382D VAL* 1.3 69.7 + - - +
383D ALA 4.2 0.4 - - - -
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Residues in contact with VAL 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310D LYS 3.7 0.2 - - - +
311D VAL* 4.6 0.4 - - - -
312D LEU 3.1 20.7 + - - +
345D VAL* 3.4 43.1 - - + -
347D GLY 4.3 2.9 - - - +
348D ILE* 4.0 22.0 - - + -
349D PHE* 5.6 0.7 - - - -
380D VAL* 4.3 1.8 - - + -
381D LEU* 1.3 80.9 - - - +
383D ALA* 1.3 58.7 + - - +
384D ALA* 3.3 1.2 + - + -
389D ALA* 3.2 29.1 - - + +
392D ALA* 3.9 6.7 - - + -
393D LEU* 3.4 32.5 - - + +
396D VAL* 5.1 0.9 - - + -
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Residues in contact with ALA 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300D ILE* 6.5 0.4 - - + -
301D ILE* 4.1 14.8 - - + -
304D VAL* 3.5 35.5 - - + +
310D LYS 3.7 6.5 - - - -
311D VAL* 4.0 21.8 - - + +
345D VAL* 4.4 9.4 - - - +
347D GLY 5.6 0.2 + - - -
349D PHE* 5.7 7.7 - - + -
381D LEU 4.2 0.6 - - - -
382D VAL* 1.3 68.2 - - - +
384D ALA* 1.3 64.7 + - - +
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Residues in contact with ALA 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304D VAL* 3.7 10.8 - - - +
309D GLY* 4.5 1.1 - - - -
310D LYS 3.1 28.1 + - - +
345D VAL* 3.9 17.3 - - + -
346D PRO* 6.2 0.7 - - + -
382D VAL 3.3 2.0 + - - -
383D ALA* 1.3 77.0 - - - +
385D GLU* 1.3 66.2 + - - +
386D GLU* 3.2 4.5 + - - -
388D LYS* 3.6 25.6 - - + -
389D ALA* 3.8 13.7 - - + +
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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
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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