Contacts of the helix formed by residues 376 - 385 (chain A) 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 TYR 376 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A LEU* 3.9 17.0 - - + -
341A HIS* 3.4 35.0 - + + -
372A ASN 5.5 0.2 + - - -
373A LEU 5.2 0.4 - - - -
374A ASN 4.1 0.7 - - - +
375A VAL* 1.3 106.4 - - + +
377A SER* 1.3 66.4 + - - +
378A THR 3.4 0.9 - - - +
379A GLY* 3.0 12.0 + - - -
380A ARG* 3.2 16.4 + - - +
147B GLU* 4.4 4.5 - - - +
204B ALA 5.1 0.3 + - - -
205B GLN 3.5 15.4 + - - -
207B SER* 4.6 17.3 + - - -
210B ARG* 5.5 2.2 + - - -
5000B ASP* 3.2 49.3 + - + +
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Residues in contact with SER 377 (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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376A TYR* 1.3 70.0 - - - +
378A THR* 1.3 67.1 + - - +
380A ARG* 3.0 24.9 + - - +
381A LYS* 2.9 35.1 + - - +
40B GLU* 3.3 20.5 + - - -
145B PHE* 4.8 18.8 - - - -
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Residues in contact with THR 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A HIS* 3.9 9.6 - - + -
342A THR 3.2 35.7 - - - +
344A ASN* 3.2 23.0 + - - +
347A ILE* 4.7 3.1 - - + -
376A TYR* 3.4 0.8 - - - +
377A SER* 1.3 77.3 - - - +
379A GLY* 1.3 62.9 + - - +
381A LYS* 3.2 9.8 + - - +
382A LEU* 3.0 26.2 + - + +
145B PHE* 4.1 5.7 - - - -
147B GLU* 2.6 37.2 + - - +
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Residues in contact with GLY 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A HIS* 3.7 16.0 + - - -
373A LEU* 3.1 32.1 - - - +
376A TYR 3.0 9.0 + - - -
378A THR* 1.3 77.0 - - - +
380A ARG* 1.3 64.2 + - - +
382A LEU* 2.9 9.0 + - - +
383A LEU* 2.8 21.7 + - - +
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Residues in contact with ARG 380 (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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373A LEU 3.2 7.0 + - - +
374A ASN* 3.0 19.9 + - - +
375A VAL 2.9 21.3 + - - -
376A TYR 3.2 5.1 + - - +
377A SER* 3.0 37.7 + - - +
379A GLY* 1.3 74.4 - - - +
381A LYS* 1.3 57.5 + - - +
383A LEU* 3.1 9.1 + - - +
384A LYS* 2.9 28.2 + - - +
39B TYR* 3.2 33.5 + - - +
40B GLU* 3.2 45.9 + - + +
41B LEU* 4.7 7.3 - - + +
436D THR* 3.6 23.6 + - - +
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Residues in contact with LYS 381 (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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344A ASN* 3.0 33.1 - - - +
347A ILE* 4.1 17.5 - - + +
351A GLU* 4.5 2.6 - - - +
377A SER* 2.9 28.9 + - - +
378A THR* 3.3 9.4 - - - +
380A ARG* 1.3 77.6 - - - +
382A LEU* 1.3 62.6 + - - +
384A LYS* 3.3 7.8 + - - +
385A ALA* 3.1 21.7 + - - +
40B GLU* 4.9 3.6 - - - +
41B LEU* 4.5 16.2 - - + -
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Residues in contact with LEU 382 (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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340A GLY 3.9 9.9 - - - +
341A HIS* 4.0 2.0 - - - -
342A THR* 3.7 26.2 - - - +
347A ILE* 3.3 30.1 - - + -
350A ILE* 3.7 24.9 - - + -
362A MSE 3.8 19.5 - - + -
373A LEU* 4.3 9.4 - - + -
378A THR* 3.0 17.8 + - + +
379A GLY* 2.9 7.5 + - - +
381A LYS* 1.3 77.5 - - - +
383A LEU* 1.3 62.9 + - - +
385A ALA* 3.5 6.2 + - - +
387A VAL* 3.0 46.6 + - + +
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Residues in contact with LEU 383 (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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373A LEU* 3.6 36.3 - - + +
374A ASN* 3.5 29.4 - - - +
379A GLY 2.8 14.7 + - - +
380A ARG* 3.3 11.7 - - + +
382A LEU* 1.3 75.2 - - - +
384A LYS* 1.3 56.8 + - - +
386A GLY* 2.5 29.6 + - - -
387A VAL 3.7 8.6 + - - +
389A PRO* 3.6 21.1 - - + -
416A ARG* 4.7 10.9 + - - +
39B TYR* 6.0 0.2 - - - +
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Residues in contact with LYS 384 (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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351A GLU* 5.1 5.2 - - - +
380A ARG 2.9 12.7 + - - +
381A LYS* 3.6 10.3 - - - +
383A LEU* 1.3 71.3 - - - +
385A ALA* 1.3 58.2 + - - +
386A GLY* 2.7 12.6 + - - -
41B LEU* 3.4 50.6 - - + +
42B SER 5.8 0.2 - - - +
43B ALA* 6.1 3.6 - - - +
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Residues in contact with ALA 385 (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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347A ILE* 4.5 5.2 - - + -
350A ILE* 4.7 1.3 - - + -
351A GLU* 3.6 46.1 + - + +
354A VAL* 3.0 32.3 - - - +
381A LYS 3.1 11.9 + - - +
382A LEU* 3.8 11.7 - - - +
383A LEU 3.1 0.8 - - - -
384A LYS* 1.3 74.8 - - - +
386A GLY* 1.3 57.0 + - - +
387A VAL* 3.5 8.0 + - + -
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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