Contacts of the helix formed by residues 337 - 347 (chain D) in PDB entry 1Z6T
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 ARG 337 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331D LEU* 4.5 1.1 - - - -
334D PHE* 3.5 45.6 + - + +
335D PRO 3.5 3.6 - - - -
336D ASN* 1.3 81.3 - - - +
338D TRP* 1.3 59.1 + - - +
339D GLU* 3.3 2.5 - - - -
340D TYR* 3.1 38.5 + - + +
341D TYR* 2.9 61.1 + - + -
374D MET* 4.4 11.7 - - - +
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Residues in contact with TRP 338 (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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295D LEU* 4.1 8.5 - - + -
299D VAL* 4.0 30.0 - - + +
301D MET* 4.2 9.6 - - + +
306D LEU* 3.8 20.4 - - + -
307D PRO* 3.4 32.2 - - + +
309D GLN* 3.5 19.1 - - + +
310D ALA* 3.5 31.0 - - + -
313D ILE* 3.6 25.0 - - + +
331D LEU* 3.7 39.2 + - + +
335D PRO 3.4 24.4 + - - -
336D ASN* 3.7 4.2 + - - -
337D ARG* 1.3 78.2 - - - +
339D GLU* 1.3 57.6 + - - +
341D TYR 4.1 0.2 - - - -
342D LEU* 3.1 29.3 + - - +
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Residues in contact with GLU 339 (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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309D GLN* 3.9 27.3 + - + +
337D ARG 3.3 0.2 - - - -
338D TRP* 1.3 75.8 - - - +
340D TYR* 1.3 67.1 - - - +
342D LEU* 3.4 4.3 + - + +
343D LYS* 3.1 58.4 + - + +
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Residues in contact with TYR 340 (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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337D ARG* 3.1 44.6 + - + +
339D GLU* 1.3 79.9 - - - +
341D TYR* 1.3 92.2 + + - +
343D LYS* 3.4 5.1 + - + +
344D GLN* 2.5 64.7 + - + +
374D MET* 4.1 16.0 - - + +
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Residues in contact with TYR 341 (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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313D ILE* 5.2 3.4 - - + -
327D ILE* 5.6 8.7 - - + -
330D LEU* 4.2 23.1 - - + -
331D LEU* 4.1 21.1 - - + -
334D PHE* 3.5 38.0 - - + +
337D ARG* 2.9 48.7 + - + +
338D TRP 4.4 2.2 - - - +
340D TYR* 1.3 98.4 - + - +
342D LEU* 1.3 66.3 + - - +
344D GLN* 3.4 5.1 + - + +
345D LEU* 3.1 29.5 + - + +
370D ILE* 3.7 32.3 - - + +
374D MET* 3.6 14.3 - - + +
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Residues in contact with LEU 342 (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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309D GLN* 3.6 26.7 - - + -
312D SER* 3.4 48.7 - - - +
313D ILE* 3.8 17.7 - - + +
316D GLU* 4.2 3.6 - - + -
338D TRP 3.1 20.2 + - - +
339D GLU* 3.8 5.8 - - + +
341D TYR* 1.3 76.2 - - - +
343D LYS* 1.3 58.8 + - + +
345D LEU* 3.3 5.7 + - - +
346D GLN* 2.9 56.9 + - + +
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Residues in contact with LYS 343 (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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339D GLU* 3.1 50.6 + - + +
340D TYR* 3.7 6.3 - - - +
342D LEU* 1.3 75.4 - - + +
344D GLN* 1.3 62.3 + - - +
346D GLN* 3.2 15.7 + - - +
347D ASN* 2.8 39.1 + - + +
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Residues in contact with GLN 344 (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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340D TYR* 2.5 69.3 + - + +
341D TYR* 3.4 10.5 + - + +
343D LYS* 1.3 81.6 - - - +
345D LEU* 1.3 59.9 + - - +
347D ASN* 3.1 35.7 - - - +
349D GLN* 5.5 1.9 - - - +
366D GLU* 3.8 12.7 - - - +
370D ILE* 3.6 30.5 - - + -
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Residues in contact with LEU 345 (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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313D ILE* 3.9 34.8 - - + +
316D GLU* 3.9 31.8 - - + +
317D CYS* 4.6 1.6 - - - -
323D VAL* 5.3 3.6 - - + -
327D ILE* 3.9 32.8 - - + -
341D TYR 3.1 16.6 + - - +
342D LEU* 3.5 7.9 - - - +
343D LYS 3.3 0.2 - - - -
344D GLN* 1.3 77.1 - - - +
346D GLN* 1.3 61.6 + - - +
348D LYS* 3.3 34.0 + - - +
363D ALA* 4.7 6.1 - - - +
366D GLU* 4.5 9.2 - - + -
367D ALA* 4.6 11.7 - - + +
370D ILE* 4.5 9.4 - - + -
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Residues in contact with GLN 346 (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 SER* 5.0 4.6 - - - -
315D LYS* 5.1 4.8 - - - +
316D GLU* 3.4 30.0 + - + +
342D LEU* 2.9 45.3 + - - +
343D LYS* 3.2 18.5 + - - +
345D LEU* 1.3 77.4 - - - +
347D ASN* 1.3 58.4 + - - +
348D LYS* 3.5 6.4 + - - +
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Residues in contact with ASN 347 (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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343D LYS* 2.8 18.4 + - + +
344D GLN* 3.1 26.8 - - - +
346D GLN* 1.3 70.2 - - + +
348D LYS* 1.3 60.0 + - - +
349D GLN* 3.4 41.0 + - - +
366D GLU* 4.2 1.2 - - - +
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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