Contacts of the helix formed by residues 337 - 347 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331B LEU* 4.3 2.0 - - - +
334B PHE* 3.3 43.6 + - + +
335B PRO 3.4 3.2 - - - -
336B ASN* 1.3 81.5 - - + +
338B TRP* 1.3 59.0 + - - +
339B GLU 3.4 2.7 - - - +
340B TYR* 3.4 43.4 + - + +
341B TYR* 3.0 45.7 + - + -
374B MET* 3.5 30.7 - - - +
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Residues in contact with TRP 338 (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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295B LEU* 4.1 9.9 - - + -
299B VAL* 4.2 19.4 - - + +
301B MET* 4.4 9.4 - - + +
306B LEU* 3.9 24.0 - - + -
307B PRO* 3.2 36.1 - - + +
309B GLN* 3.8 20.2 - - + +
310B ALA* 3.5 32.1 - - + -
313B ILE* 3.6 24.2 - - + +
331B LEU* 3.4 39.8 - - + +
335B PRO 3.9 21.3 + - - -
336B ASN* 3.6 3.8 - - - -
337B ARG* 1.3 74.1 - - - +
339B GLU* 1.3 66.1 + - - +
341B TYR 4.1 0.2 - - - -
342B LEU* 3.1 24.9 + - - +
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Residues in contact with GLU 339 (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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308B GLU* 5.3 0.9 - - - +
309B GLN* 2.7 41.6 + - - +
337B ARG 3.4 0.2 - - - -
338B TRP* 1.3 74.5 - - - +
340B TYR* 1.3 67.6 + - - +
342B LEU* 3.2 12.1 + - - +
343B LYS* 3.0 63.2 + - + +
346B GLN* 5.5 0.7 - - - +
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Residues in contact with TYR 340 (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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337B ARG* 3.4 50.9 + - + +
339B GLU* 1.3 80.0 - - - +
341B TYR* 1.3 82.9 + + - +
343B LYS* 3.5 6.7 + - - +
344B GLN* 2.9 67.8 + - + +
374B MET* 4.0 15.1 - - + +
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Residues in contact with TYR 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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313B ILE* 4.9 8.7 - - + -
327B ILE* 5.2 9.6 - - + -
330B LEU* 4.0 34.1 - - + -
331B LEU* 4.1 14.8 - - + -
334B PHE* 3.2 32.5 - - + +
337B ARG* 3.0 38.0 + - + +
338B TRP 4.5 1.8 - - - +
340B TYR* 1.3 97.6 - + - +
342B LEU* 1.3 66.8 + - - +
344B GLN* 3.3 18.6 + - - +
345B LEU* 3.1 28.9 + - + +
370B ILE* 3.7 23.3 - - + +
374B MET* 3.6 17.0 - - + +
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Residues in contact with LEU 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B GLN* 4.0 20.6 - - + -
312B SER* 3.5 49.8 - - - +
313B ILE* 3.8 19.2 - - + +
316B GLU* 4.1 4.7 - - + -
338B TRP 3.1 21.1 + - - +
339B GLU* 3.6 14.1 - - - +
341B TYR* 1.3 76.8 - - - +
343B LYS* 1.3 57.6 + - - +
345B LEU* 3.3 4.3 + - + +
346B GLN* 3.0 51.3 + - + +
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Residues in contact with LYS 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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339B GLU* 3.0 48.7 + - + +
340B TYR* 3.8 6.3 - - - +
342B LEU* 1.3 73.2 - - - +
344B GLN* 1.3 61.4 + - - +
346B GLN* 3.1 14.1 + - - +
347B ASN* 2.8 35.8 + - + +
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Residues in contact with GLN 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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340B TYR* 2.9 60.5 + - + +
341B TYR* 3.3 16.7 - - - +
342B LEU 3.4 0.2 - - - -
343B LYS* 1.3 77.1 - - + +
345B LEU* 1.3 60.5 + - - +
347B ASN* 3.1 31.8 - - - +
349B GLN* 5.5 5.1 + - - +
366B GLU* 3.8 12.7 - - - +
370B ILE* 3.6 32.5 - - + +
373B GLU* 6.1 2.4 - - - +
374B MET* 5.4 2.9 - - - +
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Residues in contact with LEU 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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313B ILE* 4.0 32.8 - - + +
316B GLU* 3.8 31.5 - - + +
317B CYS* 4.8 4.5 - - - -
323B VAL* 5.2 1.1 - - + -
327B ILE* 4.0 34.8 - - + -
341B TYR 3.1 19.5 + - - +
342B LEU* 3.5 6.7 - - - +
343B LYS 3.2 0.4 - - - -
344B GLN* 1.3 76.9 - - - +
346B GLN* 1.3 57.3 + - - +
348B LYS* 2.9 36.4 - - - +
363B ALA* 4.6 10.3 - - - +
366B GLU* 4.6 6.5 - - + -
367B ALA* 4.6 15.5 - - + +
370B ILE* 4.4 5.4 - - + -
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Residues in contact with GLN 346 (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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312B SER* 4.7 5.9 + - - -
316B GLU* 3.8 30.2 + - + +
339B GLU* 5.5 0.5 - - - +
342B LEU* 3.0 46.0 + - - +
343B LYS* 3.1 15.9 + - - +
345B LEU* 1.3 77.1 - - - +
347B ASN* 1.3 59.1 + - - +
348B LYS* 3.5 6.9 + - - +
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Residues in contact with ASN 347 (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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343B LYS 2.8 24.2 + - - +
344B GLN* 3.1 20.9 - - - +
346B GLN* 1.3 71.2 - - + +
348B LYS* 1.3 63.5 + - - +
349B GLN* 3.4 32.0 + - - +
366B GLU* 4.2 1.0 - - - +
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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