Contacts of the helix formed by residues 340 - 354 (chain F) in PDB entry 5ZR1
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 PRO 340 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405E LEU* 5.0 16.8 - - + +
336F ARG 4.4 4.3 - - - +
337F ARG 4.8 6.7 - - - +
338F LYS 3.4 11.4 - - - +
339F ASP* 1.3 81.0 - - - +
341F ARG* 1.3 61.9 + - - +
342F ILE 3.2 1.0 + - - -
343F ASP* 3.8 19.1 + - - +
344F HIS* 4.2 4.9 + - - +
417F GLN* 4.9 8.5 - - - +
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Residues in contact with ARG 341 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339F ASP* 3.1 14.1 + - + -
340F PRO* 1.3 80.3 - - - +
342F ILE* 1.3 83.7 + - + +
344F HIS* 3.2 11.1 + - - +
345F PHE* 3.1 30.6 + - - +
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Residues in contact with ILE 342 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332F PHE* 6.1 3.1 - - + -
335F ARG* 3.7 32.8 - - + +
336F ARG* 4.7 11.2 - - + -
339F ASP* 3.4 27.5 + - + +
340F PRO 3.2 1.4 - - - -
341F ARG* 1.3 96.4 - - - +
343F ASP* 1.3 60.7 + - - +
345F PHE* 2.9 17.4 + - + +
346F ILE* 2.9 51.0 + - + +
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Residues in contact with ASP 343 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404E SER* 3.7 8.1 + - - +
405E LEU* 4.4 29.1 - - + +
329F PHE* 3.4 16.5 - - + -
336F ARG* 2.4 60.6 + - - +
339F ASP 4.5 0.9 + - - -
340F PRO* 3.8 12.0 + - - +
341F ARG 3.3 0.8 - - - -
342F ILE* 1.3 77.4 - - - +
344F HIS* 1.3 59.1 + - - +
346F ILE* 4.7 2.3 - - - +
347F VAL* 3.4 24.3 + - - +
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Residues in contact with HIS 344 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404E SER* 4.3 10.8 - - - +
340F PRO 4.2 4.6 + - - +
341F ARG* 3.2 12.7 + - - +
342F ILE 3.2 0.4 - - - -
343F ASP* 1.3 76.6 - - - +
345F PHE* 1.3 65.3 + - - +
346F ILE 3.4 0.2 - - - -
347F VAL* 3.6 8.1 - - + +
348F SER* 3.3 29.8 + - - -
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Residues in contact with PHE 345 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292F PHE* 5.9 1.8 - + - -
341F ARG* 3.1 23.5 + - - +
342F ILE* 2.9 21.4 + - + +
344F HIS* 1.3 78.3 + - - +
346F ILE* 1.3 76.1 + - + +
348F SER* 3.3 5.5 + - - -
349F LYS* 2.8 64.2 + - + +
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Residues in contact with ILE 346 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292F PHE* 3.7 26.2 - - + -
325F LEU* 3.7 22.2 - - + -
328F THR* 4.1 25.6 - - - +
329F PHE* 4.9 18.4 - - + -
332F PHE* 5.7 4.9 - - + -
336F ARG* 4.9 7.2 - - + -
342F ILE* 2.9 33.9 + - + +
343F ASP* 4.1 3.6 + - - +
344F HIS 3.4 0.2 - - - -
345F PHE* 1.3 92.9 - - + +
347F VAL* 1.3 60.0 + - + +
349F LYS* 3.3 5.2 + - - +
350F MET* 2.8 29.5 + - - +
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Residues in contact with VAL 347 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404E SER* 3.7 27.8 - - - +
325F LEU* 5.1 6.1 - - + -
329F PHE* 4.5 19.1 - - + -
343F ASP 3.4 21.7 + - - +
344F HIS* 3.6 11.4 - - + +
346F ILE* 1.3 74.4 - - + +
348F SER* 1.3 65.2 + - - +
350F MET* 3.7 7.6 - - - +
351F CYS* 3.3 30.1 + - - -
359F VAL* 4.5 11.5 - - + +
362F VAL* 4.8 10.3 - - + -
363F ILE* 4.4 16.6 - - + -
366F VAL* 6.4 1.6 - - + -
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Residues in contact with SER 348 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344F HIS* 3.3 34.2 + - - -
345F PHE* 3.6 6.5 - - - -
346F ILE 3.3 0.4 - - - -
347F VAL* 1.3 77.4 - - - +
349F LYS* 1.3 62.6 + - - +
350F MET 3.5 0.2 + - - -
351F CYS* 3.7 8.0 + - - +
352F SER* 3.6 17.7 + - - -
359F VAL* 5.7 2.7 - - - -
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Residues in contact with LYS 349 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291F ASP* 3.4 48.2 + - - +
292F PHE* 4.2 23.8 - - + +
345F PHE* 2.8 51.2 + - + +
346F ILE* 3.6 7.0 - - - +
348F SER* 1.3 75.3 - - - +
350F MET* 1.3 62.1 + - - +
352F SER* 3.7 5.7 + - - -
353F LEU* 3.5 24.2 + - + +
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Residues in contact with MET 350 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288F LEU* 3.7 21.8 - - + -
292F PHE* 3.5 26.5 - - + -
321F CYS* 3.7 32.3 - - + +
324F VAL* 5.1 1.1 - - + -
325F LEU* 3.7 28.9 - - + -
346F ILE 2.8 16.2 + - - +
347F VAL* 3.9 9.9 - - - +
348F SER 3.2 0.4 - - - -
349F LYS* 1.3 75.9 - - - +
351F CYS* 1.3 65.0 + - - +
353F LEU* 3.5 5.3 + - + +
354F MET* 3.1 47.6 + - + +
362F VAL* 3.9 12.7 - - + +
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Residues in contact with CYS 351 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347F VAL 3.3 17.8 + - - +
348F SER* 4.3 5.4 - - - +
349F LYS 3.4 0.6 - - - -
350F MET* 1.3 79.3 - - - +
352F SER* 1.3 58.5 + - - +
355F LEU* 3.0 6.8 + - - -
356F THR* 3.0 53.1 + - + +
357F SER 4.9 3.4 - - - +
358F LYS 4.1 2.5 - - - -
359F VAL* 3.7 32.1 - - - -
362F VAL* 3.6 22.4 - - - -
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Residues in contact with SER 352 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348F SER 3.6 12.1 + - - -
349F LYS* 3.7 8.6 + - - -
350F MET 3.3 0.6 - - - -
351F CYS* 1.3 78.7 - - - +
353F LEU* 1.3 60.8 + - - +
355F LEU* 3.6 22.6 + - - +
356F THR 5.3 0.4 - - - -
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Residues in contact with LEU 353 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272F LEU* 4.0 8.8 - - - +
287F ARG 5.5 0.7 - - - +
288F LEU* 3.7 31.2 - - + +
291F ASP* 3.3 28.0 - - - +
292F PHE* 5.1 7.4 - - + -
317F TRP* 5.7 0.2 - - - -
349F LYS* 3.5 17.4 + - + +
350F MET* 3.5 5.7 + - + +
351F CYS 3.3 0.4 - - - -
352F SER* 1.3 78.4 - - - +
354F MET* 1.3 61.6 + - + +
355F LEU* 3.3 17.5 - - + +
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Residues in contact with MET 354 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271F SER* 3.7 2.6 - - - -
272F LEU* 3.1 40.1 + - - -
273F LEU* 3.7 22.9 - - + -
288F LEU* 3.7 29.8 - - + -
317F TRP* 3.5 38.4 - - + +
320F VAL* 4.9 0.2 - - + -
321F CYS* 3.7 31.6 - - + +
350F MET* 3.1 31.4 + - + +
351F CYS 4.5 1.3 - - - +
353F LEU* 1.3 75.9 - - - +
355F LEU* 1.3 65.7 + - - +
356F THR* 3.2 5.3 + - + -
362F VAL* 5.5 2.5 - - + -
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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