Contacts of the helix formed by residues 346 - 363 (chain L) in PDB entry 1ZUM
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 ASP 346 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196L GLN* 3.6 31.1 + - + +
344L GLN* 3.3 1.5 + - - +
345L VAL* 1.3 86.2 - - - +
347L GLU* 1.3 60.7 + - - +
348L THR* 3.8 16.3 + - - -
349L GLN* 3.0 29.4 + - - +
350L PHE* 3.1 27.2 + - - +
379L TYR* 3.6 19.0 - - + +
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Residues in contact with GLU 347 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346L ASP* 1.3 74.3 - - - +
348L THR* 1.3 66.8 + - - +
350L PHE* 3.1 6.3 + - + +
351L LYS* 3.0 56.9 + - + +
379L TYR* 3.5 38.5 + - + +
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Residues in contact with THR 348 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346L ASP* 3.3 15.5 + - - -
347L GLU* 1.3 78.5 - - - +
349L GLN* 1.3 67.2 + - - +
351L LYS* 3.5 11.3 + - - +
352L LYS* 3.0 33.5 + - + +
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Residues in contact with GLN 349 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168L TRP* 4.0 21.1 - - + +
300L GLN* 5.2 1.1 - - - +
344L GLN* 4.6 8.3 - - + +
345L VAL* 3.8 19.7 - - + -
346L ASP* 3.0 21.5 + - - +
348L THR* 1.3 80.8 - - - +
350L PHE* 1.3 60.3 + - - +
352L LYS* 3.5 26.2 - - - +
353L ILE* 2.9 41.9 + - + +
400L ILE 3.5 21.1 - - - +
401L PHE* 4.4 11.6 - - - +
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Residues in contact with PHE 350 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344L GLN* 4.6 4.2 - - - +
346L ASP 3.1 16.0 + - - +
347L GLU* 3.2 15.0 - - + +
349L GLN* 1.3 79.9 - - - +
351L LYS* 1.3 67.1 + - + +
353L ILE 3.6 0.2 + - - -
354L LEU* 3.2 40.4 + - + +
373L ILE* 3.8 36.8 - - + -
378L GLY 4.4 5.4 - - - -
379L TYR* 3.5 44.4 - + + -
380L PHE 3.4 21.1 - - - -
381L ILE* 3.5 27.2 - - + +
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Residues in contact with LYS 351 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347L GLU* 3.0 52.6 + - + +
348L THR* 4.1 7.9 - - - +
350L PHE* 1.3 83.1 - - + +
352L LYS* 1.3 59.9 + - - +
354L LEU* 3.3 12.1 + - + +
355L GLY* 2.9 26.0 + - - -
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Residues in contact with LYS 352 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348L THR* 3.0 23.8 + - + +
349L GLN* 3.5 31.6 - - - +
351L LYS* 1.3 76.7 - - - +
353L ILE* 1.3 58.3 + - + +
355L GLY* 3.4 2.5 + - - -
356L TYR* 3.0 26.9 + - - +
398L GLU* 4.2 16.4 + - - -
399L GLU 5.0 5.5 + - - -
400L ILE* 4.5 16.5 - - + +
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Residues in contact with ILE 353 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344L GLN* 3.4 41.3 - - + +
349L GLN* 2.9 26.0 + - + +
352L LYS* 1.3 75.7 - - + +
354L LEU* 1.3 59.0 + - - +
356L TYR* 3.2 7.2 + - + +
357L ILE* 2.9 31.1 + - + +
381L ILE* 3.6 20.0 - - + -
400L ILE* 4.0 21.3 - - + +
401L PHE 3.8 3.8 - - - +
402L GLY* 3.5 17.5 - - - -
403L PRO* 4.2 2.5 - - + -
404L VAL* 3.8 26.7 - - + -
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Residues in contact with LEU 354 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350L PHE* 3.2 40.5 + - + +
351L LYS* 3.3 13.4 + - + +
353L ILE* 1.3 76.2 - - - +
355L GLY* 1.3 63.9 + - - +
357L ILE* 3.3 14.9 + - + +
358L ASN* 3.1 28.9 + - - +
371L GLY 4.9 2.0 - - - +
372L GLY* 4.5 14.6 - - - -
373L ILE* 4.2 26.7 - - + +
381L ILE* 4.1 18.4 - - + -
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Residues in contact with GLY 355 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351L LYS 2.9 15.6 + - - -
352L LYS* 3.8 2.2 - - - -
353L ILE 3.3 0.2 - - - -
354L LEU* 1.3 77.1 - - - +
356L TYR* 1.3 57.7 + - - +
358L ASN* 3.2 10.6 + - - +
359L THR* 3.0 31.3 + - - -
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Residues in contact with TYR 356 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272L LYS* 3.2 11.1 + - - -
352L LYS 3.0 14.0 + - - +
353L ILE 3.2 8.3 + - - +
355L GLY* 1.3 75.1 - - - +
357L ILE* 1.3 66.3 + - - +
359L THR* 3.2 9.1 + - - -
360L GLY 3.0 17.8 + - - -
386L PHE* 5.5 0.2 - + - -
394L THR* 4.4 7.0 - - + -
395L ILE* 2.7 52.5 + - + +
398L GLU* 3.5 24.5 - - + -
400L ILE* 3.2 46.4 - - + +
404L VAL* 3.5 33.7 - - + -
406L GLN* 2.9 11.5 + - - -
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Residues in contact with ILE 357 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353L ILE* 2.9 21.6 + - + +
354L LEU* 3.3 13.9 + - + +
356L TYR* 1.3 76.1 - - + +
358L ASN* 1.3 62.5 + - - +
360L GLY 3.2 1.9 + - - -
361L LYS* 3.2 32.2 + - + +
367L LEU* 5.1 0.2 - - + -
371L GLY* 3.4 37.2 - - - +
381L ILE* 4.3 16.6 - - + -
384L THR* 3.5 24.9 - - + +
386L PHE* 3.4 20.3 - - + -
404L VAL* 3.9 22.9 - - + -
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Residues in contact with ASN 358 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354L LEU* 3.1 20.0 + - - +
355L GLY* 3.4 13.0 - - - +
357L ILE* 1.3 73.9 - - - +
359L THR* 1.3 65.5 + - - +
361L LYS* 3.1 27.2 + - - +
362L GLN* 2.9 34.4 + - + +
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Residues in contact with THR 359 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355L GLY 3.0 14.2 + - - -
356L TYR* 3.6 11.2 - - - -
358L ASN* 1.3 76.2 - - - +
360L GLY* 1.3 62.9 + - - +
362L GLN* 3.3 8.4 + - + +
363L GLU* 3.0 52.1 + - + +
394L THR* 3.9 18.4 - - + +
395L ILE* 5.0 2.5 - - + -
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Residues in contact with GLY 360 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356L TYR 3.0 10.1 + - - -
357L ILE 3.2 4.7 + - - -
358L ASN 3.1 0.4 - - - -
359L THR* 1.3 79.3 - - - +
361L LYS* 1.3 60.6 + - - +
363L GLU* 3.5 6.7 + - - +
365L ALA* 3.1 25.8 + - - +
386L PHE* 3.7 15.7 - - - -
395L ILE* 3.6 27.1 - - - +
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Residues in contact with LYS 361 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357L ILE* 3.2 31.3 + - + +
358L ASN* 3.1 22.5 + - - +
360L GLY* 1.3 76.6 - - - +
362L GLN* 1.3 61.7 + - + +
364L GLY* 3.3 13.3 + - - -
365L ALA 4.4 6.3 - - - +
367L LEU* 4.1 24.8 - - + +
371L GLY 5.2 5.6 + - - +
386L PHE* 3.8 15.0 - - + -
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Residues in contact with GLN 362 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358L ASN* 2.9 28.9 + - + +
359L THR* 3.3 9.6 + - + +
361L LYS* 1.3 77.4 - - + +
363L GLU* 1.3 62.5 + - + +
364L GLY 3.2 1.1 + - - -
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Residues in contact with GLU 363 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359L THR* 3.0 32.3 + - + +
360L GLY* 3.5 4.3 + - - +
361L LYS 3.3 0.4 - - - -
362L GLN* 1.3 78.5 - - + +
364L GLY* 1.3 59.4 + - - +
365L ALA 3.6 1.1 + - - -
393L MET* 3.4 30.5 - - + +
394L THR* 2.9 46.5 + - - -
395L ILE* 4.0 4.2 + - - +
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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