Contacts of the helix formed by residues 346 - 363 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196H GLN* 3.5 30.5 - - + +
344H GLN* 3.4 1.7 + - - +
345H VAL* 1.3 86.9 - - + +
347H GLU* 1.3 61.3 + - - +
348H THR* 3.7 14.9 + - - -
349H GLN* 2.9 31.1 + - - +
350H PHE* 3.0 26.9 + - - +
379H TYR* 3.8 16.9 - - + +
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Residues in contact with GLU 347 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346H ASP* 1.3 75.2 - - - +
348H THR* 1.3 63.6 - - - +
350H PHE* 3.2 5.1 - - + +
351H LYS* 3.0 55.1 + - + +
379H TYR* 3.6 38.7 + - + +
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Residues in contact with THR 348 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346H ASP* 3.3 15.0 + - - -
347H GLU* 1.3 78.9 - - - +
349H GLN* 1.3 67.2 + - - +
351H LYS* 3.6 8.5 + - - +
352H LYS* 3.0 36.7 + - - +
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Residues in contact with GLN 349 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168H TRP* 4.0 24.7 - - + +
300H GLN* 4.8 2.0 - - - +
344H GLN* 4.6 9.0 - - + -
345H VAL* 3.7 20.0 - - + -
346H ASP* 2.9 26.9 + - - +
348H THR* 1.3 79.5 - - - +
350H PHE* 1.3 66.6 + - - +
352H LYS* 3.1 25.2 + - - +
353H ILE* 2.9 36.3 + - + +
400H ILE 3.8 18.2 - - - +
401H PHE* 4.6 8.8 - - - +
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Residues in contact with PHE 350 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344H GLN* 4.6 4.2 - - - +
346H ASP 3.0 14.8 + - - +
347H GLU* 3.2 16.8 - - + +
349H GLN* 1.3 77.9 - - - +
351H LYS* 1.3 69.2 + - + +
353H ILE 3.5 0.2 + - - -
354H LEU* 3.2 36.9 + - + +
373H ILE* 3.7 35.9 - - + -
375H ALA 5.3 0.2 - - - -
378H GLY 4.3 5.2 - - - -
379H TYR* 3.5 46.2 - + + -
380H PHE 3.4 21.5 - - - -
381H ILE* 3.6 25.9 - - + +
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Residues in contact with LYS 351 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347H GLU* 3.0 47.0 + - + +
348H THR* 4.1 7.0 - - - +
350H PHE* 1.3 85.0 - - + +
352H LYS* 1.3 60.5 + - - +
354H LEU* 3.2 11.0 + - + +
355H GLY* 2.9 27.4 + - - -
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Residues in contact with LYS 352 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348H THR* 3.0 27.3 + - + +
349H GLN* 3.1 32.4 + - - +
351H LYS* 1.3 75.9 - - - +
353H ILE* 1.3 58.6 + - + +
355H GLY* 3.4 2.3 + - - -
356H TYR* 3.1 27.8 + - - +
398H GLU* 5.5 6.5 - - - +
400H ILE* 4.4 16.1 - - + +
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Residues in contact with ILE 353 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344H GLN* 3.3 44.4 - - + +
349H GLN* 2.9 24.4 + - + +
352H LYS* 1.3 74.8 - - + +
354H LEU* 1.3 59.8 + - - +
356H TYR* 3.2 8.0 + - - +
357H ILE* 2.9 31.0 + - + +
381H ILE* 3.5 23.6 - - + -
400H ILE* 4.0 21.1 - - + +
401H PHE 3.9 4.0 - - - +
402H GLY* 3.6 14.6 - - - -
403H PRO* 4.2 1.1 - - + -
404H VAL* 4.0 25.4 - - + -
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Residues in contact with LEU 354 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350H PHE* 3.2 43.4 + - + +
351H LYS* 3.2 12.1 + - + +
353H ILE* 1.3 75.1 - - - +
355H GLY* 1.3 62.9 + - - +
357H ILE* 3.1 12.2 + - + +
358H ASN* 3.0 24.0 + - - +
371H GLY 4.9 2.2 - - - +
372H GLY* 4.6 14.6 - - - -
373H ILE* 4.2 26.2 - - + +
381H ILE* 4.1 20.4 - - + -
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Residues in contact with GLY 355 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351H LYS 2.9 15.4 + - - -
352H LYS* 3.8 2.5 - - - -
353H ILE 3.3 0.2 - - - -
354H LEU* 1.3 75.8 - - - +
356H TYR* 1.3 57.0 + - - +
358H ASN* 3.4 10.7 + - - +
359H THR* 3.1 30.3 + - - -
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Residues in contact with TYR 356 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272H LYS* 3.2 10.0 + - - -
352H LYS 3.1 13.4 + - - +
353H ILE 3.3 10.1 - - - +
355H GLY* 1.3 75.4 - - - +
357H ILE* 1.3 67.1 + - - +
359H THR* 3.2 8.1 + - - +
360H GLY 3.0 17.8 + - - -
394H THR* 4.6 4.9 - - + -
395H ILE* 3.1 44.0 + - + +
398H GLU* 3.6 27.4 - - + +
400H ILE* 3.2 51.0 - - + +
404H VAL* 3.6 30.1 - - + -
406H GLN* 2.7 20.4 + - - -
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Residues in contact with ILE 357 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353H ILE* 2.9 19.8 + - + +
354H LEU* 3.1 13.7 + - + +
356H TYR* 1.3 76.3 - - + +
358H ASN* 1.3 62.5 + - - +
360H GLY 3.2 1.4 + - - -
361H LYS* 3.2 32.6 + - + +
367H LEU* 5.2 0.2 - - + -
371H GLY* 3.5 36.6 - - - +
381H ILE* 4.3 15.3 - - + -
384H THR* 3.5 27.1 - - + +
386H PHE* 3.4 20.3 - - + -
404H VAL* 4.0 23.3 - - + -
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Residues in contact with ASN 358 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354H LEU 3.0 12.7 + - - +
355H GLY* 3.4 13.4 - - - +
356H TYR 3.2 0.2 - - - -
357H ILE* 1.3 75.3 - - - +
359H THR* 1.3 65.9 + - - +
361H LYS* 3.0 23.7 + - - +
362H GLN* 2.9 38.0 + - + +
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Residues in contact with THR 359 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355H GLY 3.1 13.5 + - - -
356H TYR* 3.2 11.7 + - - -
358H ASN* 1.3 77.1 - - - +
360H GLY* 1.3 62.7 + - - +
362H GLN* 3.3 7.9 + - + +
363H GLU* 3.0 57.5 + - + +
394H THR* 3.8 20.6 - - + +
395H ILE* 5.3 1.1 - - + -
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Residues in contact with GLY 360 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356H TYR 3.0 11.1 + - - -
357H ILE 3.2 4.9 + - - -
358H ASN 3.1 0.4 - - - -
359H THR* 1.3 78.5 - - - +
361H LYS* 1.3 59.7 + - - +
363H GLU* 3.4 6.8 + - - +
364H GLY 3.6 0.2 + - - -
365H ALA* 3.2 25.7 + - - +
386H PHE* 3.9 14.4 - - - -
395H ILE* 3.8 28.8 - - - +
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Residues in contact with LYS 361 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357H ILE* 3.2 28.0 + - + +
358H ASN* 3.0 21.2 + - - +
360H GLY* 1.3 76.8 - - - +
362H GLN* 1.3 61.9 + - + +
364H GLY* 3.3 13.2 + - - -
365H ALA 4.4 9.2 + - - +
367H LEU* 4.1 24.8 - - + +
371H GLY 5.3 5.5 + - - -
386H PHE* 4.1 12.8 - - + -
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Residues in contact with GLN 362 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358H ASN* 2.9 32.8 + - + +
359H THR* 3.7 9.2 - - + +
361H LYS* 1.3 76.7 - - + +
363H GLU* 1.3 60.9 + - + +
364H GLY 3.3 1.5 + - - -
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Residues in contact with GLU 363 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359H THR* 3.0 32.8 + - + +
360H GLY* 3.4 5.7 + - - +
361H LYS 3.3 0.8 - - - -
362H GLN* 1.3 79.6 - - + +
364H GLY* 1.3 58.2 + - - +
365H ALA 3.6 1.1 - - - -
393H MET* 3.6 30.3 - - + +
394H THR* 2.8 49.0 + - - -
395H ILE* 3.9 2.8 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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