Contacts of the helix formed by residues 346 - 363 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196K GLN* 3.2 32.8 - - + +
344K GLN* 3.4 1.4 + - - +
345K VAL* 1.3 84.5 - - - +
347K GLU* 1.3 64.6 + - - +
348K THR* 3.8 16.2 + - - -
349K GLN* 3.0 30.1 + - - +
350K PHE* 3.1 19.1 + - - +
379K TYR* 3.5 17.5 - - + +
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Residues in contact with GLU 347 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346K ASP* 1.3 75.9 - - - +
348K THR* 1.3 64.1 + - - +
350K PHE* 3.1 8.5 + - + +
351K LYS* 3.0 56.1 + - + -
379K TYR* 3.4 39.5 + - + +
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Residues in contact with THR 348 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346K ASP* 3.3 16.1 + - - -
347K GLU* 1.3 78.3 - - - +
349K GLN* 1.3 65.9 + - - +
351K LYS* 4.2 11.0 + - - +
352K LYS* 3.1 33.7 + - + +
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Residues in contact with GLN 349 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168K TRP* 4.1 20.2 - - + +
300K GLN* 5.1 1.3 - - - +
344K GLN* 4.7 4.7 - - + -
345K VAL* 3.4 23.1 - - + -
346K ASP* 3.0 24.5 + - - +
348K THR* 1.3 80.1 - - - +
350K PHE* 1.3 60.2 + - - +
352K LYS* 3.5 24.2 - - - +
353K ILE* 2.9 45.9 + - + +
400K ILE 3.8 18.0 - - - +
401K PHE* 4.5 11.5 - - - +
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Residues in contact with PHE 350 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344K GLN* 4.6 3.8 - - - +
346K ASP 3.1 14.6 + - - +
347K GLU* 3.1 17.0 - - + +
349K GLN* 1.3 77.3 - - - +
351K LYS* 1.3 68.8 + - + +
353K ILE* 3.4 2.9 + - - +
354K LEU* 3.2 38.0 + - + +
373K ILE* 3.7 37.7 - - + -
378K GLY 4.4 5.2 - - - -
379K TYR* 3.5 46.9 - + + -
380K PHE 3.4 20.6 - - - -
381K ILE* 3.7 19.2 - - + +
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Residues in contact with LYS 351 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347K GLU* 3.0 51.8 + - + +
348K THR* 4.2 8.3 + - - +
350K PHE* 1.3 83.9 - - + +
352K LYS* 1.3 60.0 + - - +
354K LEU* 3.2 12.8 + - + +
355K GLY* 3.0 26.7 + - - -
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Residues in contact with LYS 352 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348K THR* 3.1 24.5 + - + +
349K GLN* 3.2 30.9 + - - +
351K LYS* 1.3 75.7 - - - +
353K ILE* 1.3 58.2 + - + +
355K GLY* 3.5 2.0 + - - -
356K TYR* 3.0 61.1 + - + -
399K GLU 5.2 4.4 + - - -
400K ILE* 5.9 2.3 - - - +
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Residues in contact with ILE 353 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344K GLN* 3.5 36.8 - - + +
349K GLN* 2.9 27.6 + - + +
352K LYS* 1.3 78.3 - - + +
354K LEU* 1.3 63.8 + - - +
356K TYR* 3.2 7.4 + - - +
357K ILE* 3.0 26.3 + - + +
381K ILE* 3.4 20.9 - - + -
400K ILE* 3.7 34.3 - - + +
401K PHE 3.6 6.1 - - - +
402K GLY* 3.5 17.0 - - - -
403K PRO* 4.5 1.3 - - + -
404K VAL* 4.0 13.2 - - + -
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Residues in contact with LEU 354 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350K PHE* 3.2 33.8 + - + +
351K LYS* 3.2 14.8 + - + +
353K ILE* 1.3 75.7 - - - +
355K GLY* 1.3 62.5 + - - +
357K ILE* 3.3 14.7 + - + +
358K ASN* 3.2 27.7 + - - +
371K GLY 4.9 2.0 - - - +
372K GLY* 4.5 10.5 - - - -
373K ILE* 4.0 42.0 - - + +
381K ILE* 4.6 13.7 - - + -
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Residues in contact with GLY 355 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351K LYS 3.0 15.4 + - - -
352K LYS 3.9 2.0 - - - -
354K LEU* 1.3 77.5 - - - +
356K TYR* 1.3 57.3 + - - +
358K ASN* 3.4 11.8 + - - +
359K THR* 3.1 29.6 + - - -
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Residues in contact with TYR 356 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352K LYS* 3.0 56.3 + - + -
353K ILE* 3.2 9.8 + - - +
355K GLY* 1.3 75.0 - - - +
357K ILE* 1.3 64.1 + - - +
359K THR* 3.3 6.9 + - - -
360K GLY 3.1 16.8 + - - -
394K THR* 4.1 13.5 - - + -
395K ILE* 3.4 22.5 - - + +
398K GLU* 2.6 47.8 + - + +
399K GLU 4.3 4.7 + - - -
400K ILE* 3.1 47.8 - - + -
404K VAL* 6.2 0.7 - - - -
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Residues in contact with ILE 357 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353K ILE* 3.0 17.3 + - + +
354K LEU* 3.3 14.3 + - + +
356K TYR* 1.3 75.0 - - - +
358K ASN* 1.3 66.7 + - - +
360K GLY 3.0 10.2 + - - -
361K LYS* 3.1 22.1 + - + +
367K LEU* 5.0 0.4 - - + -
371K GLY* 3.5 36.1 - - - +
381K ILE* 4.3 15.5 - - + -
384K THR* 3.7 22.0 - - - +
386K PHE* 3.4 23.5 - - + -
404K VAL* 3.9 27.1 - - + -
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Residues in contact with ASN 358 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354K LEU* 3.2 15.9 + - - +
355K GLY* 3.5 13.1 - - - +
356K TYR 3.3 0.2 - - - -
357K ILE* 1.3 80.3 - - - +
359K THR* 1.3 56.5 + - - +
361K LYS* 3.2 30.7 + - - +
362K GLN* 2.9 33.0 + - - +
371K GLY 5.7 0.2 - - - +
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Residues in contact with THR 359 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355K GLY 3.1 15.6 + - - -
356K TYR* 3.5 13.4 - - - +
357K ILE 3.3 0.2 - - - -
358K ASN* 1.3 74.8 - - - +
360K GLY* 1.3 58.0 + - - +
362K GLN* 3.7 16.8 + - - +
363K GLU* 3.0 39.6 + - + +
394K THR* 3.5 39.2 - - + +
395K ILE* 4.8 1.6 - - + -
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Residues in contact with GLY 360 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356K TYR 3.1 6.7 + - - -
357K ILE 3.0 9.1 + - - -
359K THR* 1.3 78.9 - - - +
361K LYS* 1.3 60.5 + - - +
363K GLU* 3.4 6.3 + - - +
365K ALA* 3.1 26.2 + - - +
386K PHE* 3.9 14.8 - - - -
395K ILE* 3.9 25.1 - - - -
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Residues in contact with LYS 361 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357K ILE* 3.1 27.1 + - + +
358K ASN* 3.2 27.4 + - - +
360K GLY* 1.3 74.4 - - - +
362K GLN* 1.3 63.2 + - - +
364K GLY* 3.3 12.8 + - - -
365K ALA 4.4 8.5 + - - +
367K LEU* 4.5 24.3 - - + +
371K GLY 5.2 6.4 + - - +
386K PHE* 4.0 12.3 - - + -
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Residues in contact with GLN 362 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358K ASN* 2.9 16.0 + - - +
359K THR* 3.7 19.8 + - - +
361K LYS* 1.3 77.9 - - - +
363K GLU* 1.3 66.6 + - + +
364K GLY 3.5 0.9 + - - -
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Residues in contact with GLU 363 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359K THR* 3.0 29.5 + - + +
360K GLY* 3.4 5.5 + - - +
361K LYS 3.3 0.6 - - - -
362K GLN* 1.3 82.7 - - + +
364K GLY* 1.3 59.3 + - - +
365K ALA 3.5 0.4 - - - -
392K GLY 5.0 1.0 - - - +
393K MET* 3.4 33.7 - - + +
394K THR* 2.7 50.7 + - - -
395K ILE* 4.0 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
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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