Contacts of the helix formed by residues 346 - 363 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C VAL* 6.5 0.4 - - + -
196C GLN* 3.1 33.5 - - + +
344C GLN* 3.4 1.3 + - - +
345C VAL* 1.3 87.7 - - + +
347C GLU* 1.3 63.3 + - - +
348C THR* 3.2 13.3 + - - -
349C GLN* 2.8 29.9 + - - +
350C PHE* 3.1 20.3 + - - +
379C TYR* 3.7 18.2 - - + +
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Residues in contact with GLU 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346C ASP* 1.3 73.4 - - - +
348C THR* 1.3 65.8 + - - +
350C PHE* 3.3 5.9 + - + +
351C LYS* 2.9 57.4 + - + +
379C TYR* 3.6 36.8 + - + +
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Residues in contact with THR 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C ASP* 3.2 14.8 + - - -
347C GLU* 1.3 80.4 - - - +
349C GLN* 1.3 64.8 + - - +
351C LYS* 3.5 15.7 + - - +
352C LYS* 3.1 45.3 + - + +
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Residues in contact with GLN 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C TRP* 3.9 24.6 - - + +
300C GLN* 4.8 2.0 - - - +
344C GLN* 4.7 5.2 - - + -
345C VAL* 3.7 22.0 - - + -
346C ASP* 2.8 26.2 + - - +
348C THR* 1.3 76.7 - - - +
350C PHE* 1.3 66.4 + - - +
352C LYS* 3.3 27.5 + - - +
353C ILE* 2.9 38.7 + - + +
400C ILE 4.2 14.2 - - - +
401C PHE* 4.4 12.1 - - - +
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Residues in contact with PHE 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344C GLN* 4.6 2.9 - - + +
346C ASP 3.1 14.9 + - - +
347C GLU* 3.3 17.7 - - + +
349C GLN* 1.3 76.0 - - - +
351C LYS* 1.3 69.3 + - + +
353C ILE* 3.4 2.8 + - - -
354C LEU* 3.1 41.6 + - + +
373C ILE* 3.8 34.3 - - + -
378C GLY 4.8 4.3 - - - -
379C TYR* 3.7 39.7 - + + -
380C PHE 3.7 21.8 - - - -
381C ILE* 3.7 29.2 - - + +
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Residues in contact with LYS 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C GLU* 2.9 50.0 + - + +
348C THR* 3.8 14.6 + - - +
350C PHE* 1.3 84.2 - - + +
352C LYS* 1.3 60.7 + - - +
354C LEU* 3.2 12.4 + - + +
355C GLY* 2.8 26.3 + - - -
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Residues in contact with LYS 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C THR* 3.1 29.7 + - + +
349C GLN* 3.3 33.4 + - - +
351C LYS* 1.3 76.4 - - - +
353C ILE* 1.3 59.3 + - + +
355C GLY* 3.3 2.9 + - - -
356C TYR* 3.0 48.3 + - + -
400C ILE 5.7 2.2 - - - +
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Residues in contact with ILE 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C GLN* 3.6 43.1 - - + +
349C GLN* 2.9 27.3 + - + +
352C LYS* 1.3 75.2 - - + +
354C LEU* 1.3 60.2 + - - +
356C TYR* 3.2 8.8 + - - +
357C ILE* 2.9 32.0 + - + +
381C ILE* 3.5 23.6 - - + -
400C ILE* 3.8 21.5 - - + +
401C PHE 3.9 4.5 - - - +
402C GLY* 3.8 10.5 - - - -
403C PRO* 4.4 3.8 - - + -
404C VAL* 3.9 25.8 - - + -
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Residues in contact with LEU 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350C PHE* 3.1 43.8 + - + +
351C LYS* 3.2 11.9 + - + +
353C ILE* 1.3 75.4 - - - +
355C GLY* 1.3 63.0 + - - +
357C ILE* 3.3 14.0 + - + +
358C ASN* 3.1 23.4 + - - +
371C GLY 5.2 1.8 - - - +
372C GLY* 4.8 9.9 - - - -
373C ILE* 4.1 27.4 - - + -
381C ILE* 4.0 17.3 - - + -
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Residues in contact with GLY 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351C LYS 2.8 15.2 + - - -
352C LYS* 3.3 4.7 + - - -
353C ILE 3.1 0.4 - - - -
354C LEU* 1.3 78.6 - - - +
356C TYR* 1.3 56.8 + - - +
358C ASN* 3.4 7.3 + - - +
359C THR* 2.8 31.0 + - - -
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Residues in contact with TYR 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352C LYS* 3.0 40.0 + - + +
353C ILE 3.2 6.7 + - - +
355C GLY* 1.3 72.4 - - - +
357C ILE* 1.3 61.9 + - - +
359C THR* 3.2 11.2 + - - -
360C GLY 2.9 23.4 + - - -
386C PHE* 5.5 0.2 - - - -
394C THR* 4.3 15.5 - - + -
395C ILE* 3.6 17.5 - - + +
398C GLU* 2.6 46.0 + - + +
399C GLU 4.1 6.5 + - - -
400C ILE* 3.0 52.9 - - + -
404C VAL* 6.1 0.4 - - - -
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Residues in contact with ILE 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353C ILE* 2.9 29.1 + - + +
354C LEU* 3.7 11.4 - - + +
356C TYR* 1.3 75.6 - - - +
358C ASN* 1.3 64.2 + - - +
360C GLY 3.1 10.0 + - - -
361C LYS* 3.1 25.8 + - + +
367C LEU* 5.3 0.2 - - + -
371C GLY* 3.5 34.1 - - - +
381C ILE* 4.1 13.2 - - + -
384C THR* 3.9 20.9 - - + +
386C PHE* 3.4 16.8 - - + -
404C VAL* 3.9 28.9 - - + -
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Residues in contact with ASN 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354C LEU 3.1 13.8 + - - +
355C GLY* 3.6 10.3 - - - +
357C ILE* 1.3 78.2 - - - +
359C THR* 1.3 62.5 + - - +
361C LYS* 3.3 20.9 + - - +
362C GLN* 3.0 51.3 + - - +
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Residues in contact with THR 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C GLY 2.8 19.4 + - - -
356C TYR* 3.3 16.1 - - + -
358C ASN* 1.3 77.6 - - - +
360C GLY* 1.3 62.3 + - - +
362C GLN* 3.3 6.7 + - - +
363C GLU* 3.0 45.6 + - + +
394C THR* 4.0 24.2 - - + +
395C ILE* 4.6 3.1 - - + -
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Residues in contact with GLY 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356C TYR 2.9 11.3 + - - -
357C ILE 3.1 4.2 + - - -
359C THR* 1.3 76.8 - - - +
361C LYS* 1.3 58.9 + - - +
363C GLU* 3.3 9.3 + - - +
365C ALA* 3.2 25.1 + - - +
386C PHE* 3.9 15.5 - - - -
395C ILE* 3.6 26.7 - - - +
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Residues in contact with LYS 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357C ILE* 3.1 31.1 + - + +
358C ASN* 3.7 19.1 - - - +
359C THR 3.3 0.2 - - - -
360C GLY* 1.3 74.0 - - - +
362C GLN* 1.3 64.1 + - + +
364C GLY* 3.2 13.0 + - - -
365C ALA 4.5 6.1 - - - +
367C LEU* 4.5 25.6 - - + +
371C GLY 5.1 5.9 + - - -
386C PHE* 4.0 14.4 - - + -
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Residues in contact with GLN 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358C ASN* 3.0 43.7 + - - +
359C THR* 3.8 6.1 - - - +
361C LYS* 1.3 77.7 - - + +
363C GLU* 1.3 59.7 + - + +
364C GLY 3.3 0.6 + - - -
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Residues in contact with GLU 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359C THR* 3.0 25.4 + - + +
360C GLY 3.6 6.3 - - - +
361C LYS 3.2 0.4 - - - -
362C GLN* 1.3 79.1 - - + +
364C GLY* 1.3 57.1 + - - +
365C ALA 3.5 0.9 - - - +
392C GLY 4.3 1.2 - - - +
393C MET* 3.2 33.8 - - + +
394C THR* 2.5 47.8 + - - -
395C ILE* 3.3 17.7 + - - +
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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