Contacts of the helix formed by residues 324 - 345 (chain C) in PDB entry 1ZXN
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 ARG 324 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323C GLY* 1.3 70.5 - - - -
325C HIS* 1.3 59.4 + - - +
326C VAL 3.2 0.2 - - - -
327C ASP* 3.4 17.1 + - - +
328C TYR* 3.0 30.8 + - - +
381C MET* 3.1 11.3 + - + +
382C THR* 3.9 15.8 + - - +
383C LEU 3.5 24.9 - - - +
384C GLN* 4.0 16.8 - - - +
385C PRO* 3.4 29.6 - - + +
388C PHE* 4.0 3.6 - - - -
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Residues in contact with HIS 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C TRP* 3.8 20.9 - - + -
312C SER* 3.1 17.3 + - - -
313C PHE 4.1 4.5 - - - -
314C VAL* 3.6 17.3 - - + +
319C THR* 2.9 25.9 + - - -
322C GLY 3.2 33.9 - - - -
323C GLY 3.7 4.2 - - - -
324C ARG* 1.3 80.0 - - - +
326C VAL* 1.3 71.7 + - + +
328C TYR* 3.6 3.7 - - - +
329C VAL* 3.4 25.5 + - - +
364C VAL* 4.4 9.1 - - + +
366C ALA* 4.9 1.6 - - + -
368C ILE* 4.4 7.0 - - + -
381C MET* 3.7 28.3 - - + +
388C PHE* 4.0 11.7 - - + -
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Residues in contact with VAL 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C PHE* 5.0 8.7 - - + -
310C GLN* 3.5 24.5 - - + +
312C SER* 3.4 29.6 - - - +
322C GLY* 4.2 4.7 - - - -
323C GLY 3.0 25.8 - - - +
325C HIS* 1.3 92.9 - - + +
327C ASP* 1.3 63.8 + - - +
328C TYR 3.2 0.2 - - - -
329C VAL* 3.9 4.8 - - - +
330C ALA* 2.7 40.4 + - + +
362C ILE* 5.2 3.9 - - + +
364C VAL* 4.7 12.6 - - + -
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Residues in contact with ASP 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C PHE* 6.1 0.2 - - - -
323C GLY 3.0 19.0 + - - +
324C ARG* 3.4 22.1 + - + +
325C HIS 3.4 0.2 - - - -
326C VAL* 1.3 84.0 - - - +
328C TYR* 1.3 58.1 + - - +
330C ALA* 4.3 4.9 - - - -
331C ASP* 2.8 49.7 + - - +
357C LYS* 4.1 14.9 + - - +
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Residues in contact with TYR 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C TRP* 3.9 13.9 - + - -
324C ARG 3.0 18.7 + - - +
325C HIS 3.6 4.7 - - - +
327C ASP* 1.3 79.1 - - - +
329C VAL* 1.3 61.1 + - + +
331C ASP* 4.5 2.1 - - - +
332C GLN* 3.0 41.3 + - + +
385C PRO* 4.4 20.2 - - + -
388C PHE* 3.8 24.9 - + + -
390C SER 5.4 0.2 - - - -
391C THR* 3.4 20.2 - - - +
392C CYS* 3.2 45.7 + - + -
393C GLN* 4.5 8.9 + - - -
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Residues in contact with VAL 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C TRP* 3.7 26.5 - - + -
299C VAL* 3.8 25.4 - - + -
325C HIS 3.4 15.4 + - - +
326C VAL 3.3 3.0 + - - +
327C ASP 3.3 0.2 - - - -
328C TYR* 1.3 79.7 - - + +
330C ALA* 1.3 65.6 + - - +
332C GLN* 3.2 20.0 + - - +
333C ILE* 3.5 12.1 + - - +
362C ILE* 3.3 26.5 - - + -
364C VAL* 4.2 9.0 - - + -
392C CYS* 4.0 14.4 - - - -
394C LEU* 4.2 9.4 - - + +
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Residues in contact with ALA 330 (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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308C PHE* 4.4 16.2 - - + -
326C VAL* 2.7 25.2 + - + +
327C ASP* 4.1 2.5 - - - +
329C VAL* 1.3 74.3 - - - +
331C ASP* 1.3 58.3 + - - +
333C ILE* 3.2 6.1 + - - +
334C VAL* 2.9 31.0 + - - +
357C LYS* 4.2 23.3 - - + -
360C MET* 3.8 6.1 - - + +
362C ILE* 4.1 15.0 - - + +
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Residues in contact with ASP 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C ASP* 2.8 37.8 + - - +
328C TYR* 4.5 2.9 - - - +
330C ALA* 1.3 70.1 - - - +
332C GLN* 1.3 64.3 + - - +
334C VAL* 3.7 7.3 - - - +
335C THR* 2.8 32.5 + - - +
357C LYS* 3.8 23.7 + - - +
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Residues in contact with GLN 332 (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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328C TYR* 3.0 39.5 + - + +
329C VAL* 3.2 13.8 + - - +
331C ASP* 1.3 77.8 - - - +
333C ILE* 1.3 65.2 + - - +
335C THR* 3.5 5.9 + - - -
336C LYS* 3.2 23.4 + - - +
392C CYS 2.9 20.6 + - - +
393C GLN* 3.5 23.5 + - - +
394C LEU* 3.1 37.4 + - + +
399C ILE* 5.6 2.2 - - + +
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Residues in contact with ILE 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C LEU* 3.9 20.9 - - + -
329C VAL* 3.5 8.9 + - + +
330C ALA 3.2 2.1 + - - +
332C GLN* 1.3 72.8 - - - +
334C VAL* 1.3 67.4 + - - +
336C LYS* 3.1 6.1 + - + +
337C LEU* 2.8 40.6 + - + +
360C MET* 3.5 30.1 - - + -
362C ILE* 4.0 16.4 - - + -
394C LEU* 3.2 32.3 - - + -
398C PHE* 3.7 20.2 - - + -
399C ILE* 5.2 5.4 - - + -
402C ALA* 4.5 7.2 - - + -
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Residues in contact with VAL 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C ALA 2.9 22.7 + - - +
331C ASP* 3.7 9.4 - - - +
332C GLN 3.4 0.2 - - - -
333C ILE* 1.3 76.6 - - - +
335C THR* 1.3 65.7 + - - +
337C LEU* 3.0 0.3 + - - -
338C VAL* 2.8 35.6 + - + +
353C ALA* 3.5 33.0 - - + +
356C VAL* 4.3 9.4 - - + -
357C LYS* 3.7 26.7 - - + +
360C MET* 3.6 21.1 - - - -
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Residues in contact with THR 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C ASP* 2.8 24.2 + - - +
332C GLN* 3.6 7.0 - - - -
334C VAL* 1.3 77.9 - - - +
336C LYS* 1.3 62.1 + - - +
338C VAL* 4.0 4.5 - - - +
339C ASP* 3.1 31.0 + - + +
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Residues in contact with LYS 336 (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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332C GLN 3.2 13.7 + - - +
333C ILE* 3.1 5.5 + - + +
335C THR* 1.3 79.9 - - - +
337C LEU* 1.3 63.3 + - + +
339C ASP* 3.6 6.6 - - - +
340C VAL* 3.4 26.5 + - - +
399C ILE* 3.9 35.4 - - + -
403C ILE* 4.3 4.4 - - + +
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Residues in contact with LEU 337 (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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301C LEU* 5.5 1.3 - - + -
333C ILE* 2.8 38.0 + - + +
334C VAL 3.7 2.0 - - - +
336C LYS* 1.3 71.9 - - + +
338C VAL* 1.3 65.8 + - - +
339C ASP 3.1 1.6 - - - -
340C VAL* 3.0 13.4 + - - +
341C VAL* 3.0 19.0 + - + +
356C VAL* 3.8 17.0 - - + -
360C MET* 5.0 4.7 - - + -
399C ILE* 6.1 0.4 - - + -
402C ALA* 3.8 10.1 - - + +
403C ILE* 3.2 47.3 - - + +
407C ILE* 3.4 38.8 - - + -
408C VAL* 3.9 8.6 - - + +
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Residues in contact with VAL 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C VAL* 2.8 26.8 + - + +
335C THR* 4.0 4.9 - - - +
337C LEU* 1.3 70.9 - - - +
339C ASP* 1.3 63.5 + - - +
341C VAL* 3.1 6.6 + - - +
342C LYS* 3.1 25.9 + - + +
351C VAL* 5.2 11.4 - - + +
352C LYS 4.3 2.7 - - - +
353C ALA* 3.6 31.2 - - + +
356C VAL* 3.4 32.1 - - + +
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Residues in contact with ASP 339 (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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335C THR* 3.1 22.6 + - + +
336C LYS* 3.6 8.9 - - - +
337C LEU 3.1 0.2 - - - -
338C VAL* 1.3 79.7 - - - +
340C VAL* 1.3 60.8 + - + +
341C VAL 3.6 0.2 + - - -
342C LYS* 3.8 5.3 + - - +
343C LYS* 3.6 18.7 + - - +
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Residues in contact with VAL 340 (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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336C LYS 3.4 14.3 + - - +
337C LEU* 3.0 8.8 + - - +
339C ASP* 1.3 75.8 - - + +
341C VAL* 1.3 64.3 + - - +
343C LYS* 3.5 7.3 + - - +
344C LYS* 3.4 37.4 + - + +
403C ILE* 3.7 31.4 - - + +
408C VAL* 4.3 15.9 - - + -
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Residues in contact with VAL 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C LEU* 3.0 19.0 + - + +
338C VAL* 3.1 10.7 + - - +
340C VAL* 1.3 74.7 - - - +
342C LYS* 1.3 60.6 + - - +
344C LYS* 3.1 3.1 + - - +
345C ASN* 2.8 35.0 + - + +
351C VAL* 4.0 23.6 - - + -
356C VAL* 4.8 6.5 - - + -
407C ILE* 6.0 0.4 - - + -
408C VAL* 3.9 33.0 - - + +
411C ILE* 4.6 16.6 - - + -
412C LEU* 4.5 23.7 - - + +
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Residues in contact with LYS 342 (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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338C VAL* 3.1 15.3 + - + +
339C ASP* 4.2 6.1 - - - +
341C VAL* 1.3 80.5 - - - +
343C LYS* 1.3 61.7 + - - +
345C ASN* 3.3 26.2 + - - +
346C LYS* 3.9 7.6 + - - -
351C VAL* 5.3 6.0 - - + +
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Residues in contact with LYS 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C ASP 3.6 11.2 + - - +
340C VAL* 3.5 11.6 + - - +
341C VAL 3.2 0.6 - - - -
342C LYS* 1.3 79.8 - - - +
344C LYS* 1.3 62.4 + - + +
346C LYS* 3.7 20.2 + - - +
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Residues in contact with LYS 344 (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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340C VAL* 3.4 29.1 + - + +
341C VAL 3.1 1.8 + - - -
343C LYS* 1.3 79.4 - - + +
345C ASN* 1.3 59.9 + - - +
346C LYS* 3.2 14.4 + - - +
408C VAL* 5.0 8.3 - - + +
412C LEU* 3.8 28.5 - - + +
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Residues in contact with ASN 345 (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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341C VAL* 2.8 24.5 + - + +
342C LYS* 3.3 11.9 + - - +
344C LYS* 1.3 74.1 - - - +
346C LYS* 1.3 67.7 + - - +
348C GLY* 2.9 33.7 + - - +
349C VAL 2.9 28.0 + - - -
350C ALA* 4.4 1.8 - - - +
351C VAL* 4.3 13.1 - - - +
412C LEU* 4.9 11.8 - - + +
415C VAL* 4.4 9.9 - - - +
416C LYS 5.4 0.2 + - - -
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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
------------------------------------------------------------
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