Contacts of the helix formed by residues 331 - 353 (chain C) in PDB entry 2HYE
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 GLY 331 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299C LEU* 4.6 7.9 - - - +
329C VAL* 4.9 0.4 - - - +
330C ARG* 1.3 79.9 - - - +
332C GLY* 1.3 59.1 + - - +
333C GLN 3.6 1.6 - - - -
334C GLN* 3.8 16.7 - - - +
335C ALA* 3.1 28.6 + - - +
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Residues in contact with GLY 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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299C LEU* 3.5 24.0 - - - +
326C PHE* 3.2 27.3 - - - -
329C VAL* 3.7 4.3 + - - +
330C ARG 3.2 6.3 + - - -
331C GLY* 1.3 73.5 - - - +
333C GLN* 1.3 62.0 + - - +
334C GLN 3.1 1.3 - - - -
335C ALA* 3.5 1.1 + - - -
336C LEU* 3.0 27.9 + - - +
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Residues in contact with GLN 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C TYR* 2.8 45.1 + - + -
326C PHE* 3.4 8.3 + - - -
327C SER* 3.7 23.8 + - - +
329C VAL 4.9 0.4 + - - -
330C ARG 5.0 1.0 + - - -
331C GLY* 4.6 0.2 - - - -
332C GLY* 1.3 76.5 - - - +
334C GLN* 1.3 61.8 + - - +
336C LEU* 3.5 6.6 + - - +
337C LEU* 3.3 24.0 + - + +
383C ASN* 2.9 18.8 + - - +
385C ARG* 3.0 34.0 + - - +
386C PHE* 4.0 9.3 - - + -
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Residues in contact with GLN 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C GLY* 3.8 18.3 - - - +
332C GLY 3.1 0.2 - - - -
333C GLN* 1.3 80.2 - - - +
335C ALA* 1.3 64.8 + - - +
337C LEU* 3.2 39.5 + - - +
338C GLN* 3.4 6.2 + - - +
385C ARG* 5.9 1.7 - - - +
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Residues in contact with ALA 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C LEU* 5.0 11.4 - - + -
300C THR* 5.5 5.2 - - - +
303C LEU* 4.1 14.6 - - + -
331C GLY 3.1 17.0 + - - +
332C GLY* 3.5 5.4 + - - +
334C GLN* 1.3 81.9 - - + +
336C LEU* 1.3 62.3 + - - +
337C LEU 3.3 0.2 + - - -
338C GLN* 3.5 7.3 + - - +
339C HIS* 3.5 29.4 + - + -
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Residues in contact with LEU 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C LEU* 3.7 17.6 - - + +
307C LEU* 4.4 10.1 - - + -
322C MET* 3.7 31.6 - - + -
323C TYR* 4.0 30.1 - - + +
326C PHE* 4.5 8.7 - - + -
332C GLY 3.0 17.8 + - - +
333C GLN* 3.8 7.2 - - - +
334C GLN 3.2 0.4 - - - -
335C ALA* 1.3 73.9 - - - +
337C LEU* 1.3 66.8 + - - +
339C HIS* 3.9 0.5 + - - +
340C TRP* 3.2 20.8 + - + +
380C PHE* 4.1 17.0 - - + -
386C PHE* 3.8 24.9 - - + -
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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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333C GLN* 3.3 13.6 + - + +
334C GLN* 3.2 31.6 + - - +
335C ALA 3.2 0.2 - - - -
336C LEU* 1.3 76.5 - - - +
338C GLN* 1.3 69.2 + - - +
340C TRP* 2.9 11.0 + - + +
341C SER* 2.8 26.4 + - - -
385C ARG* 4.3 27.8 - - + +
386C PHE* 3.2 44.4 - - + -
389C LEU* 4.7 19.3 - - + -
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Residues in contact with GLN 338 (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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334C GLN 3.4 6.7 + - - +
335C ALA* 3.6 13.0 - - - +
337C LEU* 1.3 78.3 - - - +
339C HIS* 1.3 95.5 + - - +
341C SER* 2.6 25.8 + - - +
342C GLU* 3.0 24.1 + - + +
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Residues in contact with HIS 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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300C THR* 4.7 10.9 + - + +
303C LEU* 3.3 35.0 - - + +
304C GLN* 4.3 32.2 + - + -
307C LEU* 3.3 23.3 - - + +
335C ALA* 3.5 10.2 + - + +
336C LEU 4.3 0.9 - - - +
337C LEU 3.2 0.6 - - - -
338C GLN* 1.3 101.2 + - - +
340C TRP* 1.3 54.3 + - - +
342C GLU* 3.0 6.2 + - - +
343C TYR* 2.7 35.7 + - - +
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Residues in contact with TRP 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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307C LEU* 3.9 9.3 - - + +
311C LEU* 3.5 28.3 - - + +
336C LEU* 3.2 19.9 + - + +
337C LEU* 2.9 10.7 + - + +
339C HIS* 1.3 74.8 - - - +
341C SER* 1.3 64.8 + - - +
343C TYR* 3.2 7.3 - - - +
344C ILE* 3.0 56.3 + - + +
372C VAL* 3.9 12.0 - - + +
375C VAL* 4.8 7.1 - - - +
376C ILE* 3.7 28.0 - - + -
380C PHE* 3.8 25.5 - + + -
386C PHE* 3.1 43.7 - + + -
389C LEU* 4.2 7.9 - - + -
390C MET* 3.2 33.4 - - + -
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Residues in contact with SER 341 (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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337C LEU 2.8 13.8 + - - -
338C GLN* 2.6 25.3 + - - +
340C TRP* 1.3 70.5 - - - +
342C GLU* 1.3 66.6 + - - +
343C TYR 2.9 5.3 + - - -
344C ILE* 3.0 14.4 + - - +
345C LYS* 3.0 30.7 + - - +
389C LEU* 3.3 36.0 - - - +
393C SER* 4.4 7.1 + - - -
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Residues in contact with GLU 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 GLN* 3.0 26.2 + - - +
339C HIS* 3.5 5.8 - - - +
341C SER* 1.3 83.0 + - - +
343C TYR* 1.3 60.1 + - - +
345C LYS* 4.1 23.4 + - + +
346C THR* 3.3 27.4 + - - +
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Residues in contact with TYR 343 (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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307C LEU* 5.6 2.5 - - + -
308C ASP* 2.9 42.2 - - - +
311C LEU* 3.6 31.3 - - + -
312C ASP* 2.8 47.9 + - - +
339C HIS 2.7 13.5 + - - +
340C TRP* 3.2 13.9 - - - +
342C GLU* 1.3 76.9 - - - +
344C ILE* 1.3 75.2 + - + +
346C THR* 3.1 6.4 + - + -
347C PHE* 2.9 43.9 + + + +
368C PHE* 4.6 14.7 - + - -
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Residues in contact with ILE 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 TRP* 3.0 61.4 + - + +
341C SER* 3.4 6.7 - - - +
343C TYR* 1.3 86.6 - - + +
345C LYS* 1.3 52.8 + - - +
347C PHE 3.8 0.2 - - - -
348C GLY* 2.7 34.7 + - - -
368C PHE* 3.7 16.3 - - + -
372C VAL* 4.0 13.5 - - + -
390C MET* 4.2 3.8 - - - -
393C SER* 3.8 22.2 - - - +
394C PHE* 3.9 25.4 - - + -
397C PHE* 4.0 7.6 - - + -
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Residues in contact with LYS 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 SER* 3.0 24.9 + - - +
342C GLU* 4.2 24.6 + - + +
344C ILE* 1.3 72.8 - - - +
346C THR* 1.3 56.7 + - - +
349C THR* 2.6 43.9 + - - +
393C SER* 3.9 27.8 - - - +
396C THR* 4.1 28.4 - - + +
397C PHE* 4.0 15.0 - - + +
400C LYS* 6.2 3.6 - - - -
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Residues in contact with THR 346 (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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342C GLU* 3.3 22.7 + - - +
343C TYR* 3.1 7.4 + - + +
345C LYS* 1.3 80.2 - - - +
347C PHE* 1.3 66.6 + - + +
349C THR* 3.5 10.5 + - - -
350C ALA* 3.5 14.0 + - - +
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Residues in contact with PHE 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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312C ASP* 5.3 9.0 - - + -
343C TYR* 2.9 41.1 + - + +
344C ILE 4.3 0.7 - - - +
346C THR* 1.3 79.5 - - + +
348C GLY* 1.3 57.9 + - - +
350C ALA* 3.8 9.8 + - + +
351C ILE* 2.9 46.9 + - + +
368C PHE* 3.3 40.4 - + + -
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Residues in contact with GLY 348 (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 ILE 2.7 20.5 + - - -
345C LYS 3.0 0.6 + - - -
347C PHE* 1.3 77.0 - - - +
349C THR* 1.3 63.7 + - - +
351C ILE* 3.0 28.7 + - - +
352C VAL 3.7 1.9 + - - -
368C PHE* 4.1 2.0 - - - -
397C PHE* 3.2 32.8 - - - -
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Residues in contact with THR 349 (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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345C LYS* 2.6 31.7 + - - +
346C THR* 3.8 7.4 + - - -
348C GLY* 1.3 67.2 - - - +
350C ALA* 1.3 53.8 + - - +
351C ILE 2.6 17.6 + - - -
352C VAL* 2.8 17.5 + - + +
353C ILE* 3.1 39.4 + - + -
397C PHE* 3.7 16.9 - - - +
400C LYS* 4.4 20.5 - - + +
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Residues in contact with ALA 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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346C THR 3.5 11.2 + - - +
347C PHE* 4.2 6.3 - - + +
348C GLY 3.4 1.2 - - - -
349C THR* 1.3 76.8 - - - +
351C ILE* 1.3 60.3 + - - +
352C VAL 3.5 0.2 - - - -
353C ILE* 4.6 11.4 - - - +
354C ASN* 5.6 2.2 + - - +
357C LYS* 4.8 17.8 + - - +
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Residues in contact with ILE 351 (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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347C PHE* 2.9 58.6 - - + +
348C GLY* 3.1 17.3 - - - +
349C THR 2.6 3.4 + - - -
350C ALA* 1.3 77.9 - - - +
352C VAL* 1.3 62.6 + - + +
353C ILE 3.8 0.7 - - - -
354C ASN 5.5 0.9 - - - -
357C LYS* 4.9 11.0 - - - +
358C ASP* 5.6 0.3 - - - +
361C MET* 3.9 23.7 - - - +
364C ASP* 3.9 28.5 - - + +
365C LEU* 4.3 14.1 - - + +
368C PHE* 4.0 18.2 - - + -
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Residues in contact with VAL 352 (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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348C GLY 4.1 7.0 - - - +
349C THR* 2.8 15.3 + - + +
351C ILE* 1.3 82.4 - - - +
353C ILE* 1.3 58.1 + - + +
354C ASN 3.7 2.2 - - - -
358C ASP* 5.3 1.3 - - - -
361C MET* 3.4 32.0 - - + +
365C LEU* 4.0 29.4 - - + -
397C PHE* 3.7 26.0 - - + +
398C ILE* 4.3 9.9 - - + +
400C LYS* 5.6 0.7 - - + -
401C ARG* 3.1 41.7 + - + +
405C PRO* 6.1 0.4 - - + -
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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
----------------------------------------------------------
349C THR* 3.1 35.0 + - + +
350C ALA* 4.6 6.7 - - - -
351C ILE 3.8 1.2 - - - +
352C VAL* 1.3 80.9 - - + +
354C ASN* 1.3 65.7 + - + +
355C PRO* 3.2 11.4 - - - +
400C LYS* 4.5 26.5 - - + +
401C ARG* 4.1 13.0 + - + +
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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