Contacts of the helix formed by residues 379 - 397 (chain C) in PDB entry 1YCH
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 379 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377C VAL* 4.2 7.6 + - + +
378C PRO* 1.3 78.7 - - - +
380C GLY* 1.3 67.9 + - - +
381C GLU* 3.3 26.7 + - - +
382C ASP* 3.0 25.5 + - - +
383C LEU* 3.1 15.8 + - - +
114D ALA* 5.6 10.9 + - - +
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Residues in contact with GLY 380 (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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379C ARG* 1.3 71.8 - - - +
381C GLU* 1.3 68.0 + - - -
383C LEU* 3.3 6.5 + - - +
384C GLN* 3.0 23.2 + - - +
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Residues in contact with GLU 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C ARG* 3.3 35.5 + - - +
380C GLY* 1.3 81.1 + - - -
382C ASP* 1.3 51.5 + - - +
384C GLN* 3.6 7.8 - - - +
385C ARG* 2.8 64.2 + - - +
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Residues in contact with ASP 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373C THR 4.6 3.5 - - - +
374C VAL* 3.6 29.6 - - + +
375C GLN 5.5 0.7 + - - -
377C VAL 4.1 2.6 - - - +
378C PRO* 3.8 7.5 - - + +
379C ARG* 3.0 39.9 + - - +
381C GLU* 1.3 77.9 - - - +
383C LEU* 1.3 63.3 + - + +
385C ARG* 3.2 35.7 + - - +
386C CYS* 3.1 25.9 + - - -
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Residues in contact with LEU 383 (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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268C LYS* 3.7 36.6 - - + +
269C MET* 4.3 9.6 - - + +
272C ALA* 3.5 11.6 - - + +
378C PRO* 3.4 29.8 - - + +
379C ARG 3.1 13.7 + - - +
380C GLY* 3.9 7.6 - - - +
382C ASP* 1.3 80.1 - - - +
384C GLN* 1.3 57.6 + - - +
386C CYS* 3.3 6.8 + - - +
387C TYR* 2.9 28.1 + - - +
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Residues in contact with GLN 384 (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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380C GLY 3.0 17.8 + - - +
381C GLU* 3.6 9.2 - - - +
383C LEU* 1.3 73.6 - - - +
385C ARG* 1.3 60.5 + - - +
387C TYR* 3.2 18.3 + - - +
388C GLU* 2.9 57.6 + - + +
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Residues in contact with ARG 385 (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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372C PRO* 5.9 1.6 - - + -
373C THR 5.7 1.8 + - - -
381C GLU* 2.8 56.9 + - - +
382C ASP* 3.2 27.7 + - - +
383C LEU 3.2 0.2 - - - -
384C GLN* 1.3 76.7 - - - +
386C CYS* 1.3 57.5 + - - +
388C GLU* 3.1 9.7 + - + +
389C LEU* 2.9 34.6 + - + +
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Residues in contact with CYS 386 (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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269C MET* 4.0 36.1 - - - -
272C ALA* 3.7 14.1 - - + -
273C LEU* 3.6 25.9 - - + +
372C PRO* 4.0 22.4 - - - +
374C VAL* 5.9 1.6 - - - -
382C ASP 3.1 17.8 + - - +
383C LEU* 3.4 9.2 - - - +
385C ARG* 1.3 72.2 - - - +
387C TYR* 1.3 67.5 + - - +
389C LEU* 3.1 8.5 + - - +
390C GLY 2.9 19.8 + - - -
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Residues in contact with TYR 387 (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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272C ALA* 3.6 13.9 + - + +
275C ASP* 3.9 18.6 - - + -
276C GLY* 3.3 27.3 - - - -
279C ALA* 3.2 24.0 - - + +
383C LEU 2.9 14.2 + - - +
384C GLN* 3.3 24.9 - - - +
386C CYS* 1.3 75.7 - - - +
388C GLU* 1.3 78.2 + - - +
391C ARG* 3.0 39.0 + - - +
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Residues in contact with GLU 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384C GLN* 2.9 38.1 + - + +
385C ARG* 3.3 11.9 - - + +
387C TYR* 1.3 90.8 - - - +
389C LEU* 1.3 53.6 + - - +
391C ARG* 3.0 15.6 - - - +
392C LYS* 2.8 33.5 + - - +
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Residues in contact with LEU 389 (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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273C LEU* 4.2 7.0 - - + -
340C LEU* 4.1 8.5 - - + -
367C ILE* 4.9 10.1 - - + -
368C ALA* 4.6 19.3 - - + -
372C PRO* 2.9 44.2 - - + -
385C ARG* 2.9 16.6 + - + +
386C CYS 3.4 8.7 - - - +
388C GLU* 1.3 75.6 - - - +
390C GLY* 1.3 58.1 + - - +
392C LYS* 2.9 25.5 + - + +
393C ILE* 2.8 34.5 + - + +
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Residues in contact with GLY 390 (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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273C LEU* 3.7 25.7 - - - +
276C GLY 3.6 7.0 - - - -
277C LEU* 3.4 17.1 - - - +
386C CYS 2.9 11.6 + - - -
387C TYR 3.7 2.5 - - - -
389C LEU* 1.3 76.7 - - - +
391C ARG* 1.3 56.5 + - - +
393C ILE* 4.5 7.2 - - - -
394C ALA* 3.1 27.5 + - - +
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Residues in contact with ARG 391 (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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276C GLY 3.2 19.1 - - - -
279C ALA* 3.4 32.4 + - - +
280C GLY* 3.8 10.9 - - - +
387C TYR* 3.0 28.6 + - + +
388C GLU* 3.0 28.3 - - - +
390C GLY* 1.3 76.9 - - - +
392C LYS* 1.3 61.9 + - - +
394C ALA* 3.4 4.0 + - - +
395C ALA* 3.1 21.7 + - - +
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Residues in contact with LYS 392 (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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367C ILE* 4.2 32.6 + - + -
368C ALA* 5.5 2.0 - - - +
388C GLU 2.8 11.8 + - - +
389C LEU* 2.9 26.5 + - + +
391C ARG* 1.3 74.6 - - - +
393C ILE* 1.3 59.4 + - - +
395C ALA* 2.9 24.7 + - + +
396C ARG* 3.1 12.5 + - + +
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Residues in contact with ILE 393 (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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273C LEU* 5.3 0.2 - - + -
277C LEU* 3.7 16.8 - - + -
306C ALA* 3.8 15.0 - - + -
308C LEU* 4.0 27.1 - - + -
338C VAL* 5.0 5.2 - - + -
339C GLY 5.4 0.2 - - - -
340C LEU* 4.1 15.9 - - + -
367C ILE* 3.6 39.3 - - + -
389C LEU* 2.8 23.5 + - + +
390C GLY* 4.0 6.3 - - - +
392C LYS* 1.3 74.3 - - - +
394C ALA* 1.3 64.4 + - - +
396C ARG* 3.1 7.4 + - - +
397C ILE* 2.9 43.3 + - + +
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Residues in contact with ALA 394 (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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277C LEU* 3.8 14.4 - - + +
280C GLY* 3.6 37.8 - - - +
282C CYS* 4.3 15.8 - - - -
390C GLY 3.1 19.6 + - - +
391C ARG 3.6 6.3 - - - +
392C LYS 3.1 0.4 - - - -
393C ILE* 1.3 77.0 - - - +
395C ALA* 1.3 62.1 + - - +
397C ILE* 3.4 2.3 + - - +
398C ALA* 3.1 20.3 + - - +
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Residues in contact with ALA 395 (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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391C ARG* 3.1 12.4 + - - +
392C LYS* 2.9 14.6 + - + +
394C ALA* 1.3 78.9 - - - +
396C ARG* 1.3 59.0 + - - +
398C ALA* 3.2 18.7 - - - +
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Residues in contact with ARG 396 (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* 3.9 22.6 - - + +
365C GLU* 2.3 50.2 + - - -
367C ILE* 3.6 30.3 - - + +
392C LYS 3.1 9.1 + - - +
393C ILE* 3.1 11.2 + - - +
395C ALA* 1.3 71.9 - - - +
397C ILE* 1.3 59.5 + - + +
398C ALA* 2.8 20.6 + - - +
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Residues in contact with ILE 397 (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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253C ALA* 3.8 19.5 - - - +
254C LYS 4.0 4.9 - - - +
282C CYS* 3.8 17.9 - - - -
305C ARG* 3.0 68.9 + - + +
306C ALA* 3.8 9.0 - - + -
338C VAL* 4.2 17.5 - - + -
393C ILE* 2.9 33.5 + - + +
394C ALA 3.7 5.2 - - - +
396C ARG* 1.3 76.1 - - + +
398C ALA* 1.3 65.9 + - - +
399C ASP* 3.6 0.4 - - - +
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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
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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