Contacts of the helix formed by residues 327 - 344 (chain C) in PDB entry 5YDI
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 ASN 327 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315C GLY 4.3 2.4 + - - -
316C PHE* 4.2 16.5 - - - +
326C GLY* 1.3 73.6 - - - +
328C ALA* 1.3 65.4 + - - +
329C GLY 3.3 2.7 - - - -
330C LEU* 3.1 27.5 + - + +
331C PHE* 3.0 32.5 + - + -
453C PRO* 3.4 7.4 - - - +
454C VAL* 2.6 51.4 + - - +
456C ASP* 3.3 20.2 + - - +
459C PHE* 4.1 5.2 - - + +
460C LEU* 4.5 4.4 - - - +
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Residues in contact with ALA 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C PHE* 4.1 18.2 - - - +
207C ARG 4.1 4.0 - - - +
208C HIS* 4.4 10.3 - - + -
310C ARG* 3.7 29.8 + - - +
314C LEU 4.5 0.7 - - - +
315C GLY* 3.0 18.9 + - - +
317C LEU 6.1 0.7 - - - +
326C GLY* 3.2 5.0 - - - -
327C ASN* 1.3 75.9 - - - +
329C GLY* 1.3 56.7 + - - +
331C PHE* 3.1 3.4 + - - +
332C ASP* 2.8 35.7 + - - +
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Residues in contact with GLY 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C TYR* 3.5 4.2 - - - +
310C ARG* 3.3 28.3 - - - -
315C GLY* 2.8 13.0 + - - -
316C PHE* 4.0 8.9 - - - -
327C ASN* 3.3 0.6 - - - +
328C ALA* 1.3 75.8 - - - +
330C LEU* 1.3 60.8 + - - +
332C ASP* 3.3 9.5 - - - +
333C GLN* 3.1 29.9 + - - +
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Residues in contact with LEU 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C PHE* 4.6 1.1 - - + -
316C PHE* 3.9 20.7 - - + -
327C ASN* 3.1 32.0 + - + +
329C GLY* 1.3 73.4 - - - +
331C PHE* 1.3 61.5 + - - +
333C GLN* 3.1 23.4 + - - +
334C ASN* 2.9 27.7 + - - +
365C SER* 4.3 14.4 - - - -
368C LEU* 3.8 22.7 - - + -
369C HIS* 4.1 3.6 - - + -
453C PRO* 4.0 13.5 - - + -
459C PHE* 3.7 42.3 - - + -
460C LEU* 5.0 0.4 - - + -
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Residues in contact with PHE 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A LEU* 4.5 17.7 - - + -
458A ALA* 5.2 2.0 - - + -
208C HIS* 3.3 46.2 - + + -
209C PRO* 3.5 19.9 - - + +
327C ASN* 3.0 28.2 + - + -
328C ALA 3.1 6.9 + - - +
330C LEU* 1.3 74.0 - - - +
332C ASP* 1.3 59.4 + - - +
334C ASN* 3.7 14.0 + - - +
335C LEU* 3.0 29.8 + - - +
338C ARG* 5.9 0.2 - - - -
374C LEU* 3.6 22.2 - - + -
456C ASP* 3.4 22.4 - - - -
458C ALA* 3.9 15.0 - - + -
459C PHE* 3.7 23.1 - + + -
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Residues in contact with ASP 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C TYR* 3.0 39.5 + - - +
209C PRO* 3.3 13.0 - - - +
256C LEU* 3.4 17.4 - - - +
309C TYR* 4.1 7.6 - - + -
310C ARG* 2.6 62.0 + - - +
328C ALA 2.8 17.3 + - - +
329C GLY 3.3 9.4 - - - +
330C LEU 3.2 0.2 - - - -
331C PHE* 1.3 74.0 - - - +
333C GLN* 1.3 64.5 + - - +
335C LEU 3.4 1.0 + - - -
336C ALA 3.1 6.1 + - - -
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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
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276C ILE* 3.4 20.8 - - + +
281C PHE* 5.3 0.2 - - - -
307C LEU* 3.9 20.3 - - + +
309C TYR* 3.4 40.8 - - + +
329C GLY 3.1 10.8 + - - +
330C LEU* 3.1 16.7 + - - +
332C ASP* 1.3 76.8 - - - +
334C ASN* 1.3 62.0 + - - +
336C ALA* 3.1 6.2 + - - +
337C LEU* 3.0 26.0 + - + +
365C SER* 3.2 32.3 - - - -
369C HIS* 2.9 26.1 + - - +
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Residues in contact with ASN 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C LEU 2.9 15.8 + - - +
331C PHE* 3.7 17.3 + - + +
333C GLN* 1.3 76.3 - - - +
335C LEU* 1.3 62.2 + - - +
337C LEU* 3.0 23.1 + - - +
338C ARG* 3.1 47.4 + - - +
369C HIS* 4.0 1.5 - - - -
374C LEU* 3.8 11.7 - - - +
375C SER* 3.2 29.5 + - - -
378C LEU* 3.2 12.3 - - - +
459C PHE* 4.3 13.0 - - + -
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Residues in contact with LEU 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A ALA 5.8 0.7 - - - +
196C TYR* 3.5 27.8 - - + +
197C ALA* 3.6 20.0 - - + -
209C PRO* 3.8 22.4 - - + +
210C ARG 4.0 0.2 - - - -
211C PRO* 4.0 33.9 - - + -
331C PHE 3.0 17.3 + - - +
332C ASP 3.7 4.9 - - - +
333C GLN 3.3 0.2 - - - -
334C ASN* 1.3 80.1 - - - +
336C ALA* 1.3 56.6 + - - +
338C ARG* 3.3 32.1 + - + +
339C TRP* 3.1 25.5 + - - +
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Residues in contact with ALA 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C TYR* 3.7 20.6 - - + -
258C ILE* 3.6 19.4 - - + +
307C LEU* 3.6 24.0 - - + -
332C ASP 3.1 11.8 + - - +
333C GLN 3.1 10.2 + - - +
335C LEU* 1.3 76.7 - - - +
337C LEU* 1.3 57.4 + - - +
339C TRP* 3.4 3.8 + - - +
340C VAL* 3.0 33.3 + - - +
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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
----------------------------------------------------------
274C LEU* 3.7 18.6 - - + -
276C ILE* 5.7 1.3 - - + -
307C LEU* 5.1 2.9 - - + -
333C GLN 3.0 14.0 + - - +
334C ASN* 3.0 8.8 + - - +
336C ALA* 1.3 75.8 - - - +
338C ARG* 1.3 54.2 + - - +
340C VAL* 3.3 5.8 + - - +
341C ARG* 2.8 33.9 + - - +
354C VAL* 5.4 0.7 - - + -
356C LEU* 3.6 33.4 - - + -
369C HIS* 3.8 39.7 - - + +
375C SER* 3.9 15.7 - - - -
378C LEU* 3.8 28.6 - - + +
379C PHE* 4.8 4.0 - - + -
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Residues in contact with ARG 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A ARG* 3.5 34.1 - - - +
373A ALA 5.6 0.6 + - - -
374A LEU* 4.1 38.6 + - - +
378A LEU* 5.6 8.1 - - - -
331C PHE* 5.9 0.4 - - - -
334C ASN* 3.1 39.6 + - - +
335C LEU* 3.6 32.8 - - + +
337C LEU* 1.3 73.4 - - - +
339C TRP* 1.3 65.0 + - - +
341C ARG* 3.5 7.3 + - - +
342C ASP* 3.2 33.3 + - - +
374C LEU* 5.3 4.0 - - - +
378C LEU* 3.7 28.8 - - + +
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Residues in contact with TRP 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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170C THR* 4.1 14.8 - - + -
171C ASP* 4.1 18.0 + - - -
172C LYS* 5.7 4.4 - - + +
194C ILE* 3.5 38.1 - - + +
195C PRO 4.4 5.6 + - - -
196C TYR* 4.0 24.5 - - + +
212C ALA* 6.3 0.7 - - + -
215C TRP* 5.6 2.8 - - - -
258C ILE* 3.8 22.9 - - + -
260C VAL* 4.1 15.3 - - + -
335C LEU 3.1 12.5 + - - +
336C ALA* 3.4 10.8 - - - +
338C ARG* 1.3 77.5 - - - +
340C VAL* 1.3 69.7 + - + +
342C ASP* 3.4 1.0 + - - -
343C ASN* 2.9 61.6 + - + +
344C ILE* 5.2 2.9 - - + -
347C PHE* 3.8 27.8 - + - -
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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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258C ILE* 4.4 2.9 - - + -
272C VAL* 4.6 5.4 - - + -
274C LEU* 3.8 30.3 - - + -
305C VAL* 4.1 17.9 - - + -
307C LEU* 6.3 0.4 - - + -
336C ALA* 3.0 16.5 + - + +
337C LEU* 3.3 7.4 + - + +
339C TRP* 1.3 91.5 - - + +
341C ARG* 1.3 62.9 + - - +
344C ILE* 3.0 46.0 + - + +
354C VAL* 4.1 21.5 - - + -
378C LEU 6.1 0.4 - - - +
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Residues in contact with ARG 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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171A ASP* 5.6 5.5 + - - +
342A ASP* 3.7 29.3 + - - +
337C LEU 2.8 17.6 + - - +
338C ARG* 3.6 11.0 - - - +
339C TRP 3.3 0.2 - - - -
340C VAL* 1.3 77.0 - - - +
342C ASP* 1.3 66.0 + - - +
345C HIS* 5.1 0.5 - - - -
351C PRO* 3.2 56.6 + - - +
352C SER* 6.1 1.1 - - - -
354C VAL* 5.7 0.7 - - - -
377C ASP* 3.4 29.7 + - - +
378C LEU* 4.4 22.8 + - + +
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Residues in contact with ASP 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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341A ARG* 3.9 28.8 + - - +
171C ASP* 4.4 10.3 - - + +
338C ARG* 3.2 19.8 + - - +
339C TRP* 5.1 0.2 - - - -
341C ARG* 1.3 86.3 + - - +
343C ASN* 1.3 73.9 + - - +
344C ILE 3.7 0.2 - - - -
345C HIS* 3.3 19.7 + - - -
346C ARG* 3.1 15.1 + - - +
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Residues in contact with ASN 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C THR* 3.3 13.0 - - - -
171C ASP* 3.1 46.4 + - - +
339C TRP* 2.9 56.0 + - + +
342C ASP* 1.3 91.5 - - - +
344C ILE* 1.3 63.5 + - - +
345C HIS 3.4 2.7 - - - -
346C ARG* 3.2 35.5 + - - +
347C PHE* 3.4 8.2 - - + -
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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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260C VAL* 3.9 16.4 - - + -
272C VAL* 4.0 22.4 - - + -
303C ILE* 3.9 14.1 - - + -
305C VAL* 3.9 26.9 - - + -
339C TRP* 5.2 3.8 - - + -
340C VAL* 3.0 33.7 + - + +
342C ASP 3.7 0.8 - - - -
343C ASN* 1.3 72.7 - - - +
345C HIS* 1.3 59.5 + - - +
346C ARG 3.0 5.6 - - - -
347C PHE* 2.8 26.6 + - + -
348C GLY 3.4 0.2 + - - -
349C GLY* 3.1 17.8 + - - -
350C ASP 4.2 4.9 - - - +
351C PRO* 3.6 31.0 - - + -
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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
------------------------------------------------------------
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