Contacts of the helix formed by residues 334 - 350 (chain C) in PDB entry 5UHE
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 THR 334 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301C PHE* 3.3 10.4 - - - -
313C ARG* 4.2 4.7 - - - +
330C SER* 4.8 4.5 - - - +
332C THR* 3.8 9.9 - - - +
333C LEU* 1.3 81.0 - - - +
335C GLU* 1.3 62.7 + - - +
336C GLU* 3.4 14.3 + - - +
337C ASP* 3.1 39.9 + - - +
338C VAL* 3.2 18.2 + - - +
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Residues in contact with GLU 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C LEU* 4.4 32.1 - - + +
243C TRP* 3.3 36.1 + - + +
301C PHE* 3.6 12.4 - - + -
334C THR* 1.3 73.6 - - - +
336C GLU* 1.3 63.0 + - - +
338C VAL* 3.0 21.8 + - - +
339C VAL* 3.1 19.3 + - - +
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Residues in contact with GLU 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C TRP* 6.5 0.2 - - - -
322C LEU* 4.2 23.5 - - + +
323C HIS* 3.3 36.0 + - - -
334C THR* 3.4 12.3 + - - +
335C GLU* 1.3 80.2 - - - +
337C ASP* 1.3 61.5 + - - +
339C VAL* 4.1 5.0 - - - +
340C ALA* 3.2 24.3 + - + +
357C VAL* 5.1 4.1 - - + +
358C PRO 4.8 8.9 - - - +
359C GLY* 5.6 2.1 - - - +
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Residues in contact with ASP 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C ARG* 2.6 45.1 + - - +
316C VAL* 4.6 3.7 - - + +
320C LEU* 3.8 13.3 - - + +
322C LEU* 3.7 19.9 - - - +
333C LEU* 3.8 18.5 - - + +
334C THR* 3.1 27.8 + - - +
335C GLU 3.2 0.4 - - - -
336C GLU* 1.3 78.9 - - - +
338C VAL* 1.3 56.0 + - - +
340C ALA* 3.5 1.1 + - - -
341C THR* 2.5 37.1 + - - +
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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
----------------------------------------------------------
212C LEU* 5.3 6.7 - - + -
214C PHE* 4.0 25.1 - - + -
237C LEU* 4.8 10.8 - - + -
238C LEU* 5.9 0.4 - - + -
241C LEU* 4.8 15.5 - - + -
301C PHE* 4.1 20.6 - - + -
333C LEU* 4.7 13.2 - - + +
334C THR 3.2 16.4 - - - +
335C GLU* 3.0 9.3 + - - +
337C ASP* 1.3 76.6 - - - +
339C VAL* 1.3 61.4 + - + +
341C THR* 3.3 8.4 + - - -
342C ILE* 3.0 36.8 + - + +
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Residues in contact with VAL 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C LEU* 4.7 11.7 - - + -
241C LEU* 5.3 1.3 - - + -
243C TRP* 4.3 28.7 - - + +
251C ARG* 3.6 31.2 - - + +
252C PHE* 3.6 24.7 - - + -
335C GLU 3.1 16.5 + - - +
336C GLU* 4.1 5.4 - - - +
338C VAL* 1.3 72.3 - - + +
340C ALA* 1.3 59.2 + - - +
341C THR 3.0 4.8 + - - -
342C ILE* 3.1 11.5 + - - +
343C GLU* 3.0 26.2 + - - +
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Residues in contact with ALA 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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251C ARG* 4.6 2.9 - - - +
320C LEU* 3.4 31.2 - - + +
322C LEU* 4.1 8.3 - - + -
336C GLU 3.2 18.0 + - - +
339C VAL* 1.3 77.9 - - - +
341C THR* 1.3 60.1 + - - +
343C GLU* 3.8 13.7 - - - +
344C TYR* 3.2 15.8 + - - +
355C MET* 4.8 2.8 - - - +
357C VAL* 3.9 26.2 - - + -
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Residues in contact with THR 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C VAL* 4.1 15.9 - - + +
187C PHE* 4.2 1.8 - - + -
202C VAL* 4.0 26.7 - - + -
204C VAL* 4.6 8.6 - - + +
214C PHE* 4.2 19.7 - - + -
320C LEU* 4.0 12.2 - - - +
337C ASP* 2.5 22.0 + - - +
338C VAL* 3.3 11.9 - - - -
339C VAL 3.0 0.2 - - - -
340C ALA* 1.3 76.4 - - - +
342C ILE* 1.3 65.6 + - - +
344C TYR* 3.0 16.6 + - - +
345C LEU* 3.0 12.6 + - - +
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Residues in contact with ILE 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C PHE* 4.5 19.3 - - + -
222C VAL* 4.9 8.1 - - + -
234C VAL* 4.3 29.2 - - + -
237C LEU* 6.1 1.1 - - + -
238C LEU* 4.4 20.0 - - + -
252C PHE* 4.0 19.5 - - + -
258C MET* 4.8 15.3 - - + -
338C VAL* 3.0 27.8 - - + +
339C VAL* 3.1 13.9 + - - +
341C THR* 1.3 75.0 - - - +
343C GLU* 1.3 61.6 + - - +
345C LEU* 3.2 12.3 + - + +
346C VAL* 3.1 25.6 + - + +
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Residues in contact with GLU 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C ARG* 2.5 43.7 + - - +
252C PHE* 4.0 10.4 - - + -
254C PHE* 4.7 6.3 - - + -
339C VAL 3.0 14.6 + - - +
340C ALA* 3.8 9.0 - - - +
341C THR 3.2 0.2 - - - -
342C ILE* 1.3 76.4 - - - +
344C TYR* 1.3 61.2 - - - +
346C VAL* 3.2 20.7 - - - +
347C ARG* 3.2 55.0 + - + +
355C MET* 3.7 19.4 - - - +
356C THR 4.2 7.3 - - - +
357C VAL* 4.6 1.6 - - - +
358C PRO* 4.0 6.6 - - - +
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Residues in contact with TYR 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C PHE* 3.3 29.2 - + + -
319C LYS* 2.6 53.6 + - - +
320C LEU* 3.7 14.1 - - + -
340C ALA 3.2 9.0 + - - +
341C THR 3.0 11.7 + - - +
343C GLU* 1.3 77.8 - - - +
345C LEU* 1.3 62.1 + - - +
347C ARG* 5.1 1.6 - - - -
348C LEU* 3.3 21.4 + - + +
355C MET* 3.5 27.1 - - + -
363C VAL* 4.3 2.5 - - + -
364C PRO 2.4 29.0 + - - -
365C VAL* 3.1 33.5 - - + +
366C GLU 4.0 5.6 - - - -
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Residues in contact with LEU 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C PHE* 4.2 7.4 - - + -
200C HIS* 3.2 35.7 - - + +
201C SER 4.4 0.2 - - - +
202C VAL* 3.6 22.7 - - + -
214C PHE* 3.6 37.7 - - + +
216C VAL* 3.6 24.2 - - + -
222C VAL* 4.1 13.9 - - + -
341C THR 3.0 8.6 + - - +
342C ILE* 3.2 12.5 + - + +
344C TYR* 1.3 76.1 - - - +
346C VAL* 1.3 66.2 + - + +
348C LEU* 3.9 3.8 - - + +
349C HIS* 3.1 19.4 + - - +
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Residues in contact with VAL 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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216C VAL* 5.9 0.2 - - - -
222C VAL* 5.9 0.9 - - + -
252C PHE* 4.7 8.7 - - + -
254C PHE* 4.1 15.7 - - + -
255C SER* 3.5 35.4 - - - +
257C ILE* 3.7 22.2 - - + -
258C MET* 4.4 7.0 - - + -
342C ILE* 3.1 16.8 + - + +
343C GLU* 3.2 15.7 - - - +
345C LEU* 1.3 77.4 - - + +
347C ARG* 1.3 63.3 + - - +
349C HIS* 2.9 22.0 + - - +
350C GLU* 3.1 18.0 + - - +
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Residues in contact with ARG 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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251C ARG 5.1 0.4 + - - -
254C PHE* 3.4 37.9 - - + -
343C GLU* 3.2 45.0 + - - +
344C TYR* 4.5 2.9 - - - +
346C VAL* 1.3 76.6 - - - +
348C LEU* 1.3 61.2 + - - +
349C HIS 3.3 0.3 + - - -
350C GLU* 3.4 10.6 + - - +
351C GLY 3.3 4.0 + - - -
352C GLN* 2.8 76.7 + - + +
354C THR 4.5 1.1 - - - +
355C MET* 3.7 27.9 - - + +
356C THR 5.8 0.2 + - - -
365C VAL* 5.1 5.4 - - + -
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Residues in contact with LEU 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C PHE* 4.3 14.8 - - + -
200C HIS* 3.2 39.8 + - + +
344C TYR* 3.3 21.2 + - + +
345C LEU* 3.9 4.0 - - + +
346C VAL 3.3 0.2 - - - -
347C ARG* 1.3 79.7 - - - +
349C HIS* 1.3 59.8 + - - +
351C GLY* 3.6 9.2 + - - -
352C GLN 4.0 10.1 - - - +
365C VAL* 3.5 33.1 - - + +
366C GLU* 3.4 35.9 - - - +
367C THR* 3.7 8.5 - - + +
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Residues in contact with HIS 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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197C LYS* 5.9 2.6 - - - +
198C THR* 3.8 29.2 + - - -
199C LEU* 4.9 1.4 - - - +
200C HIS* 4.0 22.0 + + + -
216C VAL* 3.4 38.0 - - + +
217C ASP 4.8 2.4 + - - -
220C ASP* 4.9 9.4 + - - -
257C ILE* 4.0 33.6 - - + +
345C LEU 3.1 15.0 + - - +
346C VAL* 2.9 15.8 + - - +
348C LEU* 1.3 79.6 - - - +
350C GLU* 1.3 58.4 + - - +
351C GLY 3.3 3.0 + - - -
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Residues in contact with GLU 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C PHE* 3.2 22.4 - - - +
255C SER* 3.2 28.8 - - - -
256C GLU 4.8 0.7 + - - -
257C ILE* 5.1 2.4 - - + +
346C VAL* 3.1 14.8 + - - +
347C ARG* 3.5 8.4 - - - +
349C HIS* 1.3 80.5 - - - +
351C GLY* 1.3 59.0 + - - +
352C GLN* 3.0 29.9 + - + +
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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