Contacts of the helix formed by residues 267 - 281 (chain C) in PDB entry 6UZA
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 PHE 267 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336B CYS 3.7 20.0 - - - -
337B ARG 3.3 20.6 - - - -
338B ASN 3.5 15.5 - - - +
339B THR* 4.5 7.0 - - - -
342B VAL* 4.1 10.3 - - + -
382B ASN* 3.3 36.3 - - - -
385B GLN* 4.1 32.1 - - + -
265C ASP* 3.3 11.8 + - - +
266C SER* 1.3 76.7 + - - +
268C SER* 1.3 60.1 + - - +
269C HIS 3.2 1.5 + - - -
270C SER* 3.3 6.3 + - - -
271C ARG* 3.0 41.2 + - + +
314C PHE* 5.4 11.1 - + - -
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Residues in contact with SER 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B ARG 3.8 17.3 - - - -
338B ASN* 4.6 7.6 - - - -
218C HIS* 4.3 23.1 + - - -
265C ASP* 3.4 27.2 + - - +
267C PHE* 1.3 77.8 - - - +
269C HIS* 1.3 61.8 + - - +
271C ARG* 3.8 7.9 - - - +
272C SER* 2.9 30.0 + - - -
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Residues in contact with HIS 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C CYS* 4.3 17.5 + - + +
261C LYS* 3.8 39.7 - - + +
262C GLN* 4.5 20.4 + - + -
265C ASP 3.5 16.7 + - - +
266C SER* 4.4 7.2 - - - -
267C PHE 3.2 0.8 - - - -
268C SER* 1.3 77.0 + - - +
270C SER* 1.3 63.8 + - - +
272C SER* 2.6 24.4 + - - -
273C ARG* 3.0 35.5 + - + +
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Residues in contact with SER 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C TYR* 5.9 1.2 - - - -
266C SER 3.3 14.5 + - - -
267C PHE* 3.3 8.7 + - - -
269C HIS* 1.3 78.5 - - - +
271C ARG* 1.3 59.7 + - - +
273C ARG* 3.4 10.5 + - - +
274C ILE* 3.0 29.9 + - - +
311C GLU* 4.1 14.4 + - - -
314C PHE* 3.8 30.1 - - - -
318C TYR* 5.2 0.2 + - - -
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Residues in contact with ARG 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B ASP* 4.0 14.5 + - - -
335B LEU 5.5 0.8 + - - -
336B CYS 3.0 26.6 + - - -
337B ARG* 4.1 38.3 - - - +
382B ASN* 5.2 3.0 + - - +
217C SER* 4.9 7.3 + - - +
219C ASP* 5.5 0.2 - - - +
267C PHE* 3.0 31.2 + - + +
268C SER* 3.8 7.2 - - - +
269C HIS 3.3 0.2 - - - -
270C SER* 1.3 78.3 - - - +
272C SER* 1.3 56.0 + - - +
274C ILE* 3.3 10.5 - - + +
275C ASN* 2.9 48.8 + - - +
314C PHE* 4.9 7.5 - - + -
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Residues in contact with SER 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C HIS* 5.6 5.2 - - - -
219C ASP* 3.2 33.5 - - - +
261C LYS* 5.9 1.2 - - - +
268C SER 2.9 16.8 + - - -
269C HIS* 2.6 30.3 + - - -
271C ARG* 1.3 73.2 - - - +
273C ARG* 1.3 60.3 + - - +
275C ASN* 3.3 1.7 + - - +
276C ALA* 3.0 29.5 + - - +
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Residues in contact with ARG 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C PRO* 4.2 15.7 - - + +
249C HIS* 3.1 33.9 + - - +
250C ASP* 3.3 17.0 + - - +
251C TYR* 3.9 19.3 - - - +
269C HIS* 3.0 36.7 + - + +
270C SER* 3.7 8.1 - - - +
272C SER* 1.3 77.5 + - - +
274C ILE* 1.3 56.9 + - - +
276C ALA* 3.4 3.0 + - - +
277C TYR* 3.0 41.7 + - + -
307C LEU* 3.7 22.0 - - - +
311C GLU* 3.7 19.0 + - - -
318C TYR* 3.4 22.9 - - - +
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Residues in contact with ILE 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C SER 3.0 15.5 + - - +
271C ARG* 3.3 18.2 - - + +
273C ARG* 1.3 76.2 - - - +
275C ASN* 1.3 69.6 + - - +
277C TYR* 3.8 2.4 - - - +
278C LYS* 2.9 39.8 + - - +
314C PHE* 3.7 36.6 - - + +
317C ASP* 3.7 31.6 - - + +
318C TYR* 4.1 24.9 - - + +
321C LEU* 4.6 8.3 - - + -
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Residues in contact with ASN 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C SER* 3.3 19.0 + - - -
219C ASP* 2.9 30.4 + - - +
220C VAL* 4.2 5.5 - - + +
224C ILE* 3.8 8.6 - - + +
228C HIS* 3.0 23.4 + - + -
271C ARG* 2.9 29.2 + - - +
272C SER 3.8 0.4 - - - +
274C ILE* 1.3 78.7 - - - +
276C ALA* 1.3 61.0 + - - +
278C LYS* 3.8 22.0 + - - -
279C GLY 3.0 22.9 + - - -
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Residues in contact with ALA 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C ILE* 4.5 16.5 - - + +
245C ILE* 4.0 6.3 - - + +
246C GLU 4.4 10.1 - - - +
248C PRO* 3.7 25.6 - - + -
272C SER 3.0 17.2 + - - +
273C ARG* 3.8 0.4 - - - +
274C ILE 3.4 0.2 - - - -
275C ASN* 1.3 76.8 - - - +
277C TYR* 1.3 57.5 + - - +
279C GLY* 3.3 1.4 + - - -
280C LEU* 2.9 33.9 + - - +
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Residues in contact with TYR 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C ARG* 4.4 5.4 - - - +
248C PRO* 3.9 29.8 + - + +
249C HIS 4.7 1.9 + - - -
273C ARG* 3.0 41.2 + - + +
274C ILE 4.0 3.8 - - - +
276C ALA* 1.3 73.5 - - - +
278C LYS* 1.3 59.6 + - - +
280C LEU* 3.8 11.5 - - + +
281C ALA* 2.9 33.6 + - - +
300C LEU* 4.3 14.4 - - + -
303C GLU* 2.6 36.7 + - + +
304C LEU* 3.8 26.2 - - + -
307C LEU* 3.7 27.2 - - + +
318C TYR* 4.1 15.9 - + + -
321C LEU* 4.1 7.2 - - + -
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Residues in contact with LYS 278 (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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227C ALA 4.9 0.2 - - - +
228C HIS* 3.6 31.7 - - + +
274C ILE* 2.9 31.0 + - - +
275C ASN* 3.6 16.9 + - - +
276C ALA 3.3 0.2 - - - -
277C TYR* 1.3 76.1 - - - +
279C GLY* 1.3 59.4 + - - +
281C ALA 3.9 6.3 + - - -
282C SER* 4.1 12.6 + - - -
317C ASP* 6.3 3.1 - - - -
321C LEU* 3.9 26.8 - - + +
324C GLN* 4.6 4.2 + - - +
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Residues in contact with GLY 279 (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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224C ILE* 4.6 2.2 - - - -
227C ALA* 3.6 9.0 - - - +
228C HIS* 3.3 17.0 + - - -
245C ILE* 3.5 26.2 - - - +
275C ASN 3.0 12.9 + - - -
276C ALA 3.3 2.9 + - - -
277C TYR 3.2 0.2 - - - -
278C LYS* 1.3 76.3 - - - +
280C LEU* 1.3 62.2 + - - +
282C SER* 3.5 16.1 + - - -
285C TYR* 3.8 4.2 - - - +
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Residues in contact with LEU 280 (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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245C ILE* 3.9 22.9 - - + +
247C ARG* 3.9 52.9 - - + +
248C PRO* 4.1 10.3 - - + -
276C ALA 2.9 18.9 + - - +
277C TYR* 3.3 15.7 + - + +
279C GLY* 1.3 76.1 - - - +
281C ALA* 1.3 56.6 + - - +
282C SER 3.3 4.6 + - - -
285C TYR* 3.7 33.6 - - + -
286C LEU* 3.8 13.9 - - - +
300C LEU* 3.4 18.7 - - + +
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Residues in contact with ALA 281 (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 TYR 2.9 17.7 + - - +
278C LYS 4.3 0.9 - - - -
279C GLY 3.3 1.2 - - - -
280C LEU* 1.3 75.4 - - - +
282C SER* 1.3 53.2 + - - +
283C PRO* 4.4 0.3 - - - +
286C LEU* 4.5 5.7 - - - +
300C LEU* 3.8 8.7 - - + -
304C LEU* 4.0 15.5 - - + -
321C LEU* 4.2 9.9 - - + +
324C GLN* 2.4 41.2 + - - +
325C CYS* 3.6 22.7 + - - -
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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