Contacts of the helix formed by residues 272 - 283 (chain C) in PDB entry 5C16
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 LYS 272 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270C SER 3.4 4.0 + - - +
271C VAL* 1.3 75.6 - - - +
273C ASP* 1.3 65.3 + - + +
274C ASP* 3.2 44.8 + - + +
275C ASP* 2.8 28.6 + - - +
276C LEU* 2.7 33.2 + - - +
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Residues in contact with ASP 273 (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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247C LYS* 4.0 17.7 + - - -
249C SER* 5.1 3.0 + - - -
251C ILE* 3.5 36.7 + - + +
271C VAL 4.5 0.2 - - - +
272C LYS* 1.3 86.2 - - + +
274C ASP* 1.3 60.0 + - - +
276C LEU* 3.3 14.2 + - - +
277C SER* 2.8 30.5 + - - -
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Residues in contact with ASP 274 (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 LYS* 3.1 27.0 + - + +
273C ASP* 1.3 76.8 - - - +
275C ASP* 1.3 66.5 + - - +
277C SER* 3.4 12.6 + - - -
278C LYS* 3.3 28.4 + - - +
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Residues in contact with ASP 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C VAL* 4.2 11.9 - - + -
272C LYS* 2.8 28.2 + - - +
274C ASP* 1.3 77.8 - - - +
276C LEU* 1.3 63.0 + - - +
278C LYS* 3.1 15.9 + - - +
279C VAL* 3.2 18.3 + - - +
319C GLU* 3.3 34.6 - - + +
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Residues in contact with LEU 276 (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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247C LYS* 6.3 0.4 - - - +
249C SER* 5.0 1.3 - - - +
251C ILE* 3.9 28.0 - - + -
257C PHE* 3.5 18.5 - - + -
265C ILE* 5.0 0.9 - - + -
267C VAL* 4.2 22.9 - - + -
271C VAL* 4.0 14.1 - - + +
272C LYS 2.7 11.5 + - - +
273C ASP* 3.3 15.9 - - - +
275C ASP* 1.3 77.7 - - - +
277C SER* 1.3 60.4 + - - +
279C VAL* 3.4 5.2 + - + +
280C ALA 3.1 17.2 + - - -
288C VAL* 4.2 17.5 - - + -
323C TYR* 3.6 35.9 - - + +
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Residues in contact with SER 277 (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 ILE* 4.7 2.4 - - - +
257C PHE* 4.1 15.7 - - - -
273C ASP 2.8 22.0 + - - -
274C ASP* 3.5 18.6 + - - -
275C ASP 3.2 0.6 - - - -
276C LEU* 1.3 76.3 - - - +
278C LYS* 1.3 63.5 + - - +
280C ALA* 3.3 5.7 - - - +
281C ALA* 3.2 19.1 + - - +
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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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274C ASP* 3.3 17.9 - - - +
275C ASP* 3.1 9.5 + - - +
277C SER* 1.3 76.5 - - - +
279C VAL* 1.3 66.1 + - - +
281C ALA* 3.0 19.0 + - - +
282C PHE* 3.2 12.0 + - - +
317C CYS* 4.3 7.5 - - - -
318C LYS* 5.3 6.5 - - - +
319C GLU* 3.5 40.0 + - + +
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Residues in contact with VAL 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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271C VAL* 5.7 0.2 - - + -
275C ASP 3.2 15.0 + - - +
276C LEU* 3.7 9.0 - - + +
278C LYS* 1.3 75.7 - - - +
280C ALA* 1.3 56.9 + - - +
282C PHE* 2.8 22.1 + - - +
283C ARG* 3.0 18.3 + - + +
288C VAL* 3.8 20.2 - - + -
289C PRO* 4.2 7.4 - - + -
317C CYS* 4.8 0.4 - - - -
319C GLU* 3.9 2.5 - - + -
320C ASP* 3.2 46.9 - - - +
323C TYR* 3.9 26.7 - - + -
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Residues in contact with ALA 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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257C PHE* 3.6 38.8 - - + +
276C LEU 3.1 4.9 + - - -
277C SER* 3.3 11.7 - - - +
278C LYS 3.1 0.2 - - - -
279C VAL* 1.3 77.1 - - - +
281C ALA* 1.3 62.1 + - - +
283C ARG 3.1 20.5 - - - +
286C GLY* 3.3 19.1 + - - +
288C VAL* 3.5 11.8 - - + +
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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 SER 3.2 8.0 + - - +
278C LYS* 3.0 14.4 + - - +
280C ALA* 1.3 78.0 - - - +
282C PHE* 1.3 58.7 + - - +
309C LEU* 3.5 16.5 - - - +
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Residues in contact with PHE 282 (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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278C LYS 3.2 8.9 + - - +
279C VAL* 2.8 10.8 + - - +
281C ALA* 1.3 78.1 - - - +
283C ARG* 1.3 55.2 + - - +
308C PRO* 3.5 16.1 - - + +
309C LEU* 2.7 61.6 + - + -
310C VAL* 4.1 11.4 - - + -
315C LYS* 3.5 28.7 - - + -
316C ARG* 4.2 3.4 - - - -
317C CYS* 3.4 37.5 - - + -
320C ASP* 3.5 20.6 - - - -
364C TYR* 3.6 22.4 - + - -
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Residues in contact with ARG 283 (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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279C VAL* 3.0 24.0 + - + +
280C ALA 3.1 7.5 + - - +
282C PHE* 1.3 80.5 + - - +
284C ALA* 1.3 56.0 + - - +
285C LYS 3.2 1.0 + - - -
286C GLY 2.8 26.2 + - - -
287C ARG 4.0 14.4 - - - +
288C VAL* 4.4 5.8 - - - +
289C PRO* 4.3 9.5 - - - +
305C CYS* 3.7 12.6 - - - -
306C SER* 3.1 32.1 + - - +
307C GLN 3.6 3.8 - - - -
308C PRO* 3.4 19.2 - - - +
309C LEU* 3.9 5.7 - - - +
320C ASP* 2.8 39.2 + - - +
324C LEU* 3.5 19.5 - - - +
359C GLU* 2.8 32.1 + - - +
364C TYR* 4.1 2.6 + - - -
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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