Contacts of the helix formed by residues 273 - 288 (chain C) in PDB entry 2RIB
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 SER 273 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271C PRO 3.6 1.2 - - - -
272C ARG* 1.3 80.0 + - - +
274C ALA* 1.3 60.1 + - - +
275C ALA* 3.5 9.4 + - - +
276C GLU* 3.2 26.1 + - - +
277C ASN* 2.9 28.6 + - - +
314C TYR* 3.7 16.6 - - - -
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Residues in contact with ALA 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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273C SER* 1.3 73.8 - - - +
275C ALA* 1.3 58.0 + - - +
277C ASN* 3.3 1.7 + - - +
278C ALA* 2.9 30.7 + - - +
314C TYR* 3.5 24.3 - - + +
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Residues in contact with ALA 275 (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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240C VAL* 3.9 17.6 - - + +
273C SER* 3.1 10.0 + - - +
274C ALA* 1.3 80.1 - - - +
276C GLU* 1.3 63.1 + - + +
278C ALA* 3.3 5.9 + - - +
279C ALA* 3.1 21.7 + - - +
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Residues in contact with GLU 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C VAL* 4.1 23.9 - - + +
243C LYS* 2.9 44.7 + - - +
245C PHE* 3.4 14.1 - - + -
270C SER 3.5 0.9 - - - +
271C PRO* 3.5 5.8 - - + +
272C ARG* 2.7 38.6 + - - +
273C SER* 3.2 19.8 + - - +
275C ALA* 1.3 76.6 - - - +
277C ASN* 1.3 63.7 + - - +
279C ALA* 3.1 1.6 + - - +
280C LEU* 2.9 19.9 + - - +
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Residues in contact with ASN 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C PRO* 3.6 18.7 - - + +
273C SER 2.9 12.0 + - - +
274C ALA 3.7 2.9 - - - +
275C ALA 3.3 0.2 - - - -
276C GLU* 1.3 76.9 - - - +
278C ALA* 1.3 57.2 + - - +
280C LEU* 3.3 3.6 + - - +
281C GLN* 2.8 31.8 + - - +
314C TYR* 3.5 24.0 + - + +
316C ASN* 3.4 11.5 - - - +
334C ILE* 3.6 8.1 - - - +
338C GLY* 2.9 31.7 + - - -
340C TRP* 2.8 25.5 + - - -
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Residues in contact with ALA 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 ALA 2.9 16.8 + - - +
275C ALA* 3.7 6.7 - - - +
277C ASN* 1.3 76.4 - - - +
279C ALA* 1.3 62.6 + - - +
281C GLN* 3.3 17.0 + - - +
282C GLN* 3.1 26.1 + - - +
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Residues in contact with ALA 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C GLN* 3.4 28.9 - - + +
239C SER 5.2 1.3 - - - +
240C VAL* 3.9 27.6 - - + -
245C PHE* 4.2 5.6 - - + -
275C ALA 3.1 12.0 + - - +
276C GLU 3.1 9.1 + - - +
278C ALA* 1.3 77.0 - - - +
280C LEU* 1.3 63.5 + - - +
282C GLN* 3.2 22.7 + - - +
283C LEU 3.7 0.5 + - - -
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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 PHE* 4.0 17.9 - - + -
269C ALA* 3.8 16.4 - - + -
271C PRO* 4.0 12.8 - - + -
276C GLU 2.9 13.0 + - - +
277C ASN* 3.6 7.0 - - - +
279C ALA* 1.3 76.4 - - - +
281C GLN* 1.3 64.6 + - - +
283C LEU* 3.0 17.8 + - + +
284C VAL* 3.2 13.8 + - + +
291C ALA* 5.4 0.9 - - + -
293C LEU* 3.5 32.5 - - + -
334C ILE* 3.8 22.4 - - + -
352C VAL* 3.4 38.8 - - + -
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Residues in contact with GLN 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C ASN* 2.8 19.3 + - - +
278C ALA* 3.4 16.6 - - - +
280C LEU* 1.3 76.7 - - - +
282C GLN* 1.3 56.8 + - - +
284C VAL* 3.1 9.4 + - - +
285C VAL* 2.8 40.2 + - + +
334C ILE* 4.4 4.7 - - + +
335C PHE 4.5 0.9 - - - +
336C THR 2.9 29.3 + - - +
337C ASN* 3.1 17.3 + - - +
338C GLY* 3.5 22.5 - - - +
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Residues in contact with GLN 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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263A GLN* 4.5 21.6 + - - +
238C GLN* 4.2 22.7 + - - +
278C ALA 3.1 17.8 + - - +
279C ALA* 3.3 13.5 - - - +
280C LEU 3.1 0.4 - - - -
281C GLN* 1.3 76.7 - - - +
283C LEU* 1.3 57.0 + - - +
285C VAL* 3.7 13.3 - - - +
286C ALA* 2.9 29.7 + - - +
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Residues in contact with LEU 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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235C PRO 4.2 6.7 - - - +
236C ASN* 3.5 38.8 - - - +
237C GLY 4.0 2.0 - - - +
238C GLN* 3.6 24.7 - - + +
245C PHE* 3.8 35.9 - - + +
247C THR* 4.2 15.7 - - + +
279C ALA 3.7 0.9 + - - +
280C LEU* 3.0 11.4 + - + +
282C GLN* 1.3 74.6 - - - +
284C VAL* 1.3 67.0 + - + +
286C ALA* 3.3 6.6 + - + +
287C LYS* 3.0 32.3 + - - +
350C LEU* 4.8 1.1 - - - -
352C VAL* 4.2 16.8 - - + -
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Residues in contact with VAL 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C LEU* 3.4 18.4 - - + +
281C GLN* 3.1 10.7 + - - +
283C LEU* 1.3 77.9 - - + +
285C VAL* 1.3 52.2 + - - +
287C LYS 3.6 0.2 - - - -
288C ASN* 2.7 30.1 + - - -
289C GLU 3.2 35.7 + - - +
290C ALA* 3.9 0.2 - - - -
291C ALA* 4.1 15.0 - - + -
334C ILE* 3.8 29.4 - - + +
335C PHE 3.8 28.3 - - - +
336C THR* 3.8 7.1 - - + +
350C LEU* 4.4 4.5 - - + -
352C VAL* 5.4 0.4 - - + -
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Residues in contact with VAL 285 (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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281C GLN* 2.8 25.6 + - + +
282C GLN* 3.7 14.6 - - - +
284C VAL* 1.3 76.8 - - - +
286C ALA* 1.3 64.4 + - - +
288C ASN* 3.1 15.3 + - - +
336C THR* 3.2 39.7 - - - +
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Residues in contact with ALA 286 (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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250A PHE* 6.0 2.6 - - + -
252A LYS* 5.2 8.7 + - - -
260A LEU* 5.9 7.2 - - + -
235C PRO 5.5 3.1 - - - +
282C GLN 2.9 17.4 + - - +
283C LEU* 3.3 11.2 + - + +
285C VAL* 1.3 80.0 - - - +
287C LYS* 1.3 75.1 + - - +
288C ASN* 4.9 0.9 - - - +
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Residues in contact with LYS 287 (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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250A PHE* 3.9 27.9 - - - -
235C PRO* 4.3 13.6 + - - +
236C ASN* 2.9 30.1 + - - -
247C THR* 4.1 14.1 - - + -
249C GLY* 5.3 7.9 - - - +
283C LEU* 3.0 17.8 + - - +
284C VAL 4.2 0.2 - - - +
286C ALA* 1.3 88.3 + - - +
288C ASN* 1.3 71.2 + - - +
289C GLU* 3.2 12.5 + - + +
350C LEU* 4.0 31.2 - - + -
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Residues in contact with ASN 288 (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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284C VAL 2.7 11.7 + - - -
285C VAL 3.1 13.5 + - - +
286C ALA 4.9 0.7 - - - +
287C LYS* 1.3 80.8 - - - +
289C GLU* 1.3 67.1 + - - +
336C THR* 4.1 18.3 - - - +
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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