Contacts of the helix formed by residues 269 - 281 (chain C) in PDB entry 2DB3
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 269 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225C PHE* 4.2 12.0 - - - -
228C TYR* 4.1 14.7 - - - -
267C ILE 3.4 2.1 + - - -
268C PRO* 1.3 75.5 - - - +
270C PRO* 1.3 78.2 - - + +
271C ILE* 3.2 23.6 - - + +
272C GLN* 2.9 27.2 + - - +
273C LYS* 3.0 19.5 + - - +
293C SER* 2.7 33.2 + - - +
583C VAL* 6.0 0.3 - - - +
2903C ANP 4.1 5.1 + - - -
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Residues in contact with PRO 270 (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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228C TYR* 3.5 54.3 - - + +
229C ASN* 5.2 4.5 - - - +
233C VAL* 4.9 7.2 - - + -
268C PRO 4.5 1.1 - - - +
269C THR* 1.3 90.0 - - + +
271C ILE* 1.3 61.6 + - - +
273C LYS* 3.3 14.6 + - + +
274C CYS* 3.3 27.9 + - - -
293C SER* 5.9 0.9 - - - -
455C ILE* 3.7 29.6 - - + -
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Residues in contact with ILE 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C THR* 3.2 17.8 - - + +
270C PRO* 1.3 79.3 - - - +
272C GLN* 1.3 61.0 + - - +
274C CYS* 5.1 0.2 - - - -
275C SER* 2.9 55.3 + - - +
287C ALA* 3.6 15.5 - - + -
288C CYS 4.3 2.2 - - - +
289C ALA* 3.9 22.2 - - + -
293C SER* 3.5 9.9 - - - +
294C GLY 3.7 17.0 - - - +
295C LYS* 4.0 16.6 - - + +
298C ALA* 4.1 1.6 - - + -
431C PHE* 4.3 4.9 - - + -
453C VAL* 3.5 27.1 - - + -
455C ILE* 4.0 12.4 - - + +
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Residues in contact with GLN 272 (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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244C ILE* 4.3 0.2 - - - +
247C PHE* 3.6 7.5 - - - -
265C TYR* 4.8 0.2 - - - -
268C PRO* 3.5 8.4 - - + +
269C THR* 2.9 23.5 + - + +
271C ILE* 1.3 76.4 - - - +
273C LYS* 1.3 63.7 + - - +
276C ILE* 3.0 46.4 + - + +
294C GLY* 3.0 29.8 + - - +
297C ALA* 3.6 14.7 - - - +
298C ALA* 3.8 18.6 - - - +
2903C ANP 2.8 50.7 + - - -
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Residues in contact with LYS 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C ASN* 3.9 22.2 - - - +
243C PRO* 3.2 9.5 - - + +
244C ILE* 3.0 48.1 + - - +
245C GLN* 3.1 41.9 + - - +
267C ILE* 4.6 8.4 - - - +
268C PRO* 3.5 28.3 - - + +
269C THR 3.0 15.0 + - - +
270C PRO* 3.3 15.7 + - + +
272C GLN* 1.3 77.3 - - - +
274C CYS* 1.3 58.0 + - - +
277C PRO* 3.2 12.8 - - - +
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Residues in contact with CYS 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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233C VAL* 3.7 31.0 - - - -
235C VAL* 4.3 11.7 - - + -
241C PRO 5.2 1.0 - - - +
243C PRO* 4.5 19.5 - - + -
270C PRO 3.3 16.4 + - - +
271C ILE 4.3 0.7 - - - +
273C LYS* 1.3 81.7 - - - +
275C SER* 1.3 62.5 + - - +
277C PRO* 3.5 8.3 - - - +
278C VAL* 3.3 22.1 - - - +
453C VAL* 4.1 24.2 - - + -
455C ILE* 4.3 5.4 - - - -
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Residues in contact with SER 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C ILE* 2.9 41.9 + - - +
274C CYS* 1.3 77.0 - - - +
276C ILE* 1.3 65.0 + - - +
278C VAL* 3.1 7.6 + - - +
279C ILE* 3.0 27.6 + - - +
285C LEU* 3.7 24.7 - - - +
287C ALA* 3.9 0.5 - - - +
298C ALA* 4.2 17.9 - - - -
431C PHE* 3.9 4.1 - - - -
453C VAL* 4.7 2.7 - - - +
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Residues in contact with ILE 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C ILE* 4.3 12.6 - - + -
247C PHE* 4.5 9.2 - - + -
250C ALA* 4.1 29.2 - - + +
252C LEU* 4.3 15.3 - - + -
272C GLN* 3.0 40.6 + - + +
275C SER* 1.3 76.8 - - - +
277C PRO* 1.3 68.5 - - + +
279C ILE 3.4 0.3 + - - -
280C SER* 3.1 26.4 + - - +
297C ALA 5.0 0.2 - - - +
298C ALA* 4.0 7.0 - - - +
301C LEU* 4.5 21.8 - - + -
302C PRO* 3.7 27.6 - - + +
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Residues in contact with PRO 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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241C PRO* 4.2 12.6 - - + +
242C GLN 3.3 28.9 - - - +
244C ILE* 4.0 17.3 - - + +
250C ALA 5.9 0.9 - - - +
273C LYS 3.2 20.4 - - - +
274C CYS 3.5 11.0 - - - +
276C ILE* 1.3 97.0 - - + +
278C VAL* 1.3 61.7 + - - +
280C SER* 3.8 7.0 - - - -
281C SER* 2.8 31.2 + - - -
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Residues in contact with VAL 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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240C VAL* 3.9 27.8 - - + -
241C PRO* 4.1 15.0 - - + +
274C CYS 3.3 17.7 - - - +
275C SER* 3.1 11.1 + - - +
277C PRO* 1.3 79.0 - - - +
279C ILE* 1.3 61.7 + - - +
281C SER* 3.5 4.9 + - - -
282C GLY 3.5 0.2 + - - -
283C ARG* 3.2 31.1 + - + +
285C LEU* 3.9 26.2 - - + -
451C VAL* 3.8 27.8 - - + -
453C VAL* 5.4 1.3 - - + -
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Residues in contact with ILE 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C SER 3.0 14.3 + - - +
276C ILE 3.9 3.4 - - - +
278C VAL* 1.3 77.6 - - - +
280C SER* 1.3 58.7 + - - +
282C GLY* 2.9 9.2 + - - -
283C ARG 4.4 1.3 - - - -
285C LEU* 4.5 8.7 - - + -
298C ALA 3.6 24.2 - - - +
299C PHE* 3.9 9.4 - - + -
302C PRO* 3.8 18.6 - - + -
303C ILE* 4.0 5.6 - - + +
306C LYS* 5.2 1.4 - - + +
395C PHE* 3.9 19.3 - - + -
427C GLN* 2.9 27.0 + - - +
429C LEU* 3.6 42.4 - - + -
431C PHE* 4.1 12.3 - - + -
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Residues in contact with SER 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C ALA 4.6 8.5 + - - -
251C ASP* 5.3 9.3 + - - +
252C LEU* 5.2 1.9 - - - +
276C ILE* 3.1 22.8 + - - +
277C PRO* 3.8 8.7 - - - +
279C ILE* 1.3 74.2 - - - +
281C SER* 1.3 58.1 + - - +
282C GLY* 3.0 8.2 + - - -
302C PRO* 3.8 15.5 + - - +
305C SER* 6.1 0.3 - - - -
306C LYS* 3.0 38.7 + - - +
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Residues in contact with SER 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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241C PRO* 3.2 27.7 - - - +
277C PRO* 2.8 20.9 + - - +
278C VAL 3.8 4.7 - - - -
279C ILE 3.2 0.2 - - - -
280C SER* 1.3 75.7 - - - +
282C GLY* 1.3 60.3 + - - +
283C ARG* 3.7 9.9 + - - +
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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
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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