Contacts of the helix formed by residues 272 - 281 (chain C) in PDB entry 3VBB
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 272 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225C THR* 3.8 9.1 + - - -
269C ILE* 3.7 12.9 - - - +
270C ALA 3.6 4.9 - - - +
271C THR* 1.3 79.3 + - - +
273C GLU* 1.3 58.7 + - - +
274C GLN 3.3 2.2 - - - +
275C PRO* 3.3 23.3 - - - +
276C ILE* 3.3 22.5 - - - +
296C GLY* 4.7 6.6 - - - -
298C SER* 2.8 39.6 + - - -
300C CYS* 4.4 0.2 - - - -
325C GLU* 3.5 15.2 - - - +
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Residues in contact with GLU 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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237C VAL* 4.9 5.2 - - - +
239C GLN* 4.4 10.8 + - - +
242C GLN* 5.2 1.4 - - - +
271C THR* 2.8 22.6 + - - -
272C SER* 1.3 78.6 + - - +
274C GLN* 1.3 72.9 + - - +
276C ILE* 4.2 4.7 - - - +
277C ALA* 3.1 30.9 + - - +
325C GLU* 4.3 7.6 - - - +
327C PHE* 3.3 39.3 - - + -
402C GLN* 3.2 30.4 + - - +
425C MET* 4.4 1.4 - - - +
427C ASN* 4.0 19.1 + - + -
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Residues in contact with GLN 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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229C MET* 3.5 13.6 - - - +
234C MET* 3.5 40.8 - - + +
237C VAL* 3.3 31.2 - - + +
238C ALA* 4.4 9.5 - - - +
242C GLN* 3.2 37.6 + - - +
247C LEU* 4.0 2.1 - - - +
269C ILE* 3.9 1.4 - - - +
270C ALA* 3.1 28.2 + - - +
271C THR* 3.8 16.6 + - - +
273C GLU* 1.3 86.0 + - - +
275C PRO* 1.3 67.9 - - + +
278C ALA 3.6 6.8 + - - -
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Residues in contact with PRO 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C THR* 3.0 37.7 - - + -
226C PRO* 3.7 2.9 - - + +
228C PHE 4.7 0.7 - - - +
229C MET* 3.5 13.5 - - - -
269C ILE* 3.2 25.4 - - + -
272C SER* 3.3 17.5 - - - +
274C GLN* 1.3 93.7 - - + +
276C ILE* 1.3 62.4 + - - +
278C ALA* 3.3 6.9 + - - +
279C LEU 3.2 13.5 + - - -
188D VAL* 4.0 8.6 - - + +
195D PHE* 3.6 18.4 - - + -
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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
----------------------------------------------------------
223C ILE* 3.6 29.4 - - + -
225C THR* 4.4 9.4 - - - +
272C SER* 3.3 18.8 + - - +
273C GLU* 3.5 5.9 + - - +
274C GLN 3.5 0.6 - - - -
275C PRO* 1.3 71.3 - - - +
277C ALA* 1.3 59.3 + - - +
279C LEU* 2.6 39.0 + - + +
294C TYR* 3.7 36.6 - - + -
296C GLY* 4.2 14.4 - - - +
325C GLU* 6.1 1.6 - - + -
327C PHE* 3.8 28.3 - - + -
329C TYR* 3.1 6.2 + - - +
195D PHE* 4.6 7.0 - - + -
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Residues in contact with ALA 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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237C VAL* 3.4 22.0 - - + -
273C GLU* 3.1 24.2 + - - +
276C ILE* 1.3 77.7 - - - +
278C ALA* 1.3 58.5 + - - +
279C LEU 2.9 5.5 + - - -
280C HIS 3.4 9.4 + - - -
281C ARG 3.5 7.1 + - - -
327C PHE* 4.7 4.4 - - + -
329C TYR* 3.7 11.7 + - - -
402C GLN* 5.6 0.7 - - - +
406C LEU* 3.6 24.4 - - + +
408C ILE* 4.3 1.6 - - - +
425C MET* 4.4 12.3 - - + -
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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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233C VAL* 3.8 22.0 - - + -
237C VAL* 4.2 8.7 - - + +
274C GLN 3.6 9.6 + - - +
275C PRO 3.3 10.6 + - - +
276C ILE 3.2 0.6 - - - -
277C ALA* 1.3 76.9 - - - +
279C LEU* 1.3 62.9 + - - +
280C HIS 3.5 0.2 - - - -
281C ARG* 3.8 22.7 + - - +
406C LEU* 4.5 1.1 - - - +
184D LYS* 3.8 18.0 - - - +
188D VAL* 3.6 23.6 - - + +
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Residues in contact with LEU 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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223C ILE* 4.7 13.2 - - + -
275C PRO 3.2 5.1 + - - +
276C ILE* 2.6 27.6 + - + +
277C ALA 2.9 0.2 + - - -
278C ALA* 1.3 81.2 - - - +
280C HIS* 1.3 65.0 + - + +
281C ARG 3.3 0.4 + - - -
283C GLU* 3.6 11.1 - - - +
294C TYR* 3.4 44.4 - - + +
181D GLU* 3.9 24.7 - - + +
184D LYS* 3.6 16.4 + - + +
195D PHE* 3.7 31.4 - - + -
197D LYS* 6.1 1.8 - - + +
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Residues in contact with HIS 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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276C ILE 3.8 0.4 + - - -
277C ALA 3.4 3.8 + - - -
279C LEU* 1.3 86.2 - - + +
281C ARG* 1.3 65.6 + - - +
282C ASP 3.2 2.3 + - - -
283C GLU* 3.0 40.9 + - - +
285C LEU* 4.3 11.4 - - + +
292C ILE* 4.5 18.2 - - + +
294C TYR* 2.6 45.3 + + - -
329C TYR* 3.9 33.0 - + + +
408C ILE* 3.6 17.1 - - + +
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Residues in contact with ARG 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C VAL* 3.5 33.2 - - - +
236C GLU* 3.0 39.8 + - - -
237C VAL* 5.5 0.8 - - - +
277C ALA 3.5 5.7 + - - +
278C ALA* 3.8 28.3 + - - +
279C LEU 3.3 2.6 + - - -
280C HIS* 1.3 76.8 - - - +
282C ASP* 1.3 85.8 + - + +
283C GLU* 3.9 1.4 - - - +
406C LEU* 3.7 29.0 - - + +
407C ARG* 4.7 3.3 - - - +
408C ILE* 4.0 5.1 - - - +
184D LYS* 2.9 33.1 + - - +
187D VAL* 3.9 22.8 - - - +
188D VAL* 5.9 0.2 - - - +
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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