Contacts of the helix formed by residues 271 - 280 (chain C) in PDB entry 1BI8
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 GLU 271 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270C ASP* 1.3 74.6 - - - +
272C LEU* 1.3 63.9 + - + +
274C LYS* 3.2 14.5 + - + +
275C ASP* 3.1 22.9 + - - +
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Residues in contact with LEU 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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123C LYS* 5.6 3.1 - - - +
270C ASP* 3.1 9.1 + - - +
271C GLU* 1.3 75.6 - - + +
273C GLY* 1.3 63.0 + - - +
275C ASP* 3.5 7.1 - - + +
276C LEU 3.3 4.9 + - - -
297C HIS* 2.7 38.5 + - + +
298C PRO* 2.8 47.3 - - + +
299C TYR* 4.1 11.8 - - + +
301C GLN* 3.9 15.0 - - - +
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Residues in contact with GLY 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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209C PHE* 3.9 7.0 - - - -
269C ILE* 3.2 16.4 - - - -
270C ASP* 2.7 19.4 + - - -
272C LEU* 1.3 68.4 - - - +
274C LYS* 1.3 68.1 + - - +
275C ASP 3.0 1.6 - - - -
276C LEU* 2.8 4.6 + - - +
277C LEU* 2.7 23.9 + - - +
299C TYR* 3.6 18.8 - - - -
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Residues in contact with LYS 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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261C PRO* 4.9 5.0 - - - +
262C ILE* 3.7 33.4 - - + +
263C GLU* 2.8 38.5 + - - +
269C ILE* 3.1 19.3 - - + +
270C ASP 2.8 18.5 + - - +
271C GLU* 3.2 14.8 + - + +
273C GLY* 1.3 73.7 - - - +
275C ASP* 1.3 57.6 + - - +
277C LEU* 3.4 2.3 + - - +
278C LEU* 3.0 49.7 + - + +
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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
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271C GLU 3.1 11.3 + - - +
272C LEU* 3.5 16.3 - - + +
273C GLY 2.9 0.6 + - - -
274C LYS* 1.3 78.3 - - - +
276C LEU* 1.3 51.5 + - - +
278C LEU* 3.4 6.7 + - - +
279C LYS* 2.8 63.7 + - - +
297C HIS* 2.9 18.0 + - + +
298C PRO* 5.7 0.3 - - - +
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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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126C MET* 5.5 1.3 - - + -
130C LEU* 4.8 5.8 - - + -
209C PHE* 4.1 17.7 - - + -
272C LEU 3.3 2.7 + - - +
273C GLY* 2.8 12.4 + - - +
275C ASP* 1.3 72.5 - - - +
277C LEU* 1.3 67.9 + - - +
279C LYS* 2.9 11.4 + - + -
280C CYS* 3.1 24.6 + - - -
289C ILE* 3.7 17.9 - - + -
294C ALA* 3.7 29.8 - - + +
297C HIS* 3.5 26.8 + - + +
299C TYR* 4.3 5.4 - - + -
300C PHE* 3.8 35.2 - - + -
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Residues in contact with LEU 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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206C GLY* 3.2 34.8 - - - +
209C PHE* 4.0 12.0 - - + -
210C ALA* 4.2 6.7 - - + +
262C ILE* 3.8 18.8 - - + -
266C VAL* 3.4 41.5 - - + -
269C ILE* 4.0 13.9 - - + -
273C GLY 2.7 18.8 + - - +
274C LYS 3.5 4.5 - - - +
276C LEU* 1.3 71.1 - - - +
278C LEU* 1.3 59.6 + - + +
280C CYS* 2.8 23.2 + - - +
281C LEU* 2.8 27.4 + - + -
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Residues in contact with LEU 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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234C VAL* 6.2 0.7 - - + -
235C ILE* 5.7 7.2 - - + -
262C ILE* 3.6 34.8 - - + +
274C LYS* 3.0 43.9 + - + +
275C ASP* 3.9 4.9 - - - +
277C LEU* 1.3 76.7 - - + +
279C LYS* 1.3 51.7 + - - +
280C CYS 3.2 0.3 + - - -
281C LEU* 3.5 18.0 + - + +
282C THR* 2.6 36.8 - - + +
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Residues in contact with LYS 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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275C ASP* 2.8 49.6 + - - +
276C LEU* 2.9 8.4 + - - +
278C LEU* 1.3 76.9 - - - +
280C CYS* 1.3 57.7 + - - +
282C THR* 3.8 9.8 + - + +
287C LYS 4.8 0.2 - - - +
288C ARG* 3.6 3.3 - - - +
289C ILE* 2.9 60.9 + - + +
297C HIS* 4.1 13.3 - - + -
298C PRO* 6.0 0.6 - - - +
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Residues in contact with CYS 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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126C MET* 5.8 0.2 - - - -
130C LEU* 6.4 0.2 - - - -
202C LEU* 3.6 27.8 - - - +
203C TRP* 3.8 5.5 - - - -
205C VAL* 3.7 24.5 - - - -
206C GLY* 3.6 14.4 - - - -
209C PHE* 5.3 2.0 - - - -
276C LEU* 3.1 28.2 + - - -
277C LEU* 2.8 7.5 + - - +
279C LYS* 1.3 76.4 - - - +
281C LEU* 1.3 54.2 + - - +
282C THR 2.6 17.9 + - - -
288C ARG* 3.0 25.6 + - - -
289C ILE* 3.9 8.1 - - - -
294C ALA* 5.6 0.9 - - - -
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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