Contacts of the helix formed by residues 260 - 268 (chain L) in PDB entry 6BCH
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 260 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226L LEU* 4.1 10.5 - - - +
227L ASN* 3.0 43.6 - - - +
228L CYS* 4.4 6.5 - - - -
256L ASP* 2.8 30.0 + - - +
258L LYS 3.6 0.6 - - - -
259L GLU* 1.3 96.1 + - + +
261L ILE* 1.3 66.2 + - + +
262L ILE 3.6 1.1 - - - -
263L PRO* 3.5 3.3 - - - +
264L PHE* 3.3 23.6 + - - +
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Residues in contact with ILE 261 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187L PHE* 4.5 0.2 - - + -
207L PHE* 4.1 28.3 - - + -
226L LEU* 4.2 24.2 - - + -
228L CYS* 3.9 20.4 - - - -
251L VAL* 4.3 15.5 - - + -
256L ASP 3.1 11.0 + - - +
257L ILE* 3.8 15.7 - - + +
260L LYS* 1.3 74.2 - - - +
262L ILE* 1.3 62.1 + - - +
264L PHE* 3.2 7.1 + - - +
265L PHE* 2.9 50.8 + - + -
281L TRP* 4.5 17.0 - - + -
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Residues in contact with ILE 262 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257L ILE* 3.1 20.6 + - + +
258L LYS* 4.4 6.7 - - - +
261L ILE* 1.3 75.7 - - - +
263L PRO* 1.3 74.9 - - + +
266L ASN* 2.9 39.3 + - - +
278L TYR* 3.1 15.2 + - - +
281L TRP* 4.2 13.9 - - + -
282L CYS* 3.7 36.8 - - + +
285L VAL* 4.2 24.7 - - + -
286L THR* 6.0 0.4 - - - +
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Residues in contact with PRO 263 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258L LYS 3.5 20.4 - - - +
259L GLU* 4.0 12.8 - - - +
260L LYS 3.5 14.6 - - - +
262L ILE* 1.3 96.7 - - + +
264L PHE* 1.3 61.2 + - - +
266L ASN* 3.2 9.2 + - + +
267L LYS* 3.0 29.8 + - + +
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Residues in contact with PHE 264 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174L SER* 3.8 12.3 - - - -
177L VAL* 3.6 41.1 - - + -
178L ALA 4.8 0.4 - - - -
225L TYR* 3.6 26.5 - + - -
226L LEU* 4.1 15.0 - - + -
260L LYS 3.3 13.6 + - - +
261L ILE* 3.2 11.2 + - - +
262L ILE 3.2 0.6 - - - -
263L PRO* 1.3 79.1 - - - +
265L PHE* 1.3 76.6 + + - +
267L LYS* 3.2 2.4 + - - -
268L ASN* 2.6 71.3 + - + +
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Residues in contact with PHE 265 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177L VAL* 4.5 2.7 - - + -
178L ALA* 4.5 2.2 - - - -
181L THR* 3.1 44.9 - - + -
187L PHE* 4.0 10.8 - + - -
207L PHE* 3.9 21.1 - + - -
226L LEU* 5.4 3.1 - - + -
261L ILE* 2.9 49.1 + - + -
262L ILE 3.8 0.2 - - - -
264L PHE* 1.3 97.5 - + - +
266L ASN* 1.3 63.1 + - - +
267L LYS 3.3 0.2 - - - -
268L ASN 3.1 25.9 - - - +
269L HIS* 3.6 8.7 + - - -
270L ILE* 3.7 20.1 + - + -
278L TYR* 3.2 28.5 - + + +
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Residues in contact with ASN 266 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262L ILE* 2.9 36.1 + - - +
263L PRO* 3.4 9.6 - - + +
265L PHE* 1.3 79.7 - - - +
267L LYS* 1.3 73.8 + - - +
269L HIS* 3.0 22.6 + - - -
278L TYR* 3.5 17.8 + - - -
279L ARG* 4.4 13.4 + - - +
282L CYS* 5.0 0.2 - - - -
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Residues in contact with LYS 267 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175L ASN* 5.2 0.9 - - - +
263L PRO* 3.0 18.9 + - + +
264L PHE* 3.8 3.1 - - - +
266L ASN* 1.3 97.0 + - - +
268L ASN* 1.3 68.9 + - - +
269L HIS* 3.3 16.8 + - - -
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Residues in contact with ASN 268 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174L SER* 2.7 32.6 + - - +
175L ASN* 3.6 12.4 - - - +
178L ALA* 3.9 15.5 - - + +
264L PHE* 2.6 64.8 + - + +
265L PHE* 3.1 26.1 - - - -
267L LYS* 1.3 79.8 - - - +
269L HIS* 1.3 65.8 + - - +
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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