Contacts of the helix formed by residues 256 - 262 (chain C) in PDB entry 1B3K
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 ALA 256 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10C HIS* 3.9 22.8 + - + +
13C SER* 4.0 23.1 - - - -
14C ASP* 2.8 29.0 + - - +
17C VAL* 4.9 2.0 - - - +
255C SER* 1.3 72.2 - - - +
257C GLN* 1.3 63.1 + - - +
259C ILE* 3.8 5.6 + - - +
260C SER* 3.5 18.5 + - - -
363C ARG* 5.5 0.9 + - - -
368C GLY 5.7 3.3 - - - +
370C VAL* 4.7 13.0 - - + -
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Residues in contact with GLN 257 (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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10C HIS* 4.1 21.3 + - + +
14C ASP* 4.5 0.4 + - - -
255C SER* 3.0 4.7 - - - -
256C ALA* 1.3 78.6 - - - +
258C LEU* 1.3 67.1 + - - +
260C SER* 2.8 29.6 + - - -
261C HIS* 3.0 14.0 + - + +
150D HIS* 3.0 58.8 - - + +
152D LEU* 6.0 0.7 - - + -
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Residues in contact with LEU 258 (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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213C PHE* 3.4 17.5 - - + -
250C LEU* 4.2 1.8 - - + -
253C ILE* 3.7 32.3 - - + +
254C LEU* 3.9 14.4 - - + -
255C SER* 3.1 19.4 + - - +
257C GLN* 1.3 78.7 - - - +
259C ILE* 1.3 58.4 + - - +
261C HIS* 2.8 24.0 + - + +
262C TRP* 2.8 44.4 + - + +
150D HIS* 5.2 1.2 - - - -
152D LEU* 3.1 40.2 - - + -
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Residues in contact with ILE 259 (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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17C VAL* 6.2 0.2 - - + -
236C PHE* 4.2 21.7 - - + -
254C LEU* 5.1 5.8 - - + -
255C SER 3.7 13.0 - - - +
256C ALA 4.0 5.8 - - - +
257C GLN 3.1 0.8 + - - -
258C LEU* 1.3 75.1 - - + +
260C SER* 1.3 60.2 + - - +
261C HIS 2.9 0.3 + - - -
262C TRP* 2.9 25.2 + - + +
263C LYS* 2.9 27.5 + - - +
361C VAL* 3.6 28.3 - - + -
363C ARG* 3.5 34.8 - - - +
368C GLY 5.7 0.2 - - - +
370C VAL* 3.9 26.2 - - + -
373C MET* 5.3 2.7 - - + -
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Residues in contact with SER 260 (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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10C HIS* 5.7 2.6 + - - -
256C ALA 3.5 10.9 + - - -
257C GLN* 2.8 27.3 + - - -
259C ILE* 1.3 75.7 - - - +
261C HIS* 1.3 56.2 + - - +
263C LYS* 3.7 10.9 - - - +
264C GLY* 3.1 18.4 + - - -
363C ARG* 3.6 21.4 + - - +
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Residues in contact with HIS 261 (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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213C PHE* 4.4 14.0 - + - -
257C GLN* 3.0 13.4 + - + +
258C LEU* 2.8 17.9 + - + +
260C SER* 1.3 75.8 - - - +
262C TRP* 1.3 62.1 + + - +
264C GLY* 2.8 22.4 + - - +
265C ASN* 3.4 26.3 + - - +
152D LEU* 3.9 35.6 - - + +
281D GLU* 3.6 29.8 + - - -
323D LYS* 5.9 2.0 - - - -
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Residues in contact with TRP 262 (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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211C THR* 4.0 7.1 + - + +
213C PHE* 3.3 40.2 - + + -
223C ILE* 3.5 32.7 - - + +
236C PHE* 4.3 20.2 - + + -
238C ALA* 4.3 5.4 - - + -
250C LEU* 3.6 29.2 - - + -
254C LEU* 3.4 24.2 - - + -
258C LEU* 2.8 42.1 + - + +
259C ILE* 3.6 23.1 - - + +
261C HIS* 1.3 74.5 - + - +
263C LYS* 1.3 57.1 + - - +
264C GLY 2.7 13.1 + - - -
265C ASN* 3.3 7.8 + - - +
266C MET* 2.9 35.4 + - + +
359C LEU* 5.5 1.1 - - + -
361C VAL* 5.3 7.4 - - + -
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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