Contacts of the helix formed by residues 258 - 264 (chain C) in PDB entry 4PAR
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 258 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234C TRP* 4.3 16.8 - - + -
248C LYS* 4.4 5.6 - - - +
249C SER* 4.1 13.9 - - - +
254C ILE 3.8 7.6 - - - +
255C THR* 3.1 45.3 + - - +
257C LYS* 1.3 80.7 - - - +
259C LEU* 1.3 62.4 + - - +
260C GLU 3.6 0.4 - - - -
261C GLU* 3.7 13.0 - - + +
262C TRP* 3.2 71.5 + - + +
298C LEU* 3.3 26.5 - - - +
301C GLY* 4.7 3.8 - - - -
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Residues in contact with LEU 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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255C THR 3.7 2.8 + - - +
256C LEU 4.3 8.1 - - - +
257C LYS 3.5 0.2 - - - -
258C LYS* 1.3 85.0 - - - +
260C GLU* 1.3 65.9 + - - +
262C TRP* 3.2 10.2 + - + +
263C LYS* 2.9 57.9 + - + +
296C ALA* 3.7 25.1 - - + +
298C LEU* 3.4 48.5 - - + +
301C GLY 5.9 0.2 - - - -
302C ALA 5.9 0.4 - - - +
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Residues in contact with GLU 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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256C LEU 3.5 10.0 - - - +
257C LYS* 2.8 42.0 - - - +
259C LEU* 1.3 74.3 + - - +
261C GLU* 1.3 59.1 + - + +
263C LYS* 4.3 6.5 - - - +
264C ASN* 2.8 48.5 + - - +
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Residues in contact with GLU 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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257C LYS* 3.9 32.4 + - - +
258C LYS* 3.7 16.0 - - - +
259C LEU 3.2 0.2 - - - -
260C GLU* 1.3 86.9 + - + +
262C TRP* 1.3 63.5 + - + +
264C ASN* 3.6 4.7 - - - +
265C GLY* 3.1 26.3 + - - -
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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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234C TRP* 4.6 4.7 - + - -
247C GLU* 3.3 44.6 - - + -
258C LYS* 3.2 68.5 + - + +
259C LEU* 3.7 13.0 - - + +
260C GLU 3.2 0.2 - - - -
261C GLU* 1.3 86.1 + - + +
263C LYS* 1.3 64.5 + - + +
265C GLY* 3.4 9.6 + - - -
266C PRO 5.1 1.4 - - - +
267C GLN* 3.4 13.3 + - - +
269C ARG* 3.1 29.8 - - - +
293C PHE* 3.8 23.7 - + + +
296C ALA* 5.2 0.2 - - + -
301C GLY 4.7 0.2 - - - -
302C ALA* 3.4 31.6 - - + -
304C TRP* 4.2 8.8 - + - -
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Residues in contact with LYS 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C LEU* 2.9 37.7 + - + +
260C GLU* 3.4 6.2 + - - +
262C TRP* 1.3 76.3 - - - +
264C ASN* 1.3 60.4 + - + +
267C GLN* 2.9 16.6 + - - +
293C PHE* 4.4 19.3 - - + -
296C ALA* 3.7 34.9 + - + +
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Residues in contact with ASN 264 (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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260C GLU* 2.8 36.9 + - - +
261C GLU* 3.6 5.7 - - - +
263C LYS* 1.3 75.7 - - - +
265C GLY* 1.3 68.5 + - - +
267C GLN* 3.8 1.5 + - - +
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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