Contacts of the helix formed by residues 306 - 310 (chain C) in PDB entry 1XSK
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 ASP 306 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274C THR* 4.5 0.7 - - - +
275C THR* 3.2 11.0 + - - +
276C SER 3.4 21.5 - - - +
277C PHE* 3.4 16.4 - - - -
281C TYR* 3.4 6.8 + - - +
304C HIS* 2.6 30.5 + - + +
305C PHE* 1.3 71.4 - - - +
307C CYS* 1.3 61.9 + - - +
308C PHE 3.2 3.9 + - - -
309C TRP* 2.8 31.4 + - - +
345C TRP* 3.6 12.8 - - - -
414C LYS* 3.2 12.5 + - - -
540C HIS* 3.8 7.9 - - - -
803C XYF 2.6 29.4 + - - -
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Residues in contact with CYS 307 (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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277C PHE* 3.4 18.6 - - + -
281C TYR* 3.6 0.2 + - - -
306C ASP* 1.3 78.0 - - - +
308C PHE* 1.3 60.1 + - + +
309C TRP 2.8 8.0 + - - -
310C MET* 3.1 17.7 + - - +
315C TRP* 3.4 42.8 + - + -
345C TRP* 3.3 35.3 - - - +
803C XYF 3.1 31.4 - - - -
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Residues in contact with PHE 308 (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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277C PHE* 3.3 27.1 - + - -
278C THR* 3.9 15.9 - - + -
281C TYR* 3.0 23.8 + - + +
307C CYS* 1.3 71.5 - - + +
309C TRP* 1.3 58.6 + - - +
310C MET 2.9 17.9 + - - +
312C ALA* 4.4 10.5 - - + -
315C TRP* 3.4 33.7 - + - -
321C ASP* 4.4 8.1 - - - +
324C THR* 4.9 2.3 - - - +
325C PHE* 4.0 8.8 - - - -
44D ARG* 3.4 70.5 + - + +
47D GLN* 3.8 16.4 - - + -
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Residues in contact with TRP 309 (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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281C TYR* 4.4 1.5 - - + -
305C PHE* 3.7 22.7 - - + -
306C ASP 2.8 28.0 + - - +
307C CYS 2.8 10.4 + - - -
308C PHE* 1.3 74.0 - - - +
310C MET* 1.3 81.3 + - + +
318C PHE* 3.9 22.0 - + - -
320C TRP* 3.4 68.8 - + + -
321C ASP* 2.9 22.2 + - - +
325C PHE* 3.7 13.9 - - + -
344C VAL* 3.9 14.7 - - + +
345C TRP 2.9 33.3 + - - +
346C ILE* 4.8 3.1 - - + -
405C LEU* 3.9 24.5 - - + -
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Residues in contact with MET 310 (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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307C CYS 3.1 10.1 + - - +
308C PHE* 3.5 15.1 - - - +
309C TRP* 1.3 111.7 - - + +
311C LYS* 1.3 66.6 + - - +
312C ALA 3.5 1.0 + - - -
315C TRP* 3.5 15.9 + - + -
316C CYS* 3.4 33.2 - - - +
317C ASP* 3.8 5.4 - - - +
318C PHE* 3.6 17.5 - - - -
319C GLU 3.2 23.3 - - - +
321C ASP* 4.0 6.0 - - - +
345C TRP* 3.6 38.6 - - + -
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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