Contacts of the helix formed by residues 306 - 310 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B THR* 4.3 0.2 - - + -
275B THR* 3.1 12.0 + - - +
276B SER 3.3 21.8 - - - +
277B PHE* 3.4 18.9 - - - -
281B TYR* 3.4 7.1 + - - +
304B HIS* 2.8 27.2 + - + +
305B PHE* 1.3 72.9 - - - +
307B CYS* 1.3 69.4 + - - +
308B PHE 2.9 5.3 + - - -
309B TRP* 3.1 16.6 + - - +
345B TRP* 3.4 11.5 - - - -
414B LYS* 3.2 15.8 + - - -
540B HIS* 3.7 6.5 - - - -
802B XYF 2.6 27.0 + - - -
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Residues in contact with CYS 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B PHE* 3.4 19.1 - - + -
281B TYR* 4.7 0.2 - - - +
306B ASP* 1.3 73.2 - - - +
308B PHE* 1.3 55.1 + - + +
309B TRP* 2.6 17.5 + - - -
310B MET* 3.0 15.4 + - - +
315B TRP* 3.2 34.9 + - + -
345B TRP* 3.5 35.3 - - - +
380B TRP* 4.0 7.6 - - - -
802B XYF 3.2 31.4 - - - -
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Residues in contact with PHE 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B PHE* 3.4 26.0 - + - -
278B THR* 3.9 11.0 - - + -
281B TYR* 3.3 12.8 + - + +
306B ASP 2.9 4.8 + - - -
307B CYS* 1.3 72.6 - - + +
309B TRP* 1.3 57.4 + - - +
310B MET 2.9 19.1 + - - +
312B ALA* 4.0 11.9 - - + -
315B TRP* 3.7 31.4 - + - -
321B ASP* 4.7 5.5 - - - +
324B THR* 4.7 5.5 + - - +
325B PHE* 4.0 8.8 - - - -
44F ARG* 3.4 78.6 + - + +
47F GLN* 3.7 22.2 - - + -
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Residues in contact with TRP 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B TYR* 4.6 1.1 - - + -
305B PHE* 3.6 26.2 - - + -
306B ASP 3.1 25.7 + - - +
307B CYS 2.6 11.5 + - - -
308B PHE* 1.3 74.8 - - - +
310B MET* 1.3 87.2 + - + +
318B PHE* 3.9 22.2 - + - -
320B TRP* 3.3 63.2 - + + -
321B ASP 3.0 21.1 + - - -
325B PHE* 3.6 14.0 - - + -
344B VAL* 4.2 7.2 - - + -
345B TRP* 2.9 34.3 + - + +
346B ILE* 4.7 2.9 - - + -
405B LEU* 3.7 29.6 - - + -
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Residues in contact with MET 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B CYS 3.0 5.6 + - - +
308B PHE* 3.4 21.6 - - - +
309B TRP* 1.3 113.1 - - + +
311B LYS* 1.3 67.5 + - - +
312B ALA 3.6 1.9 + - - -
315B TRP* 3.6 14.6 + - + -
316B CYS* 3.3 43.5 - - - +
317B ASP* 3.7 4.5 - - - +
318B PHE* 3.4 20.2 - - - -
319B GLU 3.4 19.7 - - - +
321B ASP* 4.3 4.8 - - - +
345B TRP* 3.6 31.4 - - + -
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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