Contacts of the helix formed by residues 306 - 310 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274F THR* 4.3 0.4 - - + -
275F THR* 3.2 11.3 + - - +
276F SER 3.3 21.8 - - - +
277F PHE* 3.5 25.2 - - - -
281F TYR* 3.3 8.1 + - - +
304F HIS* 2.6 29.1 + - + +
305F PHE* 1.3 71.3 - - - +
307F CYS* 1.3 70.3 + - - +
308F PHE 3.1 2.1 + - - -
309F TRP* 3.0 21.0 + - - +
345F TRP* 3.4 14.8 - - - -
414F LYS* 3.0 14.9 + - - -
515F PHE* 5.1 0.5 - - - -
540F HIS* 3.4 24.9 + - - -
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Residues in contact with CYS 307 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277F PHE* 3.4 33.7 - - + -
281F TYR* 3.8 0.2 + - - -
306F ASP* 1.3 76.2 - - - +
308F PHE* 1.3 61.4 + - + +
309F TRP* 2.7 11.4 + - - -
310F MET* 3.1 14.6 + - - +
315F TRP* 3.4 37.5 + - + -
345F TRP* 3.3 50.4 - - + +
380F TRP* 4.1 7.0 - - - -
416F ASP* 5.3 0.7 - - - -
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Residues in contact with PHE 308 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ARG* 3.3 72.7 + - + +
47A GLN* 3.9 16.4 - - + -
277F PHE* 3.4 25.6 - + - -
278F THR* 4.0 15.3 - - + -
281F TYR* 3.0 27.2 + - + +
306F ASP 4.0 0.2 - - - -
307F CYS* 1.3 71.9 - - + +
309F TRP* 1.3 57.8 + - - +
310F MET 2.9 18.1 + - - +
312F ALA* 4.5 9.0 - - + -
315F TRP* 3.6 34.1 - + - +
321F ASP* 4.5 6.6 - - - +
324F THR* 5.3 2.9 + - - +
325F PHE* 4.0 9.0 - - - -
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Residues in contact with TRP 309 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281F TYR* 4.4 1.1 - - + -
305F PHE* 3.6 22.0 - - + -
306F ASP 3.0 27.5 + - - +
307F CYS 2.7 11.0 + - - -
308F PHE* 1.3 75.7 - - - +
310F MET* 1.3 82.5 + - + +
318F PHE* 3.9 22.7 - + - -
320F TRP* 3.3 80.2 - + + -
321F ASP* 2.9 23.0 + - - +
325F PHE* 3.7 14.7 - - + -
344F VAL* 3.9 7.4 - - + +
345F TRP* 2.9 32.1 + - + +
346F ILE* 4.7 2.9 - - + -
405F LEU* 3.7 31.4 - - + -
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Residues in contact with MET 310 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307F CYS 3.1 7.2 + - - +
308F PHE* 2.9 18.4 - - - +
309F TRP* 1.3 113.0 - - + +
311F LYS* 1.3 65.1 + - - +
312F ALA 3.7 0.9 + - - -
315F TRP* 3.6 17.7 + - + -
316F CYS* 3.3 33.2 - - - +
317F ASP* 3.7 6.3 - - - +
318F PHE* 3.6 16.4 - - - -
319F GLU 3.4 23.8 - - - +
321F ASP* 4.2 5.3 - - - +
345F TRP* 3.5 41.1 - - + +
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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