Contacts of the helix formed by residues 306 - 310 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274D THR* 4.1 2.4 - - + +
275D THR* 5.7 2.0 - - + +
276D SER 4.0 16.5 - - - +
277D PHE* 5.0 10.0 - - - +
281D TYR* 3.9 12.9 + - - +
304D HIS* 2.4 37.6 + - + +
305D PHE* 1.3 77.5 - - - +
307D CYS* 1.3 70.6 + - + +
308D PHE 2.9 4.6 + - - -
309D TRP* 3.2 14.9 + - - +
345D TRP* 3.1 25.4 - - - -
414D LYS* 3.9 5.6 - - - +
515D PHE* 5.2 4.5 - - - -
538D ARG* 4.5 3.5 + - - -
540D HIS* 3.4 25.5 + - - -
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Residues in contact with CYS 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277D PHE* 3.4 39.0 - - + -
306D ASP* 1.3 76.4 + - - +
308D PHE* 1.3 63.3 + - + +
309D TRP* 3.2 6.3 + - - -
310D MET* 3.6 10.7 + - - +
315D TRP* 3.2 55.6 + - - -
345D TRP* 3.7 21.3 - - + +
380D TRP* 3.9 17.5 - - - -
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Residues in contact with PHE 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277D PHE* 2.9 38.4 - + - -
278D THR* 4.4 1.8 - - - -
279D THR 4.8 2.7 - - - -
281D TYR* 3.7 20.1 + - + +
306D ASP 2.9 6.6 + - - -
307D CYS* 1.3 80.5 - - + +
309D TRP* 1.3 57.4 + - - -
310D MET 3.0 17.6 + - - +
312D ALA* 4.5 5.8 - - + -
315D TRP* 3.3 35.4 - + - -
321D ASP* 4.7 4.9 - - - +
324D THR* 5.2 1.9 - - - +
325D PHE* 3.9 11.2 - - - -
44E ARG* 3.4 76.7 + - + +
47E GLN* 4.4 7.0 - - - -
48E LEU* 4.6 1.3 - - + -
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Residues in contact with TRP 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281D TYR* 4.6 0.8 + - - +
305D PHE* 3.8 23.8 - - + -
306D ASP 3.2 26.2 + - - +
307D CYS 3.2 4.1 + - - -
308D PHE* 1.3 77.0 - - - +
310D MET* 1.3 89.0 + - + +
318D PHE* 3.8 30.1 - + - -
320D TRP* 3.3 78.6 - + + -
321D ASP* 2.9 24.2 + - - +
325D PHE* 3.8 13.5 - - + -
344D VAL* 4.1 7.2 - - + +
345D TRP 2.9 31.3 + - - +
346D ILE* 4.8 0.7 - - + -
405D LEU* 4.0 25.8 - - + -
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Residues in contact with MET 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307D CYS 3.6 5.6 + - - +
308D PHE* 3.0 20.1 - - - +
309D TRP* 1.3 118.8 - - + +
311D LYS* 1.3 69.6 + - - +
312D ALA 3.7 1.2 + - - -
314D GLN 5.3 0.7 - - - +
315D TRP* 4.0 10.5 + - + -
316D CYS* 3.2 37.2 - - - +
317D ASP* 3.9 4.7 - - - +
318D PHE* 3.8 12.3 - - - -
319D GLU 3.4 20.0 - - - +
321D ASP* 4.1 6.8 - - - +
345D TRP* 3.4 39.9 - - + -
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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