Contacts of the helix formed by residues 306 - 310 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274E THR* 4.4 0.4 - - + -
275E THR* 3.5 10.7 + - - +
276E SER 3.3 21.3 - - - +
277E PHE* 3.2 24.6 - - - -
281E TYR* 3.3 8.1 + - - +
304E HIS* 3.1 14.4 + - + +
305E PHE* 1.3 72.3 - - - +
307E CYS* 1.3 65.1 + - - +
308E PHE 3.1 1.6 + - - -
309E TRP* 2.8 28.9 + - - +
345E TRP* 3.7 9.9 - - - -
414E LYS* 3.0 26.9 + - - -
540E HIS* 3.2 10.8 - - + -
804E XYF 2.9 17.1 + - - -
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Residues in contact with CYS 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277E PHE* 3.4 17.0 - - + -
306E ASP* 1.3 81.4 - - - +
308E PHE* 1.3 61.1 + - + +
309E TRP* 2.8 7.3 + - - -
310E MET* 3.2 18.0 + - - +
315E TRP* 3.4 34.9 + - + -
345E TRP* 3.5 35.0 - - - +
380E TRP* 4.0 6.5 - - - -
804E XYF 3.1 32.1 - - - -
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Residues in contact with PHE 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C ARG* 3.4 76.0 + - + +
47C GLN* 4.0 14.4 - - + -
277E PHE* 3.2 27.8 - + - -
278E THR* 3.8 16.8 - - + -
281E TYR* 3.1 15.8 + - + +
306E ASP 4.0 0.2 - - - -
307E CYS* 1.3 73.7 - - + +
309E TRP* 1.3 58.7 + - - +
310E MET 2.9 18.6 + - - +
312E ALA* 4.4 9.4 - - + -
315E TRP* 3.6 34.5 - + - +
321E ASP* 4.4 7.4 - - - +
324E THR* 4.6 5.2 + - - +
325E PHE* 4.2 8.1 - - - -
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Residues in contact with TRP 309 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281E TYR* 4.5 1.3 + - + -
305E PHE* 3.7 23.6 - - + -
306E ASP 2.8 27.1 + - - +
307E CYS 2.8 10.6 + - - -
308E PHE* 1.3 74.8 - - - +
310E MET* 1.3 84.8 + - + +
318E PHE* 4.1 16.4 - + - -
320E TRP* 3.4 79.9 - + + -
321E ASP* 3.0 21.7 + - - +
325E PHE* 3.9 15.1 - - + -
344E VAL* 4.0 7.8 - - + +
345E TRP* 2.9 34.5 + - + +
346E ILE* 4.5 3.1 - - + -
405E LEU* 3.8 31.4 - - + -
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Residues in contact with MET 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307E CYS 3.2 12.8 + - - +
308E PHE* 2.9 20.8 - - - +
309E TRP* 1.3 110.0 - - + +
311E LYS* 1.3 65.8 + - - +
312E ALA 3.7 1.0 + - - -
315E TRP* 3.6 12.2 + - + +
316E CYS* 3.4 33.4 - - - +
317E ASP* 3.9 5.2 - - - +
318E PHE* 3.7 15.0 - - - -
319E GLU 3.2 25.4 - - - +
321E ASP* 4.0 6.3 - - - +
345E TRP* 3.4 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