Contacts of the strand formed by residues 341 - 346 (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 LYS 341 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B TRP* 3.6 58.7 - - + +
301B HIS 3.1 16.6 + - - +
302B VAL* 3.3 12.8 - - + +
303B PHE 2.8 26.0 + - - -
336B LYS* 5.6 1.9 - - + +
340B LEU* 1.3 76.5 - - - +
342B ILE* 1.3 68.1 + - - +
411B ASP* 3.4 28.2 + - + +
412B CYS* 6.0 0.2 - - - -
460B GLU* 4.1 8.1 + - - -
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Residues in contact with ILE 342 (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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303B PHE* 3.4 15.3 - - + +
305B PHE* 4.3 20.6 - - + -
320B TRP* 6.4 0.2 - - + -
332B ILE* 4.8 11.2 - - + -
335B LEU* 4.1 26.5 - - + -
336B LYS* 4.2 15.0 - - + -
340B LEU* 4.2 8.1 - - + -
341B LYS* 1.3 91.6 - - - +
343B CYS* 1.3 65.0 + - - +
344B VAL* 4.1 17.7 - - + -
409B GLY 4.5 5.2 - - - +
410B VAL* 3.7 17.7 - - + +
411B ASP* 2.8 42.7 + - - +
412B CYS* 3.3 7.8 + - - -
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Residues in contact with CYS 343 (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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272B TRP* 4.0 20.6 - - + -
302B VAL* 4.5 2.7 - - + -
303B PHE 2.9 9.4 + - - +
304B HIS* 3.0 23.1 + - + +
305B PHE* 2.8 24.6 + - - +
341B LYS 4.3 0.2 + - - -
342B ILE* 1.3 72.0 - - - +
344B VAL* 1.3 68.4 + - - +
412B CYS* 3.2 29.2 - - - -
413B PHE 3.7 28.7 - - - -
414B LYS* 3.7 6.7 - - - -
464B PHE* 5.2 1.1 - - - -
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Residues in contact with VAL 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B HIS* 3.5 6.1 - - - -
305B PHE* 3.5 27.6 - - + +
309B TRP* 4.0 12.6 - - + +
320B TRP* 4.4 13.0 - - + -
342B ILE* 4.1 11.2 - - + -
343B CYS* 1.3 80.1 - - - +
345B TRP* 1.3 66.7 + - - +
346B ILE* 3.8 2.5 + - + +
405B LEU* 4.1 16.2 - - + -
410B VAL* 3.9 17.0 - - + -
412B CYS 3.4 2.8 + - - -
413B PHE* 3.7 25.7 - - + -
414B LYS 3.2 17.3 + - - -
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Residues in contact with TRP 345 (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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304B HIS* 3.1 8.2 - - + -
305B PHE 2.8 18.7 + - - +
306B ASP* 3.4 22.2 - - - -
307B CYS* 3.5 25.1 - - - +
309B TRP* 2.9 22.6 + - - +
310B MET* 3.6 27.8 - - + -
315B TRP* 4.4 11.4 - + + -
316B CYS* 4.2 4.7 - - + -
344B VAL* 1.3 72.4 - - - +
346B ILE* 1.3 82.7 + - - +
347B ASN* 3.3 38.6 - - + -
380B TRP* 3.7 29.2 - + - -
414B LYS* 4.0 11.9 - - + -
416B ASP* 3.1 20.9 + - + +
417B PHE* 4.0 4.7 - + - -
802B XYF 3.1 18.7 - - - -
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Residues in contact with ILE 346 (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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309B TRP* 4.7 2.9 - - + -
316B CYS* 3.8 9.2 - - - -
318B PHE* 4.2 17.3 - - + -
344B VAL* 3.8 11.4 - - + +
345B TRP* 1.3 95.8 - - - +
347B ASN* 1.3 66.5 + - - +
398B TYR* 4.0 14.8 - - - +
402B LEU* 4.0 14.8 - - + -
405B LEU* 5.0 0.7 - - + -
413B PHE* 3.7 32.8 - - + -
414B LYS 3.1 26.9 + - - +
415B THR* 4.0 18.4 - - + -
416B ASP* 3.2 14.2 + - - +
444B TYR* 4.2 1.8 - - - +
448B VAL* 4.1 9.0 - - + -
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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