Contacts of the strand formed by residues 341 - 346 (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 LYS 341 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267F TRP* 3.3 69.7 - - + +
301F HIS* 3.0 17.6 + - + +
302F VAL* 3.3 5.1 - - + -
303F PHE* 2.7 31.9 + - - +
336F LYS* 5.2 4.1 - - - +
339F GLY 5.8 0.2 - - - +
340F LEU* 1.3 78.6 - - - +
342F ILE* 1.3 58.2 + - - +
411F ASP* 3.4 28.9 + - - +
460F GLU* 4.1 8.1 + - - +
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Residues in contact with ILE 342 (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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302F VAL* 4.8 0.2 - - - -
303F PHE* 3.5 8.1 - - + +
305F PHE* 4.0 27.4 - - + -
332F ILE* 4.1 14.6 - - + -
335F LEU* 4.5 10.1 - - + -
336F LYS* 3.2 40.4 - - + +
340F LEU* 3.5 12.6 - - + +
341F LYS* 1.3 81.0 - - - +
343F CYS* 1.3 73.7 + - - +
344F VAL* 4.2 8.5 - - + -
409F GLY 4.2 9.0 - - - +
410F VAL* 3.8 10.2 - - + +
411F ASP* 2.8 36.1 + - - +
412F CYS* 3.2 8.4 + - - -
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Residues in contact with CYS 343 (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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272F TRP* 3.7 26.7 - - + -
302F VAL* 4.4 1.8 - - + -
303F PHE 2.8 11.9 + - - +
304F HIS* 3.2 22.1 - - + +
305F PHE 2.9 24.3 + - - -
342F ILE* 1.3 74.6 - - - +
344F VAL* 1.3 68.7 + - - +
412F CYS* 3.3 30.3 - - - -
413F PHE 3.8 3.6 - - - -
414F LYS* 3.7 22.2 - - - -
464F PHE* 5.2 1.3 - - - -
538F ARG* 6.0 0.4 - - - -
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Residues in contact with VAL 344 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304F HIS* 3.8 4.0 - - - -
305F PHE* 3.6 18.4 - - + +
309F TRP* 3.9 12.1 - - + +
320F TRP* 4.4 13.2 - - + -
342F ILE* 4.2 7.4 - - + -
343F CYS* 1.3 79.7 - - - +
345F TRP* 1.3 67.5 + - - +
346F ILE* 3.8 1.4 + - + +
405F LEU* 4.1 15.9 - - + -
410F VAL* 3.6 25.1 - - + -
412F CYS 3.3 4.6 + - - -
413F PHE* 3.5 31.2 - - + -
414F LYS 3.2 18.7 + - - -
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Residues in contact with TRP 345 (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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304F HIS* 3.4 8.4 - - + -
305F PHE 3.0 18.9 + - - +
306F ASP* 3.4 30.7 - - - -
307F CYS* 3.3 25.7 - - - -
309F TRP* 2.9 21.4 + - - +
310F MET* 3.5 27.8 - - + +
315F TRP* 4.2 14.1 - + + -
316F CYS* 4.2 6.3 - - + -
344F VAL* 1.3 71.9 - - - +
346F ILE* 1.3 84.6 + - - +
347F ASN* 3.4 39.0 - - + -
380F TRP* 3.7 24.9 - + - -
414F LYS* 4.0 12.1 - - + -
416F ASP* 3.0 32.0 + - + +
417F PHE* 4.0 4.0 - + - -
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Residues in contact with ILE 346 (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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309F TRP* 4.7 1.1 - - + -
316F CYS* 3.9 9.9 - - - -
318F PHE* 4.1 18.8 - - + -
344F VAL* 4.0 12.1 - - + +
345F TRP* 1.3 96.8 - - - +
347F ASN* 1.3 64.6 + - - +
398F TYR* 3.8 15.9 - - - +
402F LEU* 4.0 17.0 - - + -
405F LEU* 4.9 0.2 - - + -
413F PHE* 4.0 23.3 - - + -
414F LYS 3.0 14.4 + - - +
415F THR* 3.9 24.7 - - + -
416F ASP* 3.0 27.2 + - - +
444F TYR* 4.1 1.3 - - - +
448F VAL* 4.1 9.6 - - + -
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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