Contacts of the strand formed by residues 341 - 346 (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 LYS 341 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267D TRP* 3.5 71.2 - - + +
301D HIS 2.9 16.9 + - - +
302D VAL* 3.4 6.0 - - + +
303D PHE* 2.8 26.5 + - - +
336D LYS* 4.8 3.4 - - - +
340D LEU* 1.3 78.5 - - - +
342D ILE* 1.3 67.2 + - - +
411D ASP* 3.2 25.1 + - + +
460D GLU* 4.5 6.5 + - - -
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Residues in contact with ILE 342 (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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303D PHE* 3.6 8.5 - - + +
305D PHE* 4.1 23.1 - - + -
332D ILE* 4.2 13.9 - - + +
335D LEU* 4.0 26.0 - - + -
336D LYS* 3.8 20.9 - - + +
340D LEU* 4.1 9.0 - - + +
341D LYS* 1.3 81.6 - - - +
343D CYS* 1.3 60.9 + - - +
344D VAL* 4.0 19.7 - - + -
409D GLY 4.3 7.6 - - - +
410D VAL* 3.4 18.7 - - + +
411D ASP* 2.6 41.6 + - - +
412D CYS* 3.2 8.2 + - - -
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Residues in contact with CYS 343 (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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272D TRP* 3.8 21.8 - - + -
302D VAL* 4.4 1.8 - - + -
303D PHE 3.0 11.2 + - - +
304D HIS* 3.2 20.2 - - + +
305D PHE* 2.8 25.8 + - - +
341D LYS 4.1 0.6 + - - -
342D ILE* 1.3 71.6 - - - +
344D VAL* 1.3 69.3 + - - +
412D CYS* 3.1 33.9 - - - -
413D PHE 3.7 21.5 - - - -
414D LYS* 3.7 5.6 - - - -
464D PHE* 5.4 0.2 - - - -
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Residues in contact with VAL 344 (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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304D HIS* 3.7 4.9 - - - -
305D PHE* 3.5 27.8 - - + +
309D TRP* 4.1 11.9 - - + +
320D TRP* 4.4 11.0 - - + -
342D ILE* 4.0 11.0 - - + -
343D CYS* 1.3 80.8 - - - +
345D TRP* 1.3 66.8 + - - +
346D ILE 3.8 0.2 + - - -
405D LEU* 4.2 13.5 - - + -
410D VAL* 3.7 15.5 - - + -
412D CYS 3.2 4.6 + - - -
413D PHE* 3.4 34.4 - - + -
414D LYS 3.1 19.9 + - - -
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Residues in contact with TRP 345 (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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304D HIS* 3.4 4.6 - - - -
305D PHE 2.9 19.6 + - - +
306D ASP* 3.1 34.3 - - - +
307D CYS* 3.8 16.9 - - + +
309D TRP* 2.9 23.6 + - - +
310D MET* 3.4 30.3 - - + -
315D TRP* 4.2 15.9 - + + -
316D CYS* 4.4 1.3 - - + -
344D VAL* 1.3 73.8 - - - +
346D ILE* 1.3 81.6 + - - +
347D ASN* 3.5 36.3 - - + -
380D TRP* 4.0 20.1 - + - -
414D LYS* 4.0 9.6 - - + -
416D ASP* 3.1 31.3 + - + +
417D PHE* 3.9 16.8 - + - -
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Residues in contact with ILE 346 (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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309D TRP* 4.8 2.9 - - + -
316D CYS* 3.8 9.9 - - - -
318D PHE* 4.0 19.1 - - + -
344D VAL* 4.6 2.2 - - + -
345D TRP* 1.3 93.9 - - - +
347D ASN* 1.3 66.6 + - - +
398D TYR* 3.9 14.8 - - - +
402D LEU* 4.0 14.4 - - + -
405D LEU* 4.9 0.2 - - + -
413D PHE* 3.8 33.9 - - + -
414D LYS 3.2 25.8 + - - +
415D THR* 3.7 21.5 - - + -
416D ASP* 3.2 13.2 + - - +
444D TYR* 4.0 6.5 - - - +
448D VAL* 4.1 8.7 - - + -
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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