Contacts of the strand formed by residues 341 - 346 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267A TRP* 3.4 71.9 - - + +
301A HIS 2.9 16.5 + - - +
302A VAL* 3.3 5.0 - - + -
303A PHE 2.9 26.0 + - - -
336A LYS* 4.5 4.5 - - - +
339A GLY 5.2 3.4 - - - +
340A LEU* 1.3 76.2 - - - +
342A ILE* 1.3 67.6 + - - +
411A ASP* 3.3 23.8 + - - +
460A GLU* 4.5 6.3 + - - -
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Residues in contact with ILE 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A VAL* 4.9 0.2 - - - -
303A PHE* 3.6 7.0 - - + +
305A PHE* 3.9 26.9 - - + -
332A ILE* 4.2 18.6 - - + -
335A LEU* 4.3 20.6 - - + -
336A LYS* 3.2 38.4 - - + +
340A LEU* 3.4 10.8 - - + +
341A LYS* 1.3 83.3 - - - +
343A CYS* 1.3 66.2 + - - +
344A VAL* 4.4 7.9 - - + -
409A GLY 4.5 3.1 - - - +
410A VAL* 3.6 9.6 - - + +
411A ASP* 2.6 41.2 + - - +
412A CYS* 3.2 9.2 + - - -
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Residues in contact with CYS 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A TRP* 3.8 22.0 - - + -
302A VAL* 4.6 1.5 - - + +
303A PHE 3.1 9.6 + - - +
304A HIS* 3.2 19.5 - - + +
305A PHE* 2.9 26.0 + - - -
341A LYS 4.3 0.2 + - - -
342A ILE* 1.3 71.2 - - - +
344A VAL* 1.3 68.1 + - - +
412A CYS* 3.3 25.4 - - - -
413A PHE* 3.5 10.1 - - - -
414A LYS* 3.5 29.6 - - - -
464A PHE* 5.1 1.1 - - - -
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Residues in contact with VAL 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A HIS* 3.6 4.0 - - - -
305A PHE* 3.5 24.9 - - + +
309A TRP* 3.8 14.1 - - + +
320A TRP* 4.2 16.8 - - + -
342A ILE* 4.4 2.9 - - + -
343A CYS* 1.3 80.2 - - - +
345A TRP* 1.3 67.0 + - - +
346A ILE* 3.8 0.7 + - + -
405A LEU* 4.1 15.5 - - + -
410A VAL* 4.2 18.6 - - + -
412A CYS 3.4 3.2 + - - -
413A PHE* 3.6 31.0 - - + +
414A LYS 3.1 20.3 + - - -
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Residues in contact with TRP 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A HIS* 3.3 7.1 - - + -
305A PHE 2.9 18.1 + - - +
306A ASP* 3.7 29.8 - - - -
307A CYS* 3.5 18.4 - - - -
309A TRP* 2.9 22.2 + - - +
310A MET* 3.4 27.3 - - + +
315A TRP* 4.3 18.2 - + + -
316A CYS* 4.3 5.6 - - + -
344A VAL* 1.3 72.9 - - - +
346A ILE* 1.3 79.6 + - - +
347A ASN* 3.4 39.0 - - + -
380A TRP* 3.8 12.6 - + - -
414A LYS* 4.0 12.1 - - + -
416A ASP* 3.0 32.6 + - + +
417A PHE* 3.8 14.6 - + - -
801A XYF 3.4 6.7 - - - -
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Residues in contact with ILE 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A TRP* 4.8 0.7 - - + -
316A CYS* 3.9 9.2 - - - -
318A PHE* 3.9 21.1 - - + -
344A VAL* 4.3 4.7 - - + +
345A TRP* 1.3 89.1 - - - +
347A ASN* 1.3 65.5 + - - +
398A TYR* 4.0 11.4 - - - +
402A LEU* 4.0 11.9 - - + -
405A LEU* 4.8 1.1 - - + -
413A PHE* 3.8 37.5 - - + -
414A LYS 3.0 30.4 + - - +
415A THR* 4.0 4.7 - - + -
416A ASP* 3.1 17.0 + - - +
444A TYR* 4.0 6.1 - - - +
448A VAL* 4.0 26.5 - - + -
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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