Contacts of the strand formed by residues 412 - 415 (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 CYS 412 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267E TRP* 4.0 16.2 - - + -
272E TRP* 3.7 23.1 - - - -
302E VAL* 4.7 1.3 - - - -
342E ILE 3.1 4.4 + - - -
343E CYS* 3.3 47.9 - - - -
344E VAL 3.4 1.6 + - - -
410E VAL* 3.4 9.0 - - - +
411E ASP* 1.3 78.2 - - - +
413E PHE* 1.3 71.7 + - - +
452E LEU* 4.4 4.9 - - - -
462E VAL* 3.1 30.7 - - + +
463E LEU* 5.0 0.7 - - - -
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Residues in contact with PHE 413 (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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343E CYS* 3.7 5.8 - - - -
344E VAL* 3.5 29.8 - - + -
346E ILE* 3.9 26.0 - - + -
402E LEU* 3.7 36.8 - - + -
405E LEU* 3.7 17.5 - - + -
406E VAL* 3.9 11.4 - - + -
410E VAL* 3.9 10.3 - - + -
412E CYS* 1.3 81.8 - - - +
414E LYS* 1.3 60.1 + - - +
415E THR* 3.5 2.7 + - + -
448E VAL* 3.6 26.0 - - + -
451E VAL* 5.1 2.0 - - + -
452E LEU* 3.4 28.9 - - + -
462E VAL 3.9 3.4 + - - -
463E LEU* 3.3 10.9 - - + +
464E PHE 3.0 21.0 + - - -
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Residues in contact with LYS 414 (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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304E HIS* 3.3 32.8 - - + +
306E ASP* 3.0 21.8 + - - -
343E CYS* 3.5 3.0 - - - -
344E VAL 3.1 7.6 + - - +
345E TRP* 3.9 12.6 - - + -
346E ILE* 3.0 28.3 + - - +
413E PHE* 1.3 71.3 - - - +
415E THR* 1.3 57.0 + - - +
416E ASP* 3.1 3.0 + - - +
464E PHE* 3.3 24.7 - - + +
479E TRP* 3.4 24.0 - - + -
538E ARG* 3.2 17.3 - - - +
540E HIS* 3.0 14.3 + - - -
804E XYF 2.7 35.0 + - - -
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Residues in contact with THR 415 (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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346E ILE* 3.9 11.7 - - + -
413E PHE 3.5 1.4 + - - +
414E LYS* 1.3 68.0 - - - +
416E ASP* 1.3 65.3 + - - +
417E PHE 4.2 2.9 - - - +
444E TYR* 3.2 22.2 - - + +
445E ASN* 2.6 30.4 + - - +
448E VAL* 3.8 35.7 - - + -
463E LEU* 4.3 10.9 - - + +
464E PHE 3.0 6.4 + - - -
465E ALA* 3.3 13.2 + - - +
466E ARG 3.3 17.7 + - - -
467E SER 4.7 0.3 + - - -
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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