Contacts of the strand formed by residues 536 - 539 (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 HIS 536 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264F PRO* 4.0 8.7 - - + +
268F SER* 3.1 48.4 + - - +
269F PHE* 3.8 12.3 - + - -
272F TRP* 4.8 5.6 - + - +
464F PHE* 4.8 4.3 - - + -
477F VAL* 3.9 22.3 - - + +
507F PHE* 3.8 35.2 - + + +
508F TRP 3.6 2.5 + - - +
509F SER* 2.8 40.9 + - - +
510F HIS* 4.2 2.9 + - - -
531F GLY 4.2 0.5 - - - +
534F SER* 4.1 8.9 - - - -
535F SER* 1.3 104.2 + - - +
537F SER* 1.3 61.4 + - - +
566F LYS* 3.8 2.0 - - - +
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Residues in contact with SER 537 (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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270F GLY 3.8 5.7 + - - +
271F LEU* 4.3 9.9 - - - -
272F TRP* 3.0 31.9 + - - -
464F PHE* 5.3 0.4 - - - -
509F SER* 4.2 0.9 - - - -
510F HIS* 5.1 0.9 - - - -
512F ILE* 4.4 1.8 - - - -
531F GLY* 2.8 31.1 + - - -
532F LEU* 3.6 21.5 - - - +
536F HIS* 1.3 74.1 - - - +
538F ARG* 1.3 62.0 + - - +
566F LYS* 2.9 23.1 + - - +
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Residues in contact with ARG 538 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271F LEU* 4.9 0.2 - - - -
272F TRP* 3.3 32.6 - - + +
274F THR* 3.4 27.7 + - - +
304F HIS* 3.5 19.6 + - - +
343F CYS* 6.0 0.4 - - - -
414F LYS* 3.0 36.3 - - - +
464F PHE* 3.8 31.7 - - + -
479F TRP* 3.8 6.9 - - - -
510F HIS 3.5 14.2 + - - +
511F ASP* 3.3 15.7 + - - -
512F ILE* 3.0 32.6 + - - +
537F SER* 1.3 78.2 - - - +
539F LEU* 1.3 61.8 + - - +
540F HIS* 2.8 37.6 + - - +
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Residues in contact with LEU 539 (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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271F LEU* 4.1 25.8 - - + -
272F TRP 2.8 10.8 + - - +
273F LEU* 3.3 23.0 - - + +
274F THR* 2.9 24.9 + - - +
293F MET* 4.7 4.9 - - + -
512F ILE* 3.4 44.4 - - + +
524F TYR* 3.4 21.8 - - + +
528F CYS* 4.5 3.8 - - - -
538F ARG* 1.3 71.2 - - - +
540F HIS* 1.3 56.9 - - - +
546F ARG* 3.4 24.5 - - + +
548F PRO* 4.6 13.5 - - + -
559F VAL* 4.8 4.7 - - + -
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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