Contacts of the strand formed by residues 353 - 358 (chain S) in PDB entry 5KZ5
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 353 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207S ASN 4.9 1.8 - - - -
208S GLU 4.0 7.2 - - - -
209S ILE 4.0 1.3 - - - -
210S GLY* 2.9 45.2 - - - +
235S GLN* 5.5 1.8 - - + +
258S LYS* 3.6 32.1 - - + -
349S HIS* 4.1 2.4 + - - +
350S TYR* 2.9 20.1 - - + +
351S PRO 3.4 1.2 - - - -
352S GLY* 1.3 78.9 - - - +
354S ILE* 1.4 69.2 - - - +
407S ARG* 3.7 20.2 - - - -
408S PHE 3.4 8.1 - - - -
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Residues in contact with ILE 354 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209S ILE 4.0 1.3 - - - -
326S SER* 4.7 6.1 - - - +
329S LEU* 4.6 12.8 - - + -
330S ILE* 3.8 41.5 - - + -
333S ILE* 6.2 2.7 - - + -
342S MET* 4.7 9.4 - - + -
349S HIS* 4.2 4.7 - - + +
351S PRO 3.5 16.2 - - - +
353S CYS* 1.4 79.6 - - - +
355S ASN* 1.4 62.7 + - - +
356S LEU* 4.3 17.9 - - + +
406S ILE 3.8 1.4 - - - +
408S PHE* 3.0 42.1 + - + +
410S ILE* 3.5 33.9 - - + -
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Residues in contact with ASN 355 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208S GLU* 3.2 41.9 + - - +
209S ILE* 3.3 33.1 + - + +
342S MET* 4.2 4.6 - - - +
343S ASN* 2.7 50.2 + - - +
354S ILE* 1.4 74.7 - - - +
356S LEU* 1.4 68.4 + - - +
357S SER* 4.9 1.2 - - - -
392S LEU* 4.7 6.5 - - - +
405S SER* 5.0 4.6 - - - -
406S ILE 3.1 24.4 + - - +
407S ARG* 3.8 2.3 - - - +
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Residues in contact with LEU 356 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330S ILE* 5.8 4.5 - - + +
333S ILE* 3.9 33.9 - - + -
334S MET* 4.3 11.9 - - + -
340S VAL* 3.7 21.1 - - + -
341S VAL 3.6 14.1 - - - +
342S MET* 4.0 11.2 - - + -
343S ASN 4.0 2.0 - - - +
354S ILE* 4.3 17.5 - - + +
355S ASN* 1.4 81.0 + - - +
357S SER* 1.4 59.2 + - - +
358S PHE* 3.8 14.2 - - + -
405S SER* 4.1 0.5 - - - -
406S ILE* 3.4 50.3 + - + -
408S PHE* 6.1 0.2 - - + -
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Residues in contact with SER 357 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340S VAL* 4.1 1.1 - - - -
341S VAL* 2.8 36.0 + - - +
343S ASN* 3.5 24.2 - - - +
355S ASN* 4.9 0.7 - - - -
356S LEU* 1.4 72.2 - - - +
358S PHE* 1.3 68.9 + - - +
359S ALA* 3.8 4.6 - - - +
392S LEU* 5.8 3.1 - - - -
395S ILE* 5.7 5.2 - - - +
397S THR* 3.7 19.5 - - - +
405S SER* 3.6 14.3 + - - -
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Residues in contact with PHE 358 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333S ILE* 5.2 1.8 - - + -
337S LEU* 4.4 17.7 - - + -
338S PRO 5.3 2.7 - - - -
339S ASP 4.1 9.6 + - - -
340S VAL* 3.6 44.2 - - + +
341S VAL* 5.6 0.2 - - - +
356S LEU* 3.8 18.8 - - + +
357S SER* 1.3 77.6 + - - -
359S ALA* 1.3 59.9 + - - +
360S TYR* 6.2 0.4 - - - -
361S VAL* 5.1 4.0 - - + -
366S LEU* 3.4 38.9 - - + +
369S ALA* 4.1 30.1 - - + -
370S LEU* 4.5 2.2 - - + -
401S LEU* 4.0 8.1 - - - +
404S SER 4.5 5.8 - - - +
405S SER* 3.6 11.5 + - - -
406S ILE* 3.5 34.3 - - + -
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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