Contacts of the strand formed by residues 353 - 358 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205Q VAL* 5.4 0.7 - - + -
206Q ASN 5.5 0.2 - - - +
207Q ASN 4.6 2.9 - - - -
208Q GLU 3.8 17.7 - - - -
209Q ILE 4.2 1.1 - - - -
210Q GLY* 3.1 47.3 - - - +
258Q LYS* 3.5 31.4 - - + +
330Q ILE* 5.2 2.6 - - - +
349Q HIS* 5.2 0.3 - - - +
350Q TYR* 3.2 16.5 + - + +
351Q PRO 3.4 1.8 + - - -
352Q GLY* 1.3 79.7 - - - +
354Q ILE* 1.3 68.6 + - - +
407Q ARG* 4.1 12.6 - - - -
408Q PHE 4.1 5.4 - - - -
409Q GLY* 4.2 0.4 - - - -
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Residues in contact with ILE 354 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209Q ILE 4.8 0.7 - - - -
329Q LEU* 4.7 7.9 - - + -
330Q ILE* 4.1 34.3 - - + -
333Q ILE* 5.4 3.4 - - + -
342Q MET* 5.9 1.8 - - + -
350Q TYR 5.6 0.2 - - - +
351Q PRO 4.3 13.0 - - - +
353Q CYS* 1.3 84.2 - - - +
355Q ASN* 1.4 61.2 + - - +
356Q LEU* 4.5 17.9 - - + -
407Q ARG* 3.7 2.1 - - - +
408Q PHE* 3.0 82.2 + - + +
410Q ILE* 4.0 20.2 - - + -
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Residues in contact with ASN 355 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208Q GLU* 3.3 39.6 + - - +
209Q ILE* 3.3 38.6 + - - +
342Q MET* 5.5 0.5 - - - +
343Q ASN* 2.8 42.9 + - - +
353Q CYS* 4.9 0.2 - - - -
354Q ILE* 1.4 73.8 - - - +
356Q LEU* 1.3 72.6 + - - +
357Q SER* 5.5 0.2 - - - -
392Q LEU* 5.5 2.1 - - - +
405Q SER* 4.7 6.5 - - - -
406Q ILE 3.0 29.8 + - - +
407Q ARG* 3.7 4.4 - - + +
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Residues in contact with LEU 356 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330Q ILE* 5.6 3.8 - - + +
333Q ILE* 4.0 26.9 - - + -
334Q MET* 3.6 25.1 - - + -
337Q LEU* 6.1 0.7 - - + -
340Q VAL* 3.7 24.0 - - + -
341Q VAL 4.0 2.7 - - - +
342Q MET* 3.8 20.0 - - + -
343Q ASN* 4.2 5.2 - - - +
354Q ILE* 4.5 19.1 - - + -
355Q ASN* 1.3 84.6 + - - +
357Q SER* 1.4 62.8 + - - +
358Q PHE* 4.0 2.0 - - + -
405Q SER* 4.1 1.0 - - - -
406Q ILE* 3.1 46.9 + - + +
408Q PHE* 4.9 7.4 - - + -
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Residues in contact with SER 357 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341Q VAL* 3.0 29.1 + - - +
343Q ASN* 3.4 28.5 - - - +
356Q LEU* 1.4 75.5 - - - +
358Q PHE* 1.4 72.6 + - - +
392Q LEU* 6.2 1.3 - - - -
395Q ILE* 5.9 1.8 - - - -
397Q THR* 3.6 18.1 - - - +
401Q LEU 4.3 0.5 + - - -
405Q SER* 3.3 23.2 + - - -
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Residues in contact with PHE 358 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339Q ASP 4.6 6.3 - - - -
340Q VAL* 3.7 30.2 - - + +
341Q VAL* 4.4 8.9 - - - +
356Q LEU* 3.8 4.5 - - + -
357Q SER* 1.4 92.1 + - - +
359Q ALA* 1.4 63.7 + - - +
361Q VAL* 5.0 2.0 - - + -
363Q GLY* 4.5 8.7 - - - -
366Q LEU* 3.7 32.3 - - + -
367Q LEU* 3.7 15.5 - - + -
370Q LEU* 3.9 27.6 - - + -
397Q THR* 4.8 1.7 - - - +
401Q LEU* 3.9 21.6 - - + +
404Q SER* 2.9 31.9 - - - +
406Q ILE* 3.4 25.4 - - + -
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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