Contacts of the strand formed by residues 413 - 421 (chain G) in PDB entry 1RZK
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 ASN 413 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332G ASN* 4.5 13.2 - - + +
333G LEU 3.2 14.1 + - - +
334G SER* 4.5 7.1 - - - +
335G LYS* 4.0 9.5 + - - +
411G GLY* 4.5 2.6 - - - -
412G ARG* 1.3 115.5 + - - +
414G ILE* 1.3 66.5 + - - +
415G THR* 3.7 7.0 + - - +
795G NAG 3.7 23.2 + - - +
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Residues in contact with ILE 414 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331G CYS 3.4 1.0 - - - +
332G ASN* 3.2 5.7 - - - +
333G LEU* 2.6 44.0 + - + +
335G LYS* 3.6 36.3 - - + +
338G TRP* 3.6 35.2 - - + -
389G GLN* 3.9 22.7 - - + +
390G LEU* 3.7 18.2 - - + -
407G LEU* 6.1 3.8 - - + -
413G ASN* 1.3 72.0 - - - +
415G THR* 1.3 61.3 + - - +
416G LEU* 3.3 27.5 + - + +
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Residues in contact with THR 415 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330G HIS* 3.5 41.1 - - + +
331G CYS 3.2 1.6 - - - -
332G ASN* 2.9 14.3 + - - +
389G GLN* 3.1 23.1 + - - +
413G ASN* 3.7 7.4 + - - +
414G ILE* 1.3 75.8 - - - +
416G LEU* 1.3 63.3 - - - +
417G PRO* 3.5 4.4 - - + +
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Residues in contact with LEU 416 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294G ILE* 4.5 17.7 - - + -
330G HIS* 3.1 4.4 - - - +
331G CYS* 2.8 37.3 + - + +
333G LEU* 5.1 3.6 - - + -
374G HIS* 5.4 2.7 - - + -
385G CYS* 4.2 17.3 - - + -
386G ASN 3.1 22.7 - - - +
387G SER* 4.7 4.7 - - - -
389G GLN* 4.0 14.8 - - + +
390G LEU* 3.5 37.0 - - + -
414G ILE* 3.3 28.0 - - + -
415G THR* 1.3 72.5 - - - +
417G PRO* 1.4 61.5 - - - +
418G CYS* 3.0 9.2 + - - +
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Residues in contact with PRO 417 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329G GLY 3.9 7.2 - - - +
330G HIS* 4.4 2.2 - - + -
384G TYR 4.1 1.2 - - - +
385G CYS* 4.0 0.2 - - - -
386G ASN* 3.3 40.4 + - + +
389G GLN* 3.8 7.4 - - - +
415G THR* 3.5 8.9 - - + +
416G LEU* 1.4 79.1 - - - +
418G CYS* 1.3 63.5 + - - +
419G ARG* 5.5 0.2 - - - +
886G NAG 3.9 20.2 - - + -
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Residues in contact with CYS 418 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329G GLY* 2.9 25.3 + - - +
330G HIS* 3.6 21.8 - - - +
331G CYS* 4.3 0.4 - - - -
383G PHE* 3.7 20.2 - - + -
384G TYR 3.2 14.6 - - - -
385G CYS* 2.0 58.8 - - - +
416G LEU 3.0 2.6 + - - +
417G PRO* 1.3 75.0 - - - +
419G ARG* 1.3 64.4 + - - +
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Residues in contact with ARG 419 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329G GLY* 5.6 1.1 - - - -
383G PHE* 3.5 1.1 - - - -
384G TYR* 2.6 48.7 + - + +
417G PRO 5.5 0.4 - - - +
418G CYS* 1.3 77.9 - - - +
420G ILE* 1.3 72.8 + - - +
421G LYS* 4.6 9.8 - - + +
99H GLU* 2.3 54.9 + - - +
100H GLU* 3.0 52.6 + - - +
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Residues in contact with ILE 420 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298G GLY* 3.9 19.7 - - - +
329G GLY* 6.5 0.4 - - - -
381G GLU* 3.6 44.2 - - + +
382G PHE 3.4 9.4 - - - +
383G PHE* 3.7 33.7 - - + -
419G ARG* 1.3 83.6 - - - +
421G LYS* 1.3 71.0 + - - +
422G GLN* 4.0 16.7 + - - +
438G PRO* 4.2 14.8 - - + -
443G ILE* 5.3 1.8 - - + -
100H GLU* 4.9 7.8 - - - +
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Residues in contact with LYS 421 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369G PRO* 3.4 31.2 - - + +
370G GLU* 5.2 0.9 - - - +
381G GLU* 5.5 0.5 - - - +
382G PHE* 3.1 18.7 + - - +
384G TYR* 3.7 47.6 - - + -
419G ARG* 4.6 14.4 - - + +
420G ILE* 1.3 85.0 - - - +
422G GLN* 1.3 65.4 + - - +
423G ILE 4.0 11.0 - - - +
424G ILE* 4.0 8.2 - - + +
435G TYR* 5.5 0.7 - - - +
100H GLY* 3.0 46.7 - - - +
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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