Contacts of the strand formed by residues 389 - 395 (chain C) in PDB entry 1CZY
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 LYS 389 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380C ALA* 3.7 9.2 - - + -
382C TYR* 3.4 42.4 + - + +
387C GLY 3.7 1.0 + - - -
388C TYR* 1.3 70.7 - - - +
390C MET* 1.3 68.0 + - - +
413C VAL* 3.8 3.7 - - - +
414C MET* 2.9 63.0 + - + +
415C LYS 3.6 19.0 + - - +
416C GLY* 3.7 20.1 - - - -
417C PRO* 4.7 4.1 - - + +
419C ASP* 5.0 0.6 + - - -
424C TRP* 6.2 0.4 - - - -
462C ASP* 5.4 5.9 + - - -
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Residues in contact with MET 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352C GLY* 4.9 0.2 - - - -
380C ALA* 3.1 0.7 - - - -
381C PHE* 2.8 75.0 + - + +
382C TYR* 3.6 0.9 - - - -
383C THR* 3.6 39.5 - - + +
388C TYR* 4.0 7.2 - - + +
389C LYS* 1.3 82.3 - - - +
391C CYS* 1.3 58.2 + - - +
411C PHE* 3.3 39.3 - - + -
412C VAL 3.2 12.3 - - - +
413C VAL* 4.9 2.5 - - + -
414C MET* 2.9 15.5 - - - +
426C PHE* 4.2 7.4 - - + -
496C VAL* 3.8 11.0 - - + -
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Residues in contact with CYS 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C PHE* 4.0 13.2 - - - -
378C SER* 3.5 14.4 - - - +
379C PRO 3.5 16.2 - - - +
381C PHE* 4.1 4.9 - - - -
390C MET* 1.3 77.0 - - - +
392C LEU* 1.3 71.3 + - - +
411C PHE* 3.9 1.7 - - - -
412C VAL* 2.8 49.7 + - - +
414C MET* 3.5 24.7 - - + -
463C MET* 4.0 14.4 - - - -
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Residues in contact with LEU 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354C PHE* 4.4 12.1 - - + -
356C TRP* 4.2 17.0 - - + -
377C PHE* 3.4 6.6 - - - -
378C SER* 2.8 39.3 + - - +
381C PHE* 4.4 8.3 - - + -
391C CYS* 1.3 85.5 - - - +
393C ARG* 1.3 60.5 + - - +
394C ILE 4.3 0.2 - - - -
409C LEU* 4.2 6.1 - - + -
410C PHE 3.4 13.0 - - - +
411C PHE* 4.1 15.5 - - + -
412C VAL* 4.5 0.7 - - - -
432C LEU* 4.0 20.2 - - + -
492C ILE* 3.8 29.2 - - + -
493C LYS 5.2 0.2 - - - -
494C ALA* 4.0 22.2 - - + +
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Residues in contact with ARG 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374C PRO* 6.2 0.2 - - - +
375C ALA* 3.3 23.2 - - + +
376C ILE 3.4 7.0 - - - +
377C PHE* 3.3 39.8 - - + -
392C LEU* 1.3 75.4 - - - +
394C ILE* 1.3 59.4 + - - +
395C TYR* 3.1 27.2 + - + -
409C LEU* 4.4 1.3 - - - -
410C PHE* 2.7 46.6 + - + +
412C VAL* 4.0 14.3 - - + +
466C ALA* 4.2 16.6 - - + -
209E ASP* 2.8 27.7 + - - -
210E ASP* 2.7 35.2 + - - +
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Residues in contact with ILE 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356C TRP* 3.6 28.0 - - + -
358C ILE* 4.1 10.8 - - + -
375C ALA* 3.1 5.5 - - - +
376C ILE* 2.9 43.6 + - + +
392C LEU 4.3 0.2 - - - -
393C ARG* 1.3 74.6 - - - +
395C TYR* 1.3 66.2 + - - +
396C LEU* 3.9 15.4 + - + -
407C LEU* 3.3 39.3 - - + -
408C SER 3.3 13.2 - - - +
409C LEU* 4.3 9.6 - - + -
490C ILE* 4.7 1.3 - - + -
492C ILE* 4.2 24.0 - - + -
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Residues in contact with TYR 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374C PRO* 3.3 29.8 - - + +
375C ALA* 3.5 8.5 - - + -
393C ARG* 3.1 31.3 + - + -
394C ILE* 1.3 75.4 - - - +
396C LEU* 1.3 63.2 + - - +
397C ASN 3.0 5.5 + - - +
398C GLY* 3.0 29.8 + - - +
399C ASP* 3.6 21.9 + - + -
407C LEU* 3.7 3.3 - - - +
408C SER* 2.8 25.6 + - - +
410C PHE* 3.6 37.2 - + - -
207E ALA* 3.6 13.0 - - + +
209E ASP* 2.5 41.2 + - - -
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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