Contacts of the strand formed by residues 389 - 395 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380B ALA* 3.6 11.0 - - + -
381B PHE 3.6 2.9 - - - -
382B TYR* 3.4 41.1 + - + +
387B GLY 3.7 1.2 + - - -
388B TYR* 1.3 72.0 - - - +
390B MET* 1.3 66.9 + - - +
413B VAL* 3.9 3.6 - - - +
414B MET* 2.9 65.5 + - + +
415B LYS 3.5 20.3 + - - +
416B GLY* 3.8 20.3 - - - -
417B PRO* 4.7 4.1 - - + +
419B ASP* 5.1 0.6 + - - -
424B TRP* 6.2 0.2 - - - -
462B ASP* 5.1 6.7 + - - -
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Residues in contact with MET 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352B GLY* 4.8 0.4 - - - -
380B ALA* 3.1 0.5 - - - -
381B PHE* 2.8 63.7 + - + +
382B TYR* 3.5 7.2 - - - -
383B THR* 3.5 45.3 - - + +
388B TYR* 3.8 8.3 - - + +
389B LYS* 1.3 79.1 - - - +
391B CYS* 1.3 58.6 + - - +
411B PHE* 3.4 35.2 - - + -
412B VAL 3.2 11.9 - - - +
413B VAL* 4.8 2.9 - - + -
414B MET* 2.9 16.5 - - - +
426B PHE* 4.2 8.5 - - + -
496B VAL* 3.7 14.6 - - + -
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Residues in contact with CYS 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B PHE* 3.8 26.0 - - - -
378B SER* 3.6 22.2 - - - +
379B PRO 3.7 6.1 - - - +
380B ALA* 4.2 0.7 - - - -
381B PHE* 4.0 4.7 - - - -
390B MET* 1.3 76.5 - - - +
392B LEU* 1.3 71.6 + - - +
411B PHE* 4.3 1.6 - - - -
412B VAL* 2.9 48.3 + - - +
414B MET* 3.6 23.1 - - + -
463B MET* 4.0 7.2 - - - -
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Residues in contact with LEU 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B PHE* 4.3 13.5 - - + -
356B TRP* 4.0 20.4 - - + -
377B PHE* 3.3 4.3 - - - -
378B SER* 2.8 38.2 + - - +
381B PHE* 4.2 8.7 - - + -
391B CYS* 1.3 88.7 - - - +
393B ARG* 1.3 61.8 + - - +
409B LEU* 4.3 5.6 - - + -
410B PHE 3.5 12.8 - - - +
411B PHE* 4.2 13.5 - - + -
412B VAL* 4.6 0.7 - - - -
432B LEU* 4.1 13.0 - - + -
492B ILE* 4.0 25.6 - - + -
493B LYS 5.2 0.2 - - - -
494B ALA* 3.9 31.4 - - + +
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Residues in contact with ARG 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374B PRO* 6.1 0.6 - - - +
375B ALA* 3.7 20.8 - - + +
376B ILE 3.4 8.5 - - - +
377B PHE* 3.0 48.1 - - + -
392B LEU* 1.3 75.8 - - - +
394B ILE* 1.3 61.9 + - - +
395B TYR* 2.8 40.5 + - + -
409B LEU* 3.6 2.2 - - - +
410B PHE* 2.7 46.6 + - + +
412B VAL* 4.1 13.2 - - + +
466B ALA* 4.2 17.7 - - - -
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Residues in contact with ILE 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B TRP* 3.6 27.1 - - + -
358B ILE* 4.2 10.1 - - + -
375B ALA* 3.1 4.4 - - - -
376B ILE* 3.0 40.8 + - + +
392B LEU 4.4 0.2 - - - -
393B ARG* 1.3 76.5 - - - +
395B TYR* 1.3 66.5 + - - +
396B LEU* 3.8 17.2 + - + -
407B LEU* 3.4 39.9 - - + -
408B SER 3.2 14.4 - - - +
409B LEU* 4.2 15.7 - - + -
490B ILE* 4.9 0.9 - - + -
492B ILE* 4.2 17.5 - - + -
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Residues in contact with TYR 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374B PRO* 3.3 34.1 - - + +
375B ALA* 3.7 10.8 - - + -
393B ARG* 2.8 41.8 + - + -
394B ILE* 1.3 78.1 - - - +
396B LEU* 1.3 58.9 + - - +
397B ASN 3.0 8.6 + - - -
398B GLY* 3.0 31.6 + - - +
399B ASP* 3.5 38.1 + - + -
407B LEU* 3.6 2.8 - - - +
408B SER* 2.7 25.8 + - - +
410B PHE* 3.6 31.9 - + - -
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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