Contacts of the strand formed by residues 353 - 358 (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 VAL 353 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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386B TYR* 4.2 11.7 + - + -
349C THR* 2.8 29.1 + - - +
351C ASP* 3.0 26.6 + - - +
352C GLY* 1.3 81.5 - - - +
354C PHE* 1.3 66.2 + - - +
355C ILE* 5.2 1.3 - - + -
493C LYS* 3.8 29.8 - - - +
494C ALA 3.4 4.3 - - - +
495C ILE* 4.6 15.3 - - + -
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Residues in contact with PHE 354 (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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386B TYR* 3.5 14.8 - - - -
347C ALA* 3.4 27.8 - - + -
349C THR* 4.1 2.2 - - + -
352C GLY 4.2 0.2 - - - -
353C VAL* 1.3 74.8 - - - +
355C ILE* 1.3 68.2 + - - +
356C TRP* 3.5 30.3 - + + -
378C SER* 3.9 16.6 - - - -
379C PRO* 3.7 30.1 - - + -
380C ALA 4.4 3.1 - - - -
381C PHE* 3.6 51.8 - + + -
392C LEU* 4.4 9.6 - - + +
492C ILE 3.8 0.5 - - - +
493C LYS* 3.2 4.9 - - - +
494C ALA* 2.8 38.5 + - + +
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Residues in contact with ILE 355 (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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386B TYR* 3.0 59.2 + - + -
418B ASN* 4.4 9.6 - - - +
421B LEU* 4.5 9.0 - - + -
353C VAL* 5.2 2.2 - - + -
354C PHE* 1.3 85.4 - - - +
356C TRP* 1.3 60.6 + - - +
357C LYS* 3.9 2.1 + - + +
435C LEU* 4.6 9.9 - - + -
491C PHE* 3.9 30.3 - - + -
492C ILE 3.3 7.2 - - - +
493C LYS* 4.0 31.2 - - + +
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Residues in contact with TRP 356 (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* 3.5 18.3 - + + -
355C ILE* 1.3 71.4 - - - +
357C LYS* 1.3 72.8 + - - +
358C ILE* 3.6 29.2 + - + +
376C ILE* 3.5 34.8 - - + -
377C PHE 3.7 7.6 + - - -
378C SER* 3.3 34.4 - - - +
379C PRO* 3.9 19.0 - - + +
392C LEU* 4.2 20.2 - - + -
394C ILE* 3.6 30.1 - - + -
409C LEU* 5.2 0.9 - - + -
490C ILE 3.7 0.2 - - - +
491C PHE* 3.5 2.7 - - - -
492C ILE* 2.6 56.4 + - + +
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Residues in contact with LYS 357 (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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416B GLY 5.3 0.4 + - - -
417B PRO* 2.9 40.1 + - + +
418B ASN* 5.1 2.7 - - - +
355C ILE 3.9 4.0 + - - +
356C TRP* 1.3 80.8 + - - +
358C ILE* 1.3 64.9 + - - +
359C SER* 3.7 22.6 + - - +
489C ALA* 4.3 12.8 - - + -
490C ILE 3.6 6.3 - - - +
491C PHE* 3.6 33.0 - - + -
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Residues in contact with ILE 358 (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* 3.7 56.5 - - + +
357C LYS* 1.3 69.9 - - - +
359C SER* 1.3 69.5 + - - +
361C PHE* 4.4 8.1 - - + +
364C LYS* 3.9 22.4 - - + +
376C ILE* 4.9 7.6 - - + -
394C ILE* 4.1 13.7 - - + -
396C LEU* 5.0 7.9 - - + -
488C ASP 4.1 0.2 - - - +
489C ALA* 3.3 5.7 - - - -
490C ILE* 2.9 59.2 + - + +
492C ILE* 4.3 7.0 - - + -
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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