Contacts of the strand formed by residues 357 - 363 (chain C) in PDB entry 2VZE
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 ILE 357 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315C TYR* 3.6 39.7 - - + -
334C CYS* 3.3 8.7 - - + +
336C THR* 3.6 23.3 - - + -
341C LEU* 3.5 32.2 - - + +
345C THR* 4.4 4.9 - - + +
346C LEU* 3.3 28.6 - - + +
349C TRP* 3.4 42.2 - - + +
355C LEU 4.1 0.2 + - - -
356C ASP* 1.3 71.4 - - - +
358C ARG* 1.3 63.6 - - - +
359C GLU 3.7 2.1 + - - -
378C ILE* 3.5 9.2 - - - +
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Residues in contact with ARG 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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248C TRP* 4.9 1.5 + - - -
249C THR 2.8 33.9 + - - -
332C GLN 4.9 2.6 + - - -
333C ASN* 3.5 31.4 + - - +
334C CYS 2.9 12.0 + - - +
335C VAL* 3.3 21.3 - - + +
336C THR* 3.2 20.4 + - - -
356C ASP* 4.6 12.3 + - + +
357C ILE* 1.3 71.3 - - - +
359C GLU* 1.3 64.6 + - - +
360C SER* 3.9 0.7 + - - -
372C VAL* 3.4 32.7 + - + +
373C SER 3.5 15.4 - - - -
374C LYS* 3.7 28.9 + - - +
376C MET 5.3 0.9 - - - -
378C ILE* 3.6 23.1 - - + -
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Residues in contact with GLU 359 (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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336C THR* 3.6 20.9 - - + -
339C GLU 5.0 0.9 - - - +
340C SER* 3.9 2.6 + - - -
341C LEU* 3.3 45.5 + - + +
357C ILE 3.7 3.8 + - - -
358C ARG* 1.3 74.6 - - - +
360C SER* 1.3 71.9 + - - +
371C MET* 3.8 0.5 - - - +
372C VAL* 3.0 34.6 + - + +
378C ILE* 6.2 0.4 - - - +
381C GLY 4.9 1.7 + - - -
382C TYR 3.4 21.5 + - - +
383C MET* 3.5 24.6 - - + +
458C PHE* 6.0 0.2 - - - +
1571C AMP 3.1 23.1 + - - +
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Residues in contact with SER 360 (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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248C TRP* 3.7 18.3 - - - -
309C MET* 4.2 0.2 - - - +
336C THR 2.7 26.6 + - - +
337C VAL* 3.2 22.3 - - - +
359C GLU* 1.3 74.8 - - - +
361C TYR* 1.3 62.3 + - - +
368C LEU* 3.8 13.6 - - - +
370C CYS 3.4 6.5 - - - -
371C MET* 3.5 19.5 - - - +
383C MET 4.1 1.8 - - - -
1571C AMP 2.8 20.4 + - - -
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Residues in contact with TYR 361 (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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337C VAL* 4.0 5.2 - - - -
360C SER* 1.3 76.5 - - - +
362C GLY* 1.3 64.4 + - - +
368C LEU* 3.8 4.7 - - - +
369C THR* 2.8 36.8 + - + -
370C CYS* 2.8 23.7 + - + +
383C MET* 3.4 47.8 - - + -
410C ILE* 4.1 17.1 - - + +
444C LEU* 3.2 35.9 - - + +
446C ASP* 2.5 38.9 + - - +
458C PHE* 4.6 3.8 - + - -
1571C AMP 3.5 36.1 - + - +
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Residues in contact with GLY 362 (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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337C VAL* 4.3 4.7 - - - +
361C TYR* 1.3 85.4 - - - +
363C GLN* 1.3 60.5 + - - +
367C GLY 3.3 16.2 - - - -
368C LEU* 4.8 0.2 - - - -
369C THR* 3.5 8.7 - - - -
444C LEU* 4.9 0.9 - - - -
1571C AMP 3.3 34.7 + - - +
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Residues in contact with GLN 363 (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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266C ILE* 4.9 3.4 - - - +
362C GLY* 1.3 75.0 - - - +
364C THR* 1.3 61.1 + - - +
365C GLU* 3.6 22.0 - - - +
366C THR* 3.1 17.8 + - - +
367C GLY* 2.8 30.5 + - - -
442C TRP* 3.1 29.6 + - - -
443C LEU 4.3 0.2 - - - +
444C LEU* 2.8 41.0 + - + +
461C ARG* 4.3 1.0 - - - +
472C ARG* 3.9 10.1 - - - +
1571C AMP 3.3 36.1 + - - +
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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