Contacts of the strand formed by residues 353 - 359 (chain C) in PDB entry 3P9K
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 ALA 353 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180C HIS* 5.5 4.5 - - + -
184C ILE* 4.1 30.3 - - + -
293C VAL* 4.4 10.3 - - + -
294C GLN 3.8 5.4 - - - -
295C CYS* 5.2 1.8 - - - -
348C TYR* 3.7 3.5 - - - -
349C ILE* 2.8 28.6 + - + +
350C TYR 2.9 18.2 + - - +
351C ALA 3.0 2.4 + - - +
352C ASN* 1.3 78.6 - - - +
354C TRP* 1.3 60.4 + - - +
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Residues in contact with TRP 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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292C LEU 3.3 1.0 - - - +
293C VAL* 3.1 26.8 - - - +
294C GLN 2.8 17.3 + - - +
296C ILE* 3.8 46.2 + - + +
329C GLU* 5.6 4.0 - - - -
346C SER* 4.0 25.1 - - - -
347C THR 3.5 8.3 - - - -
348C TYR* 3.1 57.6 - + + -
349C ILE* 4.1 3.1 - - - -
352C ASN* 3.6 17.4 + - - +
353C ALA* 1.3 75.7 - - - +
355C ALA* 1.3 60.3 + - - +
356C ILE* 3.8 8.0 + - + +
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Residues in contact with ALA 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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188C LEU* 4.3 10.3 - - + -
192C TYR* 4.0 26.9 - - + -
291C VAL* 4.7 6.3 - - + -
292C LEU 3.2 6.7 - - - +
293C VAL* 4.7 1.6 - - + +
345C LYS 3.5 2.6 - - - +
346C SER* 3.5 1.9 - - - -
347C THR* 2.8 40.6 + - - +
349C ILE* 3.8 18.1 - - + +
354C TRP* 1.3 71.8 - - - +
356C ILE* 1.3 61.9 + - - +
357C GLU 3.9 0.4 + - - -
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Residues in contact with ILE 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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290C VAL 3.6 1.6 - - - +
291C VAL* 3.5 2.5 - - - -
292C LEU* 2.7 48.6 + - + +
294C GLN* 4.5 10.8 - - + -
296C ILE* 3.7 30.1 - - + -
329C GLU* 6.2 0.4 - - + -
332C PHE* 3.9 35.4 - - + -
344C VAL* 4.0 11.0 - - + -
345C LYS 3.6 1.8 - - - +
346C SER* 3.8 20.0 - - - +
354C TRP* 4.2 9.6 - - + +
355C ALA* 1.3 75.9 - - - +
357C GLU* 1.3 62.4 + - - +
358C PHE* 3.7 25.4 + - + -
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Residues in contact with GLU 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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192C TYR* 2.4 47.3 + - + +
194C GLY* 4.2 2.1 - - - -
289C LYS* 3.5 29.0 + - + +
290C VAL 3.5 2.0 - - - -
291C VAL* 3.7 11.9 - - + -
343C GLY 3.4 1.2 - - - +
344C VAL* 3.1 8.5 - - - +
345C LYS* 2.9 68.9 + - + +
355C ALA 3.9 0.4 + - - -
356C ILE* 1.3 72.7 - - - +
358C PHE* 1.3 63.7 + - - +
359C THR* 3.9 13.1 - - + +
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Residues in contact with PHE 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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265C LEU* 4.9 0.4 - - + -
277C LEU* 3.9 28.7 - - + -
289C LYS* 3.2 6.4 - - - +
290C VAL* 2.8 46.4 + - + +
292C LEU* 3.8 24.2 - - + -
332C PHE* 3.3 28.5 - + + -
335C LEU* 5.1 0.4 - - + -
336C ALA* 3.5 33.0 - - + -
341C PHE* 3.8 26.7 - + + -
343C GLY 3.2 2.9 - - - -
344C VAL* 3.9 11.4 - - + -
356C ILE* 3.7 23.6 - - + -
357C GLU* 1.3 80.1 - - - +
359C THR* 1.3 61.2 + - - +
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Residues in contact with THR 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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287C HIS 6.1 0.4 - - - +
288C GLY 5.1 0.9 - - - +
289C LYS* 4.0 16.6 - - + -
341C PHE* 3.6 4.5 - - - -
342C THR 2.9 6.9 + - - -
343C GLY* 2.6 58.3 + - - +
357C GLU* 3.9 23.1 - - + +
358C PHE* 1.3 78.8 - - - +
360C LYS* 1.3 65.5 + - - +
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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