Contacts of the helix formed by residues 364 - 374 (chain C) in PDB entry 3A4S
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 LEU 364 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343C LEU* 4.9 4.5 - - + -
358C LEU* 4.0 17.7 - - + -
363C PRO* 1.3 75.2 - - - +
365C LYS* 1.3 65.4 + - - +
366C VAL 3.1 2.9 - - - -
367C LEU* 3.2 13.4 + - + +
368C MET* 3.0 43.9 + - + +
391C LEU* 3.6 24.5 - - + -
393C GLY* 3.2 4.0 + - - -
395C GLU* 3.0 31.4 + - + +
396C LEU* 5.0 1.3 - - - -
397C PRO* 5.0 2.0 - - + -
400C LEU* 3.5 30.1 - - + -
402C LEU* 4.0 22.0 - - + -
408C ILE* 5.6 2.2 - - + -
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Residues in contact with LYS 365 (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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363C PRO* 3.5 4.9 - - + -
364C LEU* 1.3 77.8 - - - +
366C VAL* 1.3 57.6 + - - +
368C MET* 3.5 9.9 + - + +
369C SER* 2.8 50.5 + - - +
392C SER 5.3 3.1 - - - +
393C GLY* 3.1 27.8 + - - +
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Residues in contact with VAL 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358C LEU* 3.6 15.3 - - + -
362C SER* 3.7 15.3 - - - +
363C PRO* 3.3 30.5 - - + +
365C LYS* 1.3 79.7 - - - +
367C LEU* 1.3 63.2 + - - +
369C SER* 3.6 5.5 + - - -
370C HIS* 3.0 29.6 + - + +
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Residues in contact with LEU 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C LEU* 4.0 34.5 - - + -
345C VAL* 4.0 23.8 - - + -
356C ILE* 3.2 38.8 - - + +
358C LEU* 3.8 26.2 - - + -
364C LEU* 3.2 16.4 + - + +
366C VAL* 1.3 78.6 - - - +
368C MET* 1.3 76.4 + - + +
370C HIS* 3.3 5.7 + - - -
371C TYR* 3.0 18.0 + - - +
384C PHE* 4.9 1.8 - - + -
391C LEU* 5.9 0.9 - - + -
408C ILE* 4.8 13.5 - - + -
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Residues in contact with MET 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C LEU* 3.0 26.9 + - + +
365C LYS* 3.8 11.7 - - + +
367C LEU* 1.3 82.4 - - + +
369C SER* 1.3 62.1 + - - +
371C TYR* 3.0 13.5 + - - +
372C GLU* 3.3 21.6 + - - +
382C LEU 5.7 0.4 - - - +
384C PHE* 3.8 45.4 - - + -
391C LEU* 3.4 39.5 - - + +
392C SER 4.0 5.2 - - - +
393C GLY* 3.5 31.9 - - - +
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Residues in contact with SER 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C LYS* 2.8 41.4 + - - +
366C VAL* 4.0 5.6 - - - -
368C MET* 1.3 73.5 - - - +
370C HIS* 1.3 66.5 + - - +
372C GLU* 3.1 15.1 + - - +
373C GLU* 3.1 22.9 + - - +
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Residues in contact with HIS 370 (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 LEU* 4.1 7.7 - - + +
355C GLU 5.9 0.4 - - - -
356C ILE* 3.6 38.1 - - + +
366C VAL* 3.0 21.5 + - + +
367C LEU* 3.4 8.3 - - - +
368C MET 3.2 0.2 - - - -
369C SER* 1.3 77.8 - - - +
371C TYR* 1.3 57.1 + - - +
372C GLU 3.1 3.9 + - - -
373C GLU* 3.4 8.7 + - - +
374C ALA* 3.3 37.6 + - + +
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Residues in contact with TYR 371 (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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345C VAL* 3.7 23.3 - - + +
347C GLY 4.4 0.2 + - - -
352C GLN* 3.1 29.8 + - - +
354C LEU* 3.5 34.5 - - + -
356C ILE* 4.1 4.7 - - + -
367C LEU 3.0 14.2 + - - +
368C MET 3.0 9.6 + - - +
370C HIS* 1.3 75.9 - - - +
372C GLU* 1.3 57.6 + - - +
375C MET* 2.9 46.7 - - + +
377C LEU* 5.1 4.8 - - + +
382C LEU* 4.4 9.1 - - + +
384C PHE* 3.7 24.5 - + + -
410C VAL* 3.3 37.9 - - + +
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Residues in contact with GLU 372 (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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368C MET* 3.3 20.8 - - - +
369C SER* 3.1 11.5 + - - +
370C HIS 3.1 0.8 - - - -
371C TYR* 1.3 79.8 - - - +
373C GLU* 1.3 55.5 + - - +
375C MET* 3.8 0.9 - - - -
376C GLY* 2.8 28.9 + - - -
377C LEU* 3.0 17.0 + - - +
378C SER* 3.8 34.6 + - - +
379C GLY 4.5 2.1 + - - -
380C HIS 4.5 5.6 - - - +
382C LEU* 3.4 34.5 - - + +
384C PHE* 4.9 2.6 - - - -
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Residues in contact with GLU 373 (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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369C SER 3.1 15.0 + - - +
370C HIS* 3.9 11.8 + - - +
372C GLU* 1.3 73.5 - - - +
374C ALA* 1.3 84.1 + - - +
375C MET 2.8 10.1 + - - -
376C GLY* 3.1 12.1 + - - -
378C SER* 4.7 5.3 + - - -
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Residues in contact with ALA 374 (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 LEU* 4.3 12.2 - - + +
370C HIS* 3.3 26.9 + - + +
373C GLU* 1.3 91.9 + - - +
375C MET* 1.3 67.6 + - - +
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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