Contacts of the helix formed by residues 447 - 457 (chain B) in PDB entry 5JHQ
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 ARG 447 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410B CYS 3.5 17.0 - - - +
411B SER 3.0 22.8 + - - +
412B TYR* 3.6 27.3 + - - +
413B GLY* 3.7 10.5 + - - -
442B ALA* 3.0 19.9 + - + +
445B LYS* 3.3 20.0 + - - +
446B ASN* 1.3 71.8 + - - +
448B VAL* 1.3 64.9 + - - +
449B GLU 3.2 3.3 + - - -
450B VAL* 3.3 20.8 + - + -
451B CYS* 3.0 26.2 + - - -
269C LEU 4.1 6.3 + - - -
270C CYS* 2.6 44.5 + - - +
304C HIS* 5.9 4.4 + - - -
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Residues in contact with VAL 448 (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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446B ASN* 3.2 31.1 + - - +
447B ARG* 1.3 71.8 - - - +
449B GLU* 1.3 64.1 + - - +
451B CYS* 3.6 2.6 + - - +
452B SER* 3.1 25.3 + - - -
477B THR* 6.1 0.7 - - + -
480B LEU* 4.1 18.6 - - + +
483B ARG* 3.4 41.0 + - - +
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Residues in contact with GLU 449 (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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415B TYR* 3.4 34.0 - - + -
447B ARG 3.2 0.6 - - - -
448B VAL* 1.3 84.1 - - - +
450B VAL* 1.3 61.0 + - + +
452B SER* 3.5 18.1 + - - -
453B LEU 3.1 19.2 + - - -
483B ARG* 3.7 17.7 + - - -
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Residues in contact with VAL 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B CYS* 3.8 37.2 - - + -
413B GLY* 3.9 33.2 - - - +
414B HIS 4.2 2.7 - - - +
415B TYR* 4.3 18.2 - - + +
418B THR* 4.0 12.3 - - + -
442B ALA* 4.3 2.2 - - + -
447B ARG* 3.3 14.3 + - + -
449B GLU* 1.3 75.6 - - + +
451B CYS* 1.3 61.1 + - - +
453B LEU* 3.3 5.5 + - - +
454B LEU* 2.8 35.4 + - + +
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Residues in contact with CYS 451 (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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439B LEU* 3.7 24.9 - - + -
442B ALA* 3.7 4.3 - - - -
443B ALA* 3.7 37.0 - - - -
447B ARG 3.0 26.7 + - - +
448B VAL 3.6 5.6 - - - +
450B VAL* 1.3 74.2 - - - +
452B SER* 1.3 65.6 + - - +
454B LEU* 3.2 3.1 + - - +
455B LEU* 2.9 30.6 + - - +
480B LEU* 4.3 10.1 - - + -
483B ARG* 5.9 0.7 - - - -
484B LEU* 3.8 15.0 - - + -
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Residues in contact with SER 452 (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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448B VAL 3.1 15.4 + - - -
449B GLU* 3.5 16.6 + - - -
451B CYS* 1.3 80.5 - - - +
453B LEU* 1.3 61.2 + - - +
455B LEU* 3.6 3.1 + - - +
456B SER* 3.4 19.1 + - - -
483B ARG* 3.7 14.2 + - - +
487B GLU* 3.1 40.0 + - - +
491B HIS* 4.5 0.2 + - - -
519B PRO* 4.9 9.9 - - - +
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Residues in contact with LEU 453 (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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415B TYR* 3.6 36.3 - - + +
418B THR* 3.8 26.5 - - + -
419B GLU* 3.9 36.3 - - + +
422B LEU* 4.1 8.5 - - + -
449B GLU 3.1 11.2 + - - +
450B VAL* 3.5 7.9 - - - +
451B CYS 3.2 0.2 - - - -
452B SER* 1.3 77.0 - - - +
454B LEU* 1.3 64.7 + - - +
456B SER* 2.5 24.4 + - - +
457B HIS* 3.3 30.0 + - + +
520B GLN* 5.2 6.1 - - - +
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Residues in contact with LEU 454 (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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406B LEU* 4.5 5.6 - - + -
410B CYS* 3.8 30.5 - - - -
418B THR* 4.5 9.9 - - + -
422B LEU* 4.5 7.2 - - + -
428B VAL* 3.4 25.5 - - + +
438B PRO* 4.0 9.6 - - + +
439B LEU* 3.9 31.9 - - + +
442B ALA* 4.2 5.2 - - + -
450B VAL* 2.8 32.7 + - + +
451B CYS* 3.7 3.4 - - - +
453B LEU* 1.3 73.7 - - - +
455B LEU* 1.3 63.6 + - - +
457B HIS* 3.0 14.3 + - - +
458B GLY 3.3 0.9 + - - -
459B ALA* 3.0 27.4 + - + +
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Residues in contact with LEU 455 (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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439B LEU* 3.8 20.9 - - + -
451B CYS 2.9 24.3 + - - +
452B SER* 3.7 4.7 - - - +
453B LEU 3.3 0.2 - - - -
454B LEU* 1.3 75.9 - - - +
456B SER* 1.3 58.2 + - - +
458B GLY* 3.1 18.7 + - - -
459B ALA* 3.6 23.7 + - - +
461B PRO* 3.9 17.5 - - + -
483B ARG* 4.5 1.3 - - - +
484B LEU* 3.7 27.8 - - + +
487B GLU* 3.6 29.8 - - + +
488B PHE* 4.2 10.9 - - + -
491B HIS* 3.5 25.1 - - + +
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Residues in contact with SER 456 (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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452B SER 3.4 7.2 + - - -
453B LEU* 2.5 30.7 + - - +
455B LEU* 1.3 79.4 - - - +
457B HIS* 1.3 64.5 + - - +
458B GLY 3.2 2.6 + - - -
491B HIS* 3.3 33.2 + - - +
518B GLN* 4.5 17.1 + - - -
519B PRO* 5.1 4.4 - - - +
520B GLN* 4.6 12.3 + - - -
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Residues in contact with HIS 457 (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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419B GLU* 5.2 8.2 + - + +
422B LEU* 3.7 41.9 + - + +
423B LYS* 5.1 2.5 - - - -
428B VAL* 3.5 25.7 - - + +
453B LEU* 3.3 33.3 + - + +
454B LEU 3.0 10.4 + - - +
456B SER* 1.3 80.5 - - - +
458B GLY* 1.3 56.5 + - - +
459B ALA 3.6 0.2 - - - -
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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