Contacts of the helix formed by residues 445 - 457 (chain B) in PDB entry 1JSC
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 SER 445 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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444B ARG* 1.3 76.4 - - - +
446B GLU* 1.3 68.8 + - - +
447B TRP 3.1 2.2 - - - +
448B PHE* 3.6 8.8 + - - +
449B ALA* 3.3 23.0 + - - +
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Residues in contact with GLU 446 (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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300B LYS* 5.9 4.3 + - - +
445B SER* 1.3 79.8 + - - +
447B TRP* 1.3 63.5 + - - +
449B ALA* 4.1 6.9 - - + +
450B GLN* 3.3 23.6 + - + +
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Residues in contact with TRP 447 (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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300B LYS* 3.2 22.0 - - + +
302B PRO* 2.9 40.1 + - + -
303B VAL* 4.9 2.5 - - + -
328B GLN 4.9 5.2 - - - -
330B PRO* 3.9 19.4 - - + +
363B ALA* 4.1 9.0 - - + -
366B ASN* 2.8 46.9 - - + -
367B ALA* 3.8 20.9 - - + -
368B ASP* 5.2 0.2 - - - -
444B ARG* 4.7 13.5 - - + -
445B SER 3.1 0.8 - - - +
446B GLU* 1.3 76.3 - - - +
448B PHE* 1.3 75.1 + + + +
450B GLN* 3.4 15.1 + - + -
451B ILE* 3.2 37.3 + - + +
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Residues in contact with PHE 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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328B GLN* 4.0 29.8 - - + -
330B PRO* 5.4 7.2 - - + -
346B PRO* 4.8 18.2 - - + -
347B LYS* 3.9 31.4 - - + -
444B ARG* 4.1 32.1 - - + -
445B SER* 3.6 5.8 + - - +
447B TRP* 1.3 84.0 - + + +
449B ALA* 1.3 57.6 + - - +
451B ILE* 2.8 9.3 + - + -
452B ASN* 2.6 54.2 + - - +
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Residues in contact with ALA 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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445B SER 3.3 16.4 + - - +
446B GLU* 4.2 7.2 - - + +
448B PHE* 1.3 77.8 - - - +
450B GLN* 1.3 62.7 + - - +
452B ASN* 3.9 7.7 - - - +
453B LYS* 3.2 24.6 + - - +
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Residues in contact with GLN 450 (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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366B ASN* 5.1 11.3 - - + +
446B GLU* 3.3 19.8 + - + +
447B TRP* 3.5 23.8 - - + +
448B PHE 3.1 0.2 - - - -
449B ALA* 1.3 79.7 - - - +
451B ILE* 1.3 61.9 + - + +
453B LYS* 3.9 4.7 - - - +
454B TRP* 3.4 19.7 + - - +
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Residues in contact with ILE 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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330B PRO* 4.1 20.4 - - + -
349B LEU* 3.8 26.9 - - + -
359B THR* 3.7 26.5 - - + -
363B ALA* 4.4 14.6 - - + -
447B TRP* 3.2 34.7 + - + +
448B PHE* 2.8 10.2 + - + +
450B GLN* 1.3 75.2 - - + +
452B ASN* 1.3 55.8 + - - +
453B LYS 2.9 1.6 - - - -
454B TRP* 2.6 29.8 + - + +
455B LYS* 2.6 20.1 + - + -
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Residues in contact with ASN 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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346B PRO 5.3 4.3 - - - +
448B PHE* 2.6 55.7 + - - +
449B ALA* 3.5 7.5 - - - +
451B ILE* 1.3 74.9 - - - +
453B LYS* 1.3 51.7 + - - +
455B LYS* 4.3 6.7 - - - -
456B LYS* 2.7 37.5 + - - +
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Residues in contact with LYS 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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449B ALA 3.2 16.1 + - - +
450B GLN* 3.9 7.2 - - - +
451B ILE 2.7 4.6 + - - -
452B ASN* 1.3 74.5 - - - +
454B TRP* 1.3 65.5 + - - +
456B LYS* 3.3 6.1 + - - +
457B GLU* 3.1 24.3 + - - +
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Residues in contact with TRP 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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359B THR* 4.0 10.3 + - + -
362B LEU* 4.3 25.0 - - + +
450B GLN* 3.4 14.2 + - + +
451B ILE* 2.6 16.5 + - - +
453B LYS* 1.3 76.5 - - - +
455B LYS* 1.3 57.2 + - - +
457B GLU* 3.6 7.9 + - - +
458B TYR* 3.1 30.7 - - - -
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Residues in contact with LYS 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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359B THR* 3.2 30.9 + - + +
451B ILE* 2.6 20.6 + - + +
452B ASN* 3.8 8.3 - - - +
454B TRP* 1.3 68.8 - - - +
456B LYS* 1.3 53.2 + - - +
457B GLU 2.7 5.2 + - - -
458B TYR 2.7 34.1 + - - -
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Residues in contact with LYS 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 ASN 2.7 24.2 + - - +
453B LYS* 3.3 6.7 + - - +
455B LYS* 1.3 71.8 - - - +
457B GLU* 1.3 58.1 + - - +
458B TYR 3.4 1.4 - - - -
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Residues in contact with GLU 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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453B LYS 3.1 14.3 + - - +
454B TRP* 3.6 5.9 - - - +
455B LYS 2.7 1.2 + - - -
456B LYS* 1.3 80.2 - - - +
458B TYR* 1.3 96.9 + - + +
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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