Contacts of the helix formed by residues 440 - 452 (chain C) in PDB entry 1JLH
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 440 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26C ARG* 4.6 9.7 - - - +
439C LYS* 1.3 75.9 - - - +
441C THR* 1.3 64.8 + - - +
442C GLU* 3.4 9.5 + - - +
443C GLU* 2.7 41.6 + - - +
444C ALA* 3.0 22.7 + - - +
466C VAL* 4.2 4.5 - - - -
467C PHE 5.0 0.2 - - - -
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Residues in contact with THR 441 (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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440C SER* 1.3 73.5 - - - +
442C GLU* 1.3 59.7 + - - +
444C ALA* 3.2 3.3 + - - +
445C ARG* 2.9 39.4 + - - +
462C LEU* 3.5 26.8 - - + +
463C PRO* 6.2 0.7 - - + -
466C VAL* 3.8 25.5 - - + +
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Residues in contact with GLU 442 (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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440C SER* 3.2 10.0 + - - +
441C THR* 1.3 79.9 - - - +
443C GLU* 1.3 63.3 + - + +
445C ARG* 3.4 19.3 + - - +
446C LYS* 3.0 60.1 + - - +
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Residues in contact with GLU 443 (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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26C ARG* 3.3 16.5 + - - -
437C ARG* 3.2 22.4 + - - -
438C GLY 4.2 0.2 - - - +
439C LYS* 3.2 21.3 - - + +
440C SER* 2.7 39.7 + - - +
442C GLU* 1.3 77.1 - - + +
444C ALA* 1.3 64.1 + - - +
446C LYS* 3.4 12.8 + - + +
447C GLU* 3.2 29.1 + - - +
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Residues in contact with ALA 444 (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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439C LYS* 4.1 9.6 - - + +
440C SER 3.0 13.2 + - - +
441C THR 3.4 8.5 - - - +
443C GLU* 1.3 77.5 - - - +
445C ARG* 1.3 62.4 + - - +
447C GLU* 3.2 8.5 + - - +
448C LEU* 3.0 25.0 + - - +
462C LEU* 3.5 16.8 - - + +
465C LYS* 3.8 29.8 - - + +
466C VAL* 4.3 5.6 - - + -
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Residues in contact with ARG 445 (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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441C THR* 2.9 26.1 + - - +
442C GLU* 3.6 29.3 + - - +
443C GLU 3.4 0.2 - - - -
444C ALA* 1.3 75.5 - - - +
446C LYS* 1.3 57.1 + - - +
448C LEU* 3.0 7.9 + - - +
449C GLN* 2.7 66.5 + - + +
458C LEU* 4.2 15.5 - - + +
462C LEU* 3.4 23.5 - - + +
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Residues in contact with LYS 446 (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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442C GLU* 3.0 50.1 + - + +
443C GLU* 3.6 13.0 - - + +
444C ALA 3.3 0.2 - - - -
445C ARG* 1.3 77.8 - - + +
447C GLU* 1.3 57.9 + - + +
449C GLN* 3.4 17.7 + - - +
450C ALA* 2.9 30.3 + - - +
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Residues in contact with GLU 447 (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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439C LYS* 2.9 37.2 + - - +
443C GLU* 3.2 15.0 + - - +
444C ALA* 3.2 8.6 + - - +
445C ARG 3.1 0.6 - - - -
446C LYS* 1.3 78.2 - - + +
448C LEU* 1.3 54.8 + - + +
450C ALA* 3.3 6.7 + - - +
451C ALA* 2.8 34.6 + - - +
465C LYS* 5.9 3.1 - - - +
519D GLN* 3.1 21.4 - - - +
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Residues in contact with LEU 448 (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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444C ALA 3.0 16.9 + - - +
445C ARG 3.0 6.6 + - - +
447C GLU* 1.3 73.6 - - + +
449C GLN* 1.3 66.0 + - - +
451C ALA* 3.0 16.7 + - + +
452C GLY 3.0 9.9 + - - -
453C LYS* 3.1 33.4 + - + -
458C LEU* 3.9 22.4 - - + +
461C LEU* 3.9 9.2 - - + -
462C LEU* 3.6 44.9 - - + +
465C LYS* 3.7 33.7 - - + +
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Residues in contact with GLN 449 (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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445C ARG* 2.7 41.6 + - + +
446C LYS* 3.6 24.5 + - - +
448C LEU* 1.3 70.8 - - - +
450C ALA* 1.3 58.3 + - - +
452C GLY* 2.8 22.3 + - - -
453C LYS 5.0 2.5 - - - +
458C LEU* 3.7 21.1 - - + +
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Residues in contact with ALA 450 (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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446C LYS 2.9 17.3 + - - +
447C GLU* 3.7 7.0 - - - +
449C GLN* 1.3 76.3 - - - +
451C ALA* 1.3 60.0 + - - +
452C GLY* 3.2 0.6 + - - -
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Residues in contact with ALA 451 (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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447C GLU 2.8 14.5 + - - +
448C LEU* 3.0 20.2 - - + +
449C GLN 2.9 0.2 - - - -
450C ALA* 1.3 78.9 - - - +
452C GLY* 1.3 57.7 - - - +
453C LYS* 3.3 18.2 + - + +
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Residues in contact with GLY 452 (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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449C GLN 2.8 15.0 + - - -
450C ALA 3.2 1.0 - - - -
451C ALA* 1.3 79.7 - - - +
453C LYS* 1.3 67.0 + - - +
454C SER* 3.0 6.8 + - - -
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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