Contacts of the helix formed by residues 451 - 466 (chain A) in PDB entry 1J1V
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 451 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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447A LEU* 2.7 23.7 + - - +
448A ARG 4.6 1.6 - - - -
449A GLU 3.6 1.2 - - - -
450A GLU* 1.3 77.3 - - - +
452A HIS* 1.3 59.7 + - - +
453A ASP* 3.2 9.2 + - - +
454A ILE* 3.0 30.3 + - - +
455A LYS* 2.9 27.0 + - - +
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Residues in contact with HIS 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450A GLU 4.3 0.6 - - - -
451A SER* 1.3 72.5 - - - +
453A ASP* 1.3 62.3 + - - +
455A LYS* 3.4 27.1 + - + +
456A GLU* 2.9 34.0 + - - +
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Residues in contact with ASP 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451A SER* 3.1 7.0 + - - +
452A HIS* 1.3 79.7 - - - +
454A ILE* 1.3 63.0 + - + +
456A GLU* 3.2 13.8 + - - +
457A ASP* 2.9 39.2 + - - +
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Residues in contact with ILE 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A TYR* 5.3 2.5 - - + +
405A ARG* 5.0 11.9 - - + +
409A MSE 3.7 21.3 - - + -
444A ILE* 4.7 8.7 - - + +
447A LEU* 3.9 37.5 - - + +
448A ARG* 4.2 10.1 - - + +
451A SER* 3.0 26.9 + - - +
453A ASP* 1.3 77.2 - - + +
455A LYS* 1.3 66.0 + - - +
457A ASP* 3.1 15.1 + - - +
458A PHE* 2.9 23.9 + - - +
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Residues in contact with LYS 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448A ARG* 3.0 57.0 + - - +
449A GLU* 5.0 7.2 + - - +
451A SER 2.9 15.9 + - - +
452A HIS* 3.5 26.4 + - + +
453A ASP 3.2 0.2 - - - -
454A ILE* 1.3 78.0 - - - +
456A GLU* 1.3 59.9 + - - +
458A PHE* 3.6 3.6 - - - +
459A SER* 3.3 20.5 + - - -
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Residues in contact with GLU 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452A HIS* 2.9 20.7 + - - +
453A ASP* 3.4 14.5 - - - +
454A ILE 3.1 0.2 - - - -
455A LYS* 1.3 75.0 - - + +
457A ASP* 1.3 61.6 + - - +
458A PHE 3.1 1.3 - - - -
459A SER* 3.2 5.1 + - - -
460A ASN* 2.7 50.8 + - - +
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Residues in contact with ASP 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A TYR* 2.7 37.2 + - + -
387A TYR* 3.2 36.1 + - - +
409A MSE 4.1 3.8 - - + -
453A ASP* 2.9 26.3 + - - +
454A ILE* 3.7 14.2 - - - +
456A GLU* 1.3 78.3 - - - +
458A PHE* 1.3 57.9 + - - +
460A ASN* 3.8 0.2 - - - +
461A LEU* 2.9 38.2 + - + +
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Residues in contact with PHE 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409A MSE 3.9 25.2 - - + +
412A ALA* 5.4 2.7 - - + -
413A LEU* 3.9 18.6 - - + -
416A GLU* 4.5 25.8 - - + -
444A ILE* 4.5 10.3 - - + -
448A ARG* 3.4 49.6 - - + -
454A ILE 2.9 15.7 + - - +
455A LYS 3.6 5.2 - - - +
457A ASP* 1.3 78.6 - - - +
459A SER* 1.3 65.2 + - - +
461A LEU* 3.9 2.2 - - - +
462A ILE* 3.1 51.1 + - + +
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Residues in contact with SER 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455A LYS* 3.3 11.0 + - - -
456A GLU* 3.2 10.2 + - - -
458A PHE* 1.3 80.7 - - - +
460A ASN* 1.3 69.1 + - - +
462A ILE* 3.2 6.4 + - - +
463A ARG* 2.9 24.5 + - - +
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Residues in contact with ASN 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A TYR* 3.0 36.3 + - + +
456A GLU* 2.7 40.4 + - - +
457A ASP 3.8 0.9 - - - +
459A SER* 1.3 75.7 + - - +
461A LEU* 1.3 61.7 + - - +
463A ARG* 3.2 9.4 - - - +
464A THR* 3.1 27.0 + - - -
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Residues in contact with LEU 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A THR* 4.0 21.3 - - + -
383A VAL* 4.1 13.9 - - + -
386A TYR* 3.7 37.7 - - + -
387A TYR* 4.3 11.9 - - + +
409A MSE 3.6 32.3 - - + -
413A LEU* 3.7 20.9 - - + -
457A ASP 2.9 22.8 + - - +
458A PHE 3.9 2.2 - - - +
460A ASN* 1.3 74.7 - - - +
462A ILE* 1.3 58.3 + - - +
464A THR* 3.2 5.3 + - - +
465A LEU* 2.8 35.0 + - + +
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Residues in contact with ILE 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A LEU* 3.7 17.5 - - + -
416A GLU* 5.8 0.9 - - + -
417A LEU* 4.1 21.1 - - + -
458A PHE* 3.1 57.0 + - + +
459A SER* 3.8 5.4 - - - +
461A LEU* 1.3 75.9 - - - +
463A ARG* 1.3 64.5 + - - +
465A LEU* 4.1 5.1 - - - +
466A SER* 2.9 37.7 + - - +
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Residues in contact with ARG 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459A SER 2.9 13.5 + - - +
460A ASN* 3.2 16.4 - - - +
462A ILE* 1.3 78.5 - - - +
464A THR* 1.3 61.1 + - - +
466A SER* 3.8 5.5 + - - -
467A SER* 2.9 24.2 + - - +
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Residues in contact with THR 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A THR* 3.9 26.4 - - + +
386A TYR* 6.0 1.9 - - - -
460A ASN 3.1 12.7 + - - -
461A LEU* 3.2 9.0 + - - +
463A ARG* 1.3 80.9 - - - +
465A LEU* 1.3 63.8 + - - +
467A SER* 3.1 24.8 + - - -
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Residues in contact with LEU 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A VAL* 3.8 22.3 - - + +
378A ASN* 3.6 18.6 - - - +
379A ILE* 3.9 28.7 - - + +
382A THR* 3.4 36.6 - - + +
383A VAL* 5.4 0.7 - - + -
413A LEU* 3.9 18.2 - - + -
417A LEU* 3.3 35.2 - - + -
461A LEU* 2.8 25.5 + - + +
462A ILE 4.1 1.1 - - - +
464A THR* 1.3 73.0 - - + +
466A SER* 1.3 58.4 + - - +
467A SER* 3.3 3.3 + - - +
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Residues in contact with SER 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A VAL* 5.0 7.2 - - - -
417A LEU* 6.1 3.1 - - - -
462A ILE* 2.9 29.0 + - - +
463A ARG* 3.8 5.5 + - - -
465A LEU* 1.3 76.1 - - - +
467A SER* 1.3 63.9 + - - +
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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