Contacts of the helix formed by residues 477 - 490 (chain B) in PDB entry 5J3V
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 TYR 477 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437B PRO* 3.3 29.6 + - + +
440B ILE* 3.8 21.9 - - + +
441B PRO* 3.6 31.3 - - + +
444B ILE* 4.2 6.8 - - + +
468B TRP* 3.6 22.7 - + + -
469B VAL* 3.8 23.1 - - + +
472B GLN* 3.5 25.4 - - + -
473B PRO* 3.7 1.7 + - + -
476B THR* 1.3 108.9 + - - +
478B LEU* 1.3 67.8 + - - +
480B PRO* 3.3 3.2 - - - +
481B LEU* 3.1 26.0 + - - +
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Residues in contact with LEU 478 (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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469B VAL* 3.7 18.5 + - + +
470B VAL* 3.9 26.5 - - + -
472B GLN 5.5 0.2 - - - +
473B PRO 4.4 2.8 + - - -
474B PRO* 3.8 22.0 - - + +
477B TYR* 1.3 78.0 - - - +
479B LYS* 1.3 64.9 + - - +
481B LEU* 3.2 3.4 + - - +
482B MET* 3.1 33.6 + - + +
507B LEU* 4.1 23.8 - - + -
511B ALA* 4.7 6.1 - - + -
514B GLU* 3.3 47.3 - - + +
515B LEU* 5.2 3.6 - - + -
518B TYR* 5.3 4.3 - - + -
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Residues in contact with LYS 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B PRO 3.3 17.6 + - - +
475B ASP* 4.1 20.0 - - + +
478B LEU* 1.3 81.2 - - - +
480B PRO* 1.4 65.2 - - + +
482B MET* 3.6 9.2 - - + +
483B THR* 2.6 40.3 + - - +
518B TYR* 3.3 39.4 - - + +
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Residues in contact with PRO 480 (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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444B ILE* 4.3 18.6 - - + -
475B ASP 3.8 10.8 - - - +
476B THR 3.5 19.3 - - - +
477B TYR 3.3 15.9 - - - +
479B LYS* 1.4 95.9 - - + +
481B LEU* 1.3 60.6 + - - +
483B THR* 3.7 4.9 - - - +
484B GLU* 3.1 29.7 + - + +
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Residues in contact with LEU 481 (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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440B ILE* 5.7 1.6 - - + -
444B ILE* 4.0 16.8 - - + +
447B LEU* 4.6 2.0 - - + -
462B LEU* 3.6 53.8 - - + +
469B VAL* 3.9 31.4 - - + -
477B TYR 3.1 18.2 + - - +
478B LEU 3.2 3.6 + - - +
480B PRO* 1.3 78.3 - - - +
482B MET* 1.3 58.9 + - - +
484B GLU* 3.4 2.9 + - - +
485B LEU* 3.0 40.6 + - + +
507B LEU* 4.0 24.9 - - + -
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Residues in contact with MET 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B LEU* 3.1 20.6 + - + +
479B LYS* 3.6 9.6 - - - +
481B LEU* 1.3 77.0 - - - +
483B THR* 1.3 64.8 + - - +
485B LEU* 3.5 9.3 - - - +
486B LEU* 2.9 52.2 + - + +
504B PHE* 3.8 13.4 - - + -
507B LEU* 3.9 15.3 - - + -
515B LEU* 4.3 17.5 - - + -
518B TYR* 4.1 35.7 - - + -
521B TYR* 4.4 7.4 - - + -
522B ILE* 3.6 31.9 - - + -
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Residues in contact with THR 483 (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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479B LYS* 2.6 31.3 + - - +
480B PRO* 3.7 6.7 - - - -
481B LEU 3.2 0.8 - - - -
482B MET* 1.3 84.2 - - - +
484B GLU* 1.3 63.7 + - + +
486B LEU* 3.5 9.0 + - - +
487B LYS* 3.5 25.2 + - + +
518B TYR* 6.1 0.9 - - - -
521B TYR* 3.8 32.7 + - + +
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Residues in contact with GLU 484 (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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444B ILE* 3.8 25.2 - - + +
445B GLN* 5.0 6.1 - - - +
447B LEU* 3.6 23.1 - - + +
448B SER* 3.5 23.5 + - - -
480B PRO* 3.1 17.9 + - + +
481B LEU 3.8 0.4 - - - +
483B THR* 1.3 79.7 - - + +
485B LEU* 1.3 63.1 + - - +
487B LYS* 3.3 32.3 + - - +
488B ARG* 3.2 32.6 + - - +
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Residues in contact with LEU 485 (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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447B LEU* 4.5 10.8 - - + -
459B CYS* 3.9 37.2 - - + +
462B LEU* 5.4 2.9 - - + -
463B SER* 6.4 0.2 - - - -
481B LEU* 3.0 31.9 + - + +
482B MET 3.5 5.6 - - - +
483B THR 3.2 0.2 - - - -
484B GLU* 1.3 75.2 - - - +
486B LEU* 1.3 58.5 + - - +
488B ARG* 2.9 19.4 + - - +
489B ILE* 2.9 19.2 + - - +
500B ALA* 4.1 12.1 - - + +
503B ALA* 4.6 7.0 - - + +
504B PHE* 3.9 28.9 - - + +
507B LEU* 4.1 24.9 - - + -
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Residues in contact with LEU 486 (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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482B MET* 2.9 33.8 + - + +
483B THR 3.8 4.9 - - - +
484B GLU 3.4 0.4 - - - -
485B LEU* 1.3 76.5 - - - +
487B LYS* 1.3 61.6 + - - +
489B ILE* 3.3 27.6 + - + +
490B LEU* 3.6 4.6 + - - +
504B PHE* 3.6 25.4 - - + -
521B TYR* 3.5 39.0 - - + +
522B ILE* 3.8 21.3 - - + +
525B THR* 3.3 42.8 - - + +
526B LEU* 4.9 1.3 - - + -
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Residues in contact with LYS 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B THR* 3.5 24.1 + - + +
484B GLU* 3.3 36.7 + - - +
485B LEU 3.2 0.8 - - - -
486B LEU* 1.3 78.0 - - - +
488B ARG* 1.3 84.3 + - - +
490B LEU* 3.4 17.8 + - - +
491B ASP* 3.4 6.4 + - - -
521B TYR* 4.5 11.9 - - - +
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Residues in contact with ARG 488 (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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447B LEU* 2.7 42.6 + - + +
448B SER* 4.1 17.4 + - - +
455B ARG* 4.2 8.4 - - + +
459B CYS* 4.7 2.7 - - - -
484B GLU* 3.2 22.3 + - - +
485B LEU* 2.9 10.6 + - - +
487B LYS* 1.3 108.1 + - - +
489B ILE* 1.3 64.2 + - - +
490B LEU 3.2 1.6 - - - -
491B ASP* 3.2 41.5 + - - +
496B VAL* 3.7 19.4 - - + +
497B GLN* 3.8 1.9 - - - -
500B ALA* 3.5 23.0 - - + +
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Residues in contact with ILE 489 (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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485B LEU 2.9 17.3 + - - +
486B LEU* 3.4 35.7 - - + +
488B ARG* 1.3 78.4 - - - +
490B LEU* 1.3 56.0 + - - +
491B ASP 3.2 0.7 - - - -
497B GLN* 3.4 14.5 - - - +
500B ALA* 4.3 4.9 - - - -
501B CYS* 4.1 26.2 - - + +
504B PHE* 4.2 19.7 - - + -
525B THR* 4.6 4.9 - - + -
526B LEU* 4.0 20.4 - - + -
529B ALA* 4.2 17.3 - - + -
533B TYR* 3.0 40.1 + - - +
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Residues in contact with LEU 490 (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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486B LEU 3.6 3.3 + - - +
487B LYS* 3.4 13.4 + - - +
488B ARG 3.2 0.2 - - - -
489B ILE* 1.3 77.0 - - - +
491B ASP* 1.3 63.9 + - - +
492B SER 3.7 0.3 + - - -
497B GLN* 4.6 2.5 - - - +
525B THR* 3.8 30.5 - - + +
528B PHE* 3.6 38.8 - - + -
529B ALA* 3.7 29.2 - - + -
532B LYS* 3.2 26.8 + - + +
533B TYR* 5.9 0.4 - - + -
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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