Contacts of the helix formed by residues 470 - 488 (chain B) in PDB entry 2R8J
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 470 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420B CYS* 3.5 13.1 - - - -
424B THR* 4.1 24.6 + - - +
468B PHE* 4.7 11.9 - - - -
469B GLN* 1.3 86.5 - - - +
471B HIS* 1.3 72.6 + - - +
473B LEU* 3.0 15.0 + - - +
474B LEU 3.1 9.9 + - - -
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Residues in contact with HIS 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B PHE* 5.6 5.2 - - + -
469B GLN 2.7 5.0 + - - +
470B SER* 1.3 83.0 + - - +
472B GLU* 1.3 78.4 + - + +
473B LEU 3.1 4.5 + - - -
474B LEU* 3.2 22.0 + - + +
475B LYS* 3.2 45.7 + - + +
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Residues in contact with GLU 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B VAL* 3.6 17.0 - - - +
462B ALA 4.1 10.2 - - - +
463B TYR* 4.2 20.4 - - + -
464B LYS* 4.1 34.5 - - + +
468B PHE* 4.9 7.4 - - + +
469B GLN* 3.1 12.6 + - - +
471B HIS* 1.3 103.6 + - + +
473B LEU* 1.3 57.6 + - - +
475B LYS* 4.3 13.1 - - - +
476B VAL* 4.0 6.9 - - - +
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Residues in contact with LEU 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B CYS* 3.8 16.2 - - - +
423B LEU* 5.1 3.8 - - + -
424B THR* 5.8 1.6 - - - +
427B ILE* 6.1 1.3 - - + -
440B PRO* 4.5 5.4 - - + -
443B VAL* 3.6 27.4 - - + +
461B VAL* 4.2 5.6 - - + -
463B TYR* 3.9 16.4 - - - +
469B GLN* 4.2 21.5 - - + -
470B SER 3.0 11.3 + - - +
472B GLU* 1.3 75.7 - - - +
474B LEU* 1.3 67.5 + - - +
475B LYS 3.2 2.1 + - - -
476B VAL* 3.6 10.2 + - - +
477B GLY 3.6 7.4 + - - -
501B MET* 3.7 30.3 - - + +
503B ILE* 4.0 18.6 - - + -
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Residues in contact with LEU 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B ILE* 4.9 1.8 - - + +
416B LEU* 3.5 44.9 - - + +
417B GLU* 3.9 22.4 - - + +
420B CYS* 3.8 19.3 - - + -
470B SER 3.1 6.0 + - - +
471B HIS* 3.2 17.0 + - + +
473B LEU* 1.3 78.8 - - - +
475B LYS* 1.3 65.6 + - - +
477B GLY* 3.2 2.5 + - - +
478B ILE* 2.9 48.1 + - + +
501B MET* 4.7 4.3 - - + -
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Residues in contact with LYS 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B HIS* 3.2 43.7 + - + +
472B GLU* 4.5 13.7 - - - +
473B LEU 3.2 0.6 - - - -
474B LEU* 1.3 75.6 - - - +
476B VAL* 1.3 69.2 + - + +
478B ILE* 3.0 24.3 + - + +
479B LYS* 2.9 22.8 + - - +
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Residues in contact with VAL 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B VAL* 4.3 16.2 - - + -
460B PRO 3.9 12.6 - - - +
461B VAL* 3.5 35.9 - - + -
462B ALA 4.8 2.5 - - - +
472B GLU 4.0 7.6 - - - +
473B LEU 3.9 5.6 - - - +
474B LEU 3.4 0.2 - - - -
475B LYS* 1.3 75.7 - - + +
477B GLY* 1.3 66.0 + - - +
479B LYS* 3.0 7.4 + - - +
480B PHE* 2.8 59.1 + - + -
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Residues in contact with GLY 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B LEU* 4.7 4.0 - - - -
443B VAL* 5.1 2.2 - - - +
445B ILE* 4.0 15.0 - - - +
473B LEU 3.6 4.2 + - - -
474B LEU 3.2 6.8 + - - -
475B LYS 3.1 0.6 - - - -
476B VAL* 1.3 78.8 - - - +
478B ILE* 1.3 52.3 + - - +
480B PHE* 3.0 3.6 + - - +
481B VAL* 2.7 38.2 + - - +
501B MET* 3.9 22.8 - - - +
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Residues in contact with ILE 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B ILE* 3.7 46.9 - - + -
416B LEU* 5.2 2.9 - - + -
474B LEU* 2.9 43.4 + - + +
475B LYS* 3.5 24.9 - - + +
477B GLY* 1.3 74.4 - - - +
479B LYS* 1.3 57.8 + - - +
481B VAL* 3.1 8.0 - - - +
482B THR* 2.7 38.9 + - - +
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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
----------------------------------------------------------
475B LYS* 2.9 12.6 + - - +
476B VAL* 3.3 11.0 - - - +
478B ILE* 1.3 76.2 - - - +
480B PHE* 1.3 58.9 + - + +
482B THR* 3.0 12.5 + - + -
483B ASP* 2.7 57.6 + - - +
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Residues in contact with PHE 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B VAL* 3.7 10.8 - - + -
444B SER* 4.8 0.2 - - - -
445B ILE* 3.8 22.0 - - + -
457B LYS* 3.1 53.6 - - + -
459B GLY* 3.0 41.5 - - - -
460B PRO* 5.0 1.8 - - + -
476B VAL* 2.8 39.6 + - + +
477B GLY* 3.2 7.4 - - - +
479B LYS* 1.3 78.8 - - + +
481B VAL* 1.3 56.5 + - - +
482B THR 2.7 15.2 + - - -
483B ASP* 2.8 19.5 + - - +
484B LEU* 3.0 16.9 + - - +
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Residues in contact with VAL 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B ILE* 4.3 9.8 - - + +
412B CYS* 3.5 36.1 - - + -
413B ILE* 4.7 7.6 - - + -
416B LEU* 4.7 8.5 - - + -
445B ILE* 4.4 14.2 - - + +
447B LEU* 4.4 15.0 - - + -
477B GLY 2.7 18.6 + - - +
478B ILE* 3.1 27.8 - - + +
480B PHE* 1.3 72.4 - - - +
482B THR* 1.3 58.5 + - - +
484B LEU* 3.9 8.8 + - - +
485B ASP* 3.2 24.1 + - - +
493B TYR* 4.3 2.1 + - + +
499B LEU* 4.7 7.2 - - + -
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Residues in contact with THR 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B ILE* 4.2 15.4 - - + +
413B ILE* 5.5 0.3 - - - +
478B ILE* 2.7 28.1 + - - +
479B LYS* 3.0 14.3 + - + +
480B PHE 2.7 1.8 + - - -
481B VAL* 1.3 75.3 - - - +
483B ASP* 1.3 66.4 + - - +
484B LEU 3.0 1.8 - - - -
485B ASP* 3.1 17.3 + - + +
486B ILE* 3.2 26.4 + - + +
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Residues in contact with ASP 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B LYS* 2.9 37.9 + - + +
479B LYS* 2.7 52.6 + - - +
480B PHE* 2.8 9.6 + - - +
482B THR* 1.3 74.9 - - - +
484B LEU* 1.3 62.5 - - + +
486B ILE* 3.4 14.3 + - - +
487B LYS* 3.3 27.3 + - + +
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Residues in contact with LEU 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B ILE* 3.8 24.5 - - + +
447B LEU* 4.0 17.7 - - + -
455B TYR* 4.0 16.1 - - + -
456B ARG* 4.0 34.3 - - - +
457B LYS* 4.2 12.8 - - + +
480B PHE 3.0 19.9 + - - +
481B VAL* 3.9 7.2 - - - +
483B ASP* 1.3 73.0 - - - +
485B ASP* 1.3 63.4 + - - +
486B ILE 2.9 4.7 - - - -
487B LYS* 2.9 35.8 + - + +
488B GLY 3.2 7.6 + - - -
493B TYR* 3.5 19.4 + - - +
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Residues in contact with ASP 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B ILE* 4.4 17.2 - - + +
481B VAL 3.2 16.4 + - - +
482B THR* 3.1 12.5 + - + +
484B LEU* 1.3 78.5 - - - +
486B ILE* 1.3 60.8 + - + +
488B GLY 3.8 15.5 + - - +
489B LYS* 3.8 8.5 + - - +
493B TYR* 3.5 12.0 + - + -
494B TYR* 2.8 43.3 + - - +
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Residues in contact with ILE 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 THR* 3.3 26.7 - - + +
483B ASP* 3.5 16.2 - - - +
484B LEU 2.9 0.4 - - - -
485B ASP* 1.3 78.8 - - + +
487B LYS* 1.3 59.8 + - + +
488B GLY 2.9 10.9 + - - -
489B LYS* 3.3 18.7 + - + +
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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
----------------------------------------------------------
455B TYR* 4.0 26.6 + - + -
457B LYS* 6.4 0.9 - - + -
483B ASP* 3.3 18.4 - - + +
484B LEU* 2.9 29.0 + - + +
486B ILE* 1.3 77.3 - - + +
488B GLY* 1.3 55.5 + - - +
489B LYS 3.8 0.7 - - - -
491B LYS* 4.7 7.1 - - - +
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Residues in contact with GLY 488 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B TYR* 4.1 13.0 - - - -
484B LEU 3.2 6.8 + - - -
485B ASP* 3.8 6.0 - - - +
486B ILE 2.9 0.8 + - - -
487B LYS* 1.3 80.9 - - - +
489B LYS* 1.3 62.5 + - - +
490B ASN 3.5 1.3 - - - -
491B LYS* 3.3 21.5 - - - +
493B TYR* 3.5 28.5 - - - +
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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
------------------------------------------------------------
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