Contacts of the helix formed by residues 473 - 493 (chain B) in PDB entry 5DKB
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 ASP 473 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471B GLU* 3.0 8.7 + - + +
472B LYS* 1.3 75.7 - - - +
474B HIS* 1.3 61.6 + - - +
475B ILE 3.4 3.6 - - - +
476B HIS* 3.6 14.0 + - - +
477B ARG* 2.7 37.2 + - - +
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Residues in contact with HIS 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B LEU 6.3 0.4 - - - -
307B ALA 6.0 0.2 - - - -
308B LEU* 3.8 28.0 - - + +
366B GLY* 3.3 29.1 + - - -
369B ASP* 3.4 28.9 + - + +
370B LEU* 4.0 18.6 - - + -
471B GLU* 3.4 12.2 + - + +
473B ASP* 1.3 81.9 + - - +
475B ILE* 1.3 59.5 + - + +
477B ARG* 3.1 8.1 + - - +
478B VAL* 2.8 39.5 + - + +
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Residues in contact with ILE 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B LEU* 3.6 42.6 - - + -
374B ASP* 5.6 5.2 - - + +
378B LEU* 4.4 11.0 - - + -
454B LEU* 3.6 39.5 - - + +
458B VAL* 3.9 27.8 - - + -
471B GLU 5.4 0.7 - - - +
472B LYS* 5.1 10.3 - - + -
473B ASP 3.4 3.1 - - - +
474B HIS* 1.3 76.7 - - + +
476B HIS* 1.3 58.0 + - - +
478B VAL* 3.1 9.2 + - - +
479B LEU* 2.8 33.0 + - + +
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Residues in contact with HIS 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A ARG* 3.5 36.0 + - - +
506A GLN* 5.8 3.1 - - + +
455B ASN* 6.1 0.2 - - - -
458B VAL* 4.3 14.1 - - + +
459B TYR* 3.5 32.0 + + - -
472B LYS* 4.0 32.2 + - + +
473B ASP* 3.5 10.6 + - - +
474B HIS 3.3 0.2 - - - -
475B ILE* 1.3 79.0 - - - +
477B ARG* 1.3 57.3 + - - +
479B LEU* 3.6 19.9 - - + +
480B ASP* 2.9 39.1 + - - +
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Residues in contact with ARG 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B LEU* 3.9 29.2 - - + +
473B ASP* 2.7 25.4 + - - +
474B HIS* 3.1 9.4 + - - +
476B HIS* 1.3 72.3 - - - +
478B VAL* 1.3 61.9 + - - +
480B ASP* 3.5 10.5 + - - +
481B LYS* 3.2 19.9 + - - +
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Residues in contact with VAL 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ALA* 4.9 4.0 - - + +
308B LEU* 4.2 11.0 - - + -
315B MET* 5.2 7.4 - - + -
365B PRO* 3.4 21.8 - - + +
366B GLY* 4.3 10.1 - - - -
454B LEU* 3.6 21.8 - - + -
474B HIS* 2.8 43.9 + - + +
475B ILE* 3.5 7.4 - - - +
477B ARG* 1.3 75.6 - - - +
479B LEU* 1.3 64.9 + - - +
481B LYS* 3.0 9.4 + - - +
482B ILE* 3.0 29.0 + - + +
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Residues in contact with LEU 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A GLN* 6.5 0.2 - - + -
509A LEU* 4.2 13.2 - - + -
451B ILE* 4.0 46.0 - - + +
454B LEU* 4.0 17.7 - - + +
455B ASN* 4.4 22.7 - - + +
458B VAL* 5.4 1.6 - - + -
475B ILE* 2.8 32.6 + - + +
476B HIS* 3.6 23.8 - - + +
478B VAL* 1.3 77.6 - - - +
480B ASP* 1.3 59.0 + - - +
482B ILE* 3.2 7.8 + - + +
483B THR* 3.0 30.5 + - - -
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Residues in contact with ASP 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A GLN* 3.9 28.4 + - - +
505A ALA* 6.0 0.2 - - - +
506A GLN* 2.8 38.8 + - - +
476B HIS* 2.9 26.0 + - - +
477B ARG* 3.6 9.3 - - - +
478B VAL 3.2 0.2 - - - -
479B LEU* 1.3 78.5 - - - +
481B LYS* 1.3 57.1 + - - +
483B THR* 3.3 8.8 + - - -
484B ASP* 3.0 34.7 + - - +
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Residues in contact with LYS 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ALA 5.3 5.8 - - - +
308B LEU* 5.8 6.3 - - + -
310B LEU 5.8 3.6 - - - +
315B MET* 4.2 16.8 - - + -
477B ARG 3.2 12.6 + - - +
478B VAL* 3.0 13.5 + - + +
480B ASP* 1.3 77.9 - - - +
482B ILE* 1.3 56.9 + - - +
484B ASP* 3.3 13.3 + - - +
485B THR* 2.9 30.7 + - - -
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Residues in contact with ILE 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B MET* 4.4 19.5 - - + -
319B LEU* 5.4 1.6 - - + -
364B VAL* 5.7 1.3 - - + -
447B CYS* 3.7 27.4 - - + +
450B SER* 3.9 24.0 - - - -
451B ILE* 3.6 33.0 - - + +
454B LEU* 4.1 21.1 - - + -
478B VAL* 3.0 16.3 + - + +
479B LEU* 3.2 9.4 + - - +
481B LYS* 1.3 74.0 - - - +
483B THR* 1.3 61.2 + - - +
485B THR* 3.1 7.5 + - - -
486B LEU* 2.9 28.4 + - + +
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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
----------------------------------------------------------
501A HIS* 3.5 40.6 - - + +
502A GLN* 4.1 2.9 - - - -
505A ALA* 3.4 24.1 - - + +
509A LEU* 5.9 1.7 - - - +
451B ILE* 5.2 5.1 - - - +
479B LEU 3.0 15.0 + - - -
480B ASP* 3.4 14.0 + - - -
482B ILE* 1.3 77.1 - - - +
484B ASP* 1.3 62.1 + - - +
486B LEU* 3.2 13.0 + - - +
487B ILE* 3.0 22.3 + - - +
504B LEU* 4.1 13.1 - - + +
508B LEU* 5.6 0.2 - - - +
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Residues in contact with ASP 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A GLN* 3.1 18.5 + - - +
501A HIS* 2.6 36.1 + - + -
502A GLN* 3.0 26.3 + - - -
312B ALA* 5.3 2.5 - - + -
480B ASP 3.0 19.3 + - - +
481B LYS* 3.5 12.1 - - - +
483B THR* 1.3 75.5 - - - +
485B THR* 1.3 57.1 + - - +
487B ILE* 3.5 3.2 + - - +
488B HIS* 3.0 29.5 + - - +
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Residues in contact with THR 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B THR 5.4 0.2 - - - -
312B ALA* 3.8 18.7 - - + +
315B MET* 3.5 25.1 - - + +
316B VAL* 3.6 30.1 - - + -
447B CYS* 3.8 17.0 - - - -
481B LYS 2.9 17.4 + - - -
482B ILE* 3.1 12.5 + - - -
484B ASP* 1.3 75.2 - - - +
486B LEU* 1.3 63.9 + - - +
488B HIS* 3.3 7.6 + - - +
489B LEU* 3.0 23.7 + - + +
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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
----------------------------------------------------------
444B GLU* 4.1 30.3 - - + +
447B CYS* 3.7 25.6 - - + -
448B LEU* 4.6 9.9 - - + +
451B ILE* 3.9 27.4 - - + -
482B ILE 2.9 13.4 + - - +
483B THR* 3.2 10.5 + - - +
485B THR* 1.3 77.8 - - - +
487B ILE* 1.3 61.8 + - - +
489B LEU* 3.2 8.0 + - + +
490B MET* 3.1 32.5 + - + +
504B LEU* 3.8 27.4 - - + -
507B LEU* 4.4 13.2 - - + -
508B LEU* 4.8 1.6 - - + -
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Residues in contact with ILE 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A HIS* 3.6 41.7 - - + +
483B THR 3.0 16.3 + - - +
484B ASP 3.8 4.3 - - - +
486B LEU* 1.3 75.5 - - + +
488B HIS* 1.3 64.0 + - - +
490B MET* 3.2 6.9 + - - +
491B ALA* 3.0 24.4 + - + +
500B GLN* 3.4 34.8 - - + +
501B HIS* 4.4 7.0 - - + +
504B LEU* 3.8 34.1 - - + -
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Residues in contact with HIS 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ALA* 3.4 29.1 - - + +
313B ASP* 2.9 26.7 + - - -
316B VAL* 5.8 0.7 - - + -
484B ASP 3.0 18.4 + - - +
485B THR 3.4 6.1 - - - +
487B ILE* 1.3 77.7 - - - +
489B LEU* 1.3 70.5 + - + +
491B ALA* 3.7 5.8 + - - +
492B LYS* 3.2 40.8 + - + +
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Residues in contact with LEU 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ASP* 6.0 0.2 - - - +
316B VAL* 4.0 22.9 - - + -
443B GLU* 3.6 49.1 - - + +
444B GLU* 4.1 17.7 - - + +
447B CYS* 4.3 11.4 - - - -
485B THR 3.0 20.5 + - - +
486B LEU* 3.2 9.8 + - - +
488B HIS* 1.3 84.5 - - + +
490B MET* 1.3 57.1 + - + +
492B LYS* 3.2 17.3 + - - +
493B ALA* 3.1 26.4 + - - +
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Residues in contact with MET 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B GLU* 4.0 15.5 - - - +
486B LEU* 3.1 28.4 + - + +
487B ILE* 3.2 8.2 + - - +
489B LEU* 1.3 73.0 - - + +
491B ALA* 1.3 65.9 + - - +
493B ALA* 3.2 10.8 + - - +
495B LEU* 3.1 40.3 + - + +
500B GLN* 3.4 34.1 - - + +
503B ARG* 3.7 19.3 - - + -
504B LEU* 3.7 23.6 - - + +
507B LEU* 3.6 31.0 - - + -
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Residues in contact with ALA 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B ILE* 3.0 17.6 + - + +
488B HIS* 4.0 7.2 - - - +
490B MET* 1.3 76.2 - - - +
492B LYS* 1.3 61.9 + - - +
494B GLY* 3.3 13.2 + - - -
495B LEU 4.3 2.1 - - - +
500B GLN* 3.7 26.6 - - - +
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Residues in contact with LYS 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ASP* 5.1 7.2 - - - +
488B HIS* 3.2 35.6 + - + +
489B LEU* 3.2 20.8 + - - +
490B MET 3.2 0.4 - - - -
491B ALA* 1.3 79.9 - - - +
493B ALA* 1.3 58.3 + - - +
494B GLY* 3.2 1.3 + - - -
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Residues in contact with ALA 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B GLN* 6.5 1.1 - - + -
489B LEU 3.1 11.6 + - - +
490B MET* 3.2 12.0 + - - +
492B LYS* 1.3 76.6 - - - +
494B GLY* 1.3 60.2 + - - +
495B LEU* 3.5 10.3 - - + +
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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
------------------------------------------------------------
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