Contacts of the helix formed by residues 475 - 489 (chain B) in PDB entry 6MBZ
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 475 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B VAL* 4.8 14.4 - - + -
343B LYS* 6.3 2.7 - - - -
469B ILE* 4.6 15.3 - - + -
473B SER 3.3 5.8 + - - +
474B GLN* 1.3 70.9 - - - +
476B ASN* 1.3 65.8 + - - +
477B ASN 3.1 0.2 - - - -
478B ALA* 2.9 16.2 + - - +
479B THR* 2.8 20.1 + - - +
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Residues in contact with ASN 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B GLN* 3.1 10.3 - - + +
475B ASP* 1.3 77.1 - - - +
477B ASN* 1.3 56.8 + - - +
479B THR* 3.3 6.6 + - - -
480B ALA 2.9 12.1 + - - -
571B TRP* 2.8 32.4 + - + +
572B GLN* 5.5 9.2 - - + -
575B ASP* 3.4 24.0 - - + +
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Residues in contact with ASN 477 (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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436B THR* 3.3 33.7 - - + +
437B GLU* 3.8 18.3 + - - +
474B GLN* 3.7 7.6 + - + +
475B ASP 3.0 1.0 + - - -
476B ASN* 1.3 77.2 - - - +
478B ALA* 1.3 62.8 + - - +
480B ALA* 3.2 6.2 + - - +
481B THR* 3.0 26.3 + - - -
555B TRP* 5.2 0.2 - - - -
559B ASN* 3.0 28.8 + - - +
571B TRP* 5.6 0.2 - - - -
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Residues in contact with ALA 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B VAL* 4.1 11.0 - - + -
436B THR* 2.9 24.1 + - - +
467B VAL* 3.6 21.0 - - + +
469B ILE* 3.5 24.9 - - + -
475B ASP 2.9 7.3 + - - +
477B ASN* 1.3 75.1 - - - +
479B THR* 1.3 57.7 + - - +
481B THR* 3.3 2.9 + - - -
482B VAL* 2.9 33.4 + - - +
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Residues in contact with THR 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B VAL* 4.4 12.5 - - + +
475B ASP* 2.8 24.7 + - - +
476B ASN* 3.6 9.3 - - - -
478B ALA* 1.3 76.6 - - - +
480B ALA* 1.3 62.7 + - - +
482B VAL* 3.9 3.2 - - + +
483B LEU* 2.9 27.2 + - - +
514B LYS* 4.8 18.6 - - + +
518B GLU* 6.1 2.0 - - - +
571B TRP* 3.9 19.7 - - + -
575B ASP* 4.6 7.6 + - - +
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Residues in contact with ALA 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B ASN 2.9 7.0 + - - +
477B ASN 3.2 8.3 + - - +
479B THR* 1.3 76.7 - - - +
481B THR* 1.3 63.0 + - - +
483B LEU* 3.4 3.3 + - - +
484B TRP* 2.9 25.8 + - - +
555B TRP* 3.9 8.4 - - + -
558B PHE* 4.3 7.7 - - + -
559B ASN* 3.3 31.2 - - - +
571B TRP* 3.3 27.7 - - + +
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Residues in contact with THR 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B THR 4.0 6.5 + - - +
437B GLU* 3.3 38.2 + - - +
439B LYS* 4.3 25.1 - - + +
467B VAL* 4.7 9.4 - - + -
477B ASN* 3.0 14.8 + - - -
478B ALA* 3.3 10.1 + - - -
480B ALA* 1.3 77.0 - - - +
482B VAL* 1.3 57.7 + - - +
484B TRP* 3.3 2.9 + - - +
485B ASP* 2.9 28.9 + - + +
555B TRP* 3.9 14.7 - - + -
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Residues in contact with VAL 482 (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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263B GLY 5.3 2.0 - - - +
264B ASN* 4.5 4.0 - - - +
340B GLN* 4.0 37.7 - - + +
341B VAL* 3.7 18.8 - - + -
465B PRO* 4.8 5.4 - - + +
467B VAL* 3.6 27.4 - - + -
478B ALA 2.9 17.0 + - - +
479B THR* 4.0 4.7 - - + +
481B THR* 1.3 73.1 - - - +
483B LEU* 1.3 66.2 + - - +
485B ASP* 3.3 4.4 + - - +
486B ASN* 2.9 32.1 + - - +
514B LYS* 6.4 1.6 - - - -
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Residues in contact with LEU 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ASN* 3.1 27.8 + - - +
479B THR 2.9 19.3 + - - +
480B ALA* 3.8 3.6 - - - +
482B VAL* 1.3 76.4 - - - +
484B TRP* 1.3 69.0 + - + +
487B ALA* 2.9 24.7 + - + +
488B PHE* 5.5 1.1 - - + -
507B LEU* 4.8 5.4 - - + -
510B ALA* 4.1 22.7 - - + +
511B LEU* 4.5 12.3 - - + -
514B LYS* 3.5 44.4 - - + -
558B PHE* 4.3 24.2 - - + -
571B TRP* 4.6 11.0 - - + -
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Residues in contact with TRP 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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480B ALA 2.9 17.0 + - - +
481B THR 3.6 3.4 - - - +
483B LEU* 1.3 81.2 - - + +
485B ASP* 1.3 63.7 + - - +
488B PHE* 2.9 57.0 + + + +
498B VAL* 3.8 26.9 - - + +
499B PRO* 2.9 31.4 + - - +
500B ASP 4.4 1.6 - - - -
501B LYS 4.3 0.4 - - - -
502B VAL* 3.4 28.9 - - + -
507B LEU* 4.8 5.4 - - + -
553B VAL* 3.9 9.9 - - + -
555B TRP* 3.3 60.6 - + + +
558B PHE* 3.9 31.0 - + + -
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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
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260B GLN* 4.3 1.7 + - - -
439B LYS* 2.7 30.6 + - + +
465B PRO* 3.4 23.0 - - + +
481B THR* 2.9 17.9 + - + +
482B VAL* 3.8 5.4 - - - +
484B TRP* 1.3 77.3 - - - +
486B ASN* 1.3 65.3 + - - +
489B ALA* 2.9 26.9 + - - +
493B ARG* 2.6 38.8 + - - -
496B PHE* 4.4 0.7 - - - -
498B VAL* 3.6 13.5 - - + -
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Residues in contact with ASN 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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257B ARG* 3.0 29.3 + - - -
260B GLN* 3.6 43.2 + - - +
261B LEU* 4.1 4.0 - - - +
263B GLY* 4.0 7.1 + - - -
264B ASN* 3.5 23.7 + - - +
340B GLN* 3.0 38.5 + - - +
464B LEU* 4.9 3.5 - - - +
465B PRO* 4.6 5.0 - - - +
482B VAL* 2.9 24.4 + - - +
485B ASP* 1.3 75.1 - - - +
487B ALA* 1.3 58.8 + - - +
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Residues in contact with ALA 487 (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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257B ARG* 2.8 21.3 + - - +
261B LEU* 4.8 5.7 - - - +
264B ASN* 3.6 9.8 - - - +
483B LEU 2.9 20.7 + - - +
484B TRP 3.9 2.0 - - - +
486B ASN* 1.3 77.5 - - - +
488B PHE* 1.3 82.0 + - + +
510B ALA* 3.8 24.0 - - + -
513B MET* 5.6 2.2 - - + -
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Residues in contact with PHE 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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483B LEU* 5.5 1.6 - - + -
484B TRP* 2.9 57.4 + + + +
485B ASP 3.8 0.9 - - - -
487B ALA* 1.3 97.0 - - + +
489B ALA* 1.3 66.0 + - - +
490B GLU* 3.4 1.2 + - - +
498B VAL* 4.9 1.1 - - - -
499B PRO* 3.1 38.4 - - + +
502B VAL* 3.5 34.8 - - + -
506B GLN* 3.4 30.5 - - + -
507B LEU* 3.6 26.5 - - + -
509B GLU* 6.0 0.4 - - - -
510B ALA* 4.6 2.2 - - + -
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Residues in contact with ALA 489 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ARG* 4.5 13.6 + - - +
260B GLN* 3.7 22.2 - - - +
485B ASP* 2.9 19.5 + - - +
486B ASN 4.3 0.6 + - - -
487B ALA 3.6 2.0 - - - -
488B PHE* 1.3 77.8 - - - +
490B GLU* 1.3 65.1 + - - +
491B PRO* 4.0 0.9 - - - +
493B ARG* 3.6 32.5 - - - +
497B ALA 5.0 0.4 - - - -
498B VAL* 4.7 4.0 - - - -
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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