Contacts of the helix formed by residues 461 - 492 (chain U) in PDB entry 5MQF
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 THR 461 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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460U LEU* 3.8 28.3 - - - +
462U LEU* 3.8 29.2 - - - +
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Residues in contact with LEU 462 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461U THR* 3.8 28.5 - - - +
463U HIS* 3.8 25.1 - - - +
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Residues in contact with HIS 463 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462U LEU* 3.8 28.9 - - - +
464U ASP* 3.8 26.5 - - - +
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Residues in contact with ASP 464 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463U HIS* 3.8 29.2 - - - +
465U TYR* 3.8 25.6 - - - +
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Residues in contact with TYR 465 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464U ASP* 3.8 26.2 - - - +
466U LEU* 3.8 28.9 - - - +
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Residues in contact with LEU 466 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465U TYR* 3.8 28.9 - - - +
467U LEU* 3.8 26.9 - - - +
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Residues in contact with LEU 467 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466U LEU* 3.8 28.9 - - - +
468U ARG* 3.8 27.4 - - - +
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Residues in contact with ARG 468 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467U LEU* 3.8 24.9 - - - +
469U ASN* 3.8 28.7 - - - +
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Residues in contact with ASN 469 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468U ARG* 3.8 29.2 - - - +
470U PHE* 3.8 26.2 - - - +
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Residues in contact with PHE 470 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469U ASN* 3.8 26.9 - - - +
471U ASN* 3.8 28.9 - - - +
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Residues in contact with ASN 471 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470U PHE* 3.8 28.9 - - - +
472U LEU* 3.8 26.5 - - - +
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Residues in contact with LEU 472 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471U ASN* 3.8 25.8 - - - +
473U PHE* 3.8 28.7 - - - +
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Residues in contact with PHE 473 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472U LEU* 3.8 28.5 - - - +
474U ARG* 3.8 26.2 - - - +
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Residues in contact with ARG 474 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473U PHE* 3.8 27.4 - - - +
475U LEU* 3.8 29.2 - - - +
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Residues in contact with LEU 475 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474U ARG* 3.8 29.4 - - - +
476U GLU* 3.8 26.9 - - - +
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Residues in contact with GLU 476 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475U LEU* 3.8 25.4 - - - +
477U SER* 3.8 29.6 - - - +
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Residues in contact with SER 477 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476U GLU* 3.8 29.4 - - - +
478U THR* 3.8 25.1 - - - +
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Residues in contact with THR 478 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477U SER* 3.8 28.9 - - - +
479U TYR* 3.8 25.4 - - - +
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Residues in contact with TYR 479 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478U THR* 3.8 26.5 - - - +
480U GLU* 3.8 29.4 - - - +
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Residues in contact with GLU 480 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479U TYR* 3.8 25.8 - - - +
481U ILE* 3.8 28.7 - - - +
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Residues in contact with ILE 481 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480U GLU* 3.8 29.4 - - - +
482U ARG* 3.8 25.6 - - - +
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Residues in contact with ARG 482 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481U ILE* 3.8 25.6 - - - +
483U GLN* 3.8 29.4 - - - +
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Residues in contact with GLN 483 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482U ARG* 3.8 29.8 - - - +
484U ASP* 3.8 26.0 - - - +
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Residues in contact with ASP 484 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483U GLN* 3.8 25.6 - - - +
485U ILE* 3.8 29.6 - - - +
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Residues in contact with ILE 485 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484U ASP* 3.8 26.5 - - - +
486U GLU* 3.8 28.9 - - - +
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Residues in contact with GLU 486 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485U ILE* 3.8 28.7 - - - +
487U ASP* 3.8 26.5 - - - +
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Residues in contact with ASP 487 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486U GLU* 3.8 29.2 - - - +
488U SER* 3.8 28.0 - - - +
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Residues in contact with SER 488 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487U ASP* 3.8 29.6 - - - +
489U VAL* 3.8 27.4 - - - +
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Residues in contact with VAL 489 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488U SER* 3.8 28.5 - - - +
490U SER* 3.8 26.2 - - - +
----------------------------------------------------------
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Residues in contact with SER 490 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489U VAL* 3.8 25.6 - - - +
491U ARG* 3.8 29.2 - - - +
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Residues in contact with ARG 491 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490U SER* 3.8 29.4 - - - +
492U MSE 3.8 25.6 - - - +
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Residues in contact with MSE 492 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491U ARG* 3.8 28.9 - - - +
493U LYS* 3.8 25.6 - - - +
506U GLY* 4.2 19.3 - - - +
507U TRP* 4.7 10.8 - - - +
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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