Contacts of the helix formed by residues 483 - 493 (chain B) in PDB entry 6HBU
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 MET 483 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478B LEU* 2.9 17.2 + - + +
479B LEU* 3.7 32.3 - - + +
482B ARG* 1.3 76.8 - - - +
484B LEU* 1.3 64.5 + - - +
486B SER* 3.2 13.6 + - - -
487B ILE* 3.2 30.5 + - + +
514B MET* 4.0 24.8 - - + +
518B TYR* 3.3 35.2 + - + +
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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
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399B ILE* 4.2 22.7 - - + -
479B LEU 3.3 12.7 + - - +
480B PRO* 4.4 11.4 - - + +
483B MET* 1.3 81.5 - - + +
485B PRO* 1.3 66.6 - - + +
487B ILE* 3.4 16.5 + - + +
488B ILE* 3.3 43.2 + - + +
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Residues in contact with PRO 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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398B GLN* 3.6 34.3 - - + +
399B ILE* 4.7 10.1 - - + -
402B THR* 3.6 16.7 - - + +
437B GLN* 4.2 6.4 - - - +
480B PRO 3.9 6.3 - - - +
481B MET 3.4 33.2 - - - +
482B ARG* 3.8 1.3 - - - +
484B LEU* 1.3 91.8 - - + +
486B SER* 1.3 59.4 + - - +
487B ILE 3.6 0.2 - - - -
488B ILE* 4.7 6.3 - - + +
489B PHE* 3.2 24.1 - - - +
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Residues in contact with SER 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B GLN* 2.5 30.8 + - - +
482B ARG* 2.9 20.8 + - - -
483B MET 3.2 5.3 + - - -
484B LEU 3.2 1.4 - - - -
485B PRO* 1.3 76.0 - - - +
487B ILE* 1.3 60.9 + - - +
489B PHE* 4.1 4.9 - - - -
490B THR* 2.7 29.3 + - - -
510B MET* 4.1 6.4 - - - +
513B LEU* 3.6 10.2 + - - -
514B MET* 3.8 20.2 - - - -
517B ALA* 4.0 0.5 - - - +
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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
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483B MET* 3.2 35.1 + - + +
484B LEU* 3.4 18.4 + - + +
486B SER* 1.3 76.9 - - - +
488B ILE* 1.3 68.2 + - + +
490B THR 3.5 0.7 + - - -
491B CYS* 3.1 36.6 + - - -
510B MET* 3.8 25.3 - - + +
514B MET* 3.7 17.5 - - + -
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Residues in contact with ILE 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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399B ILE* 4.0 25.4 - - + -
402B THR* 5.3 4.9 - - + -
403B VAL* 3.9 27.4 - - + -
484B LEU* 3.3 40.4 + - + +
485B PRO* 4.7 4.5 - - + -
487B ILE* 1.3 78.6 - - + +
489B PHE* 1.3 58.4 + - - +
491B CYS* 3.3 6.0 + - - +
492B ILE* 3.1 37.4 + - + +
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Residues in contact with PHE 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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402B THR* 3.7 28.2 - - + +
405B LEU* 4.3 3.6 - - + -
406B GLY* 3.6 27.6 - - - -
409B ILE* 4.2 13.5 - - + -
433B LEU* 3.5 41.1 - - + -
436B ASN* 3.2 26.5 - - + -
437B GLN* 3.8 9.4 - - - -
485B PRO 3.2 21.7 + - - +
486B SER* 4.5 2.0 - - - -
487B ILE 3.3 0.4 - - - -
488B ILE* 1.3 78.7 - - - +
490B THR* 1.3 61.6 + - - +
492B ILE* 4.4 3.5 - - - +
493B VAL* 3.2 25.1 + - + +
513B LEU* 3.6 26.0 - - + -
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Residues in contact with THR 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 SER 2.7 23.3 + - - -
487B ILE 3.5 4.0 + - - -
488B ILE 3.3 0.4 - - - -
489B PHE* 1.3 76.9 - - - +
491B CYS* 1.3 62.9 + - - +
493B VAL* 3.7 8.2 + - - +
494B TYR* 3.3 22.0 + - - +
506B PHE* 3.7 20.0 - - + +
509B MET* 3.9 20.8 - - + +
510B MET* 3.8 35.5 - - + +
513B LEU* 3.7 17.5 - - - +
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Residues in contact with CYS 491 (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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487B ILE* 3.1 33.3 + - - +
488B ILE* 3.3 6.9 + - - +
490B THR* 1.3 77.3 - - - +
492B ILE* 1.3 63.0 + - + +
494B TYR* 3.3 9.4 + - - +
495B PHE* 3.1 23.7 + - + -
506B PHE* 3.6 27.8 - - - -
510B MET* 4.2 5.6 - - - -
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Residues in contact with ILE 492 (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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402B THR 4.8 2.9 - - - +
403B VAL* 3.8 46.7 - - + -
406B GLY* 3.4 30.5 - - - +
407B LEU* 4.0 11.2 - - + +
488B ILE* 3.1 24.2 + - + +
489B PHE* 4.4 4.5 - - - +
490B THR 3.4 0.2 - - - -
491B CYS* 1.3 78.6 - - + +
493B VAL* 1.3 56.6 + - + +
494B TYR 3.2 4.2 + - - -
495B PHE* 3.7 22.8 + - + -
496B MET* 3.2 31.1 + - - +
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Residues in contact with VAL 493 (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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406B GLY* 3.4 31.2 - - - +
409B ILE* 4.7 4.5 - - + -
410B GLY 4.7 5.4 - - - +
433B LEU* 4.0 21.8 - - + -
489B PHE* 3.2 22.6 + - + +
490B THR 3.8 2.7 - - - +
492B ILE* 1.3 73.3 - - - +
494B TYR* 1.3 58.3 + - - +
496B MET* 4.4 5.4 - - - -
497B LEU* 3.3 43.5 - - + +
499B LEU* 3.8 5.4 - - - +
509B MET* 3.7 27.1 - - + -
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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