Contacts of the helix formed by residues 483 - 494 (chain B) in PDB entry 5B2R
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 483 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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466B THR* 2.9 24.2 + - - +
467B ARG 4.3 1.6 - - - +
468B LYS* 3.8 30.3 - - + +
481B VAL 3.7 2.6 + - - -
482B VAL* 1.3 67.9 - - - +
484B LYS* 1.3 61.5 + - - +
485B GLY* 3.3 5.4 + - - -
486B ALA* 2.9 32.1 + - - +
487B SER* 2.8 28.5 + - - -
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Residues in contact with LYS 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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449B PRO* 4.4 8.7 - - + +
451B TYR* 4.0 23.6 + - + +
452B VAL* 4.6 4.0 - - + -
468B LYS* 4.8 2.0 - - - +
478B PHE* 3.8 25.8 - - + -
479B GLU* 2.9 44.6 + - - +
482B VAL* 3.2 17.6 + - + +
483B ASP* 1.3 73.4 + - - +
485B GLY* 1.3 58.9 + - - +
487B SER* 3.8 2.9 - - - -
488B ALA* 2.8 33.8 + - - +
628B ASP* 5.0 5.1 + - - -
631B MET* 3.5 23.7 - - + +
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Residues in contact with GLY 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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483B ASP* 3.3 5.1 + - - -
484B LYS* 1.3 79.2 - - - +
486B ALA* 1.3 62.4 + - - +
488B ALA* 3.8 1.7 - - - +
489B GLN* 2.9 25.9 + - - +
626B PHE* 3.9 12.4 - - - -
631B MET* 3.6 15.1 - - - +
635B ARG* 6.0 0.4 - - - -
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Residues in contact with ALA 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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466B THR* 3.6 14.1 - - - +
483B ASP* 2.9 33.9 + - - +
485B GLY* 1.3 72.3 - - - +
487B SER* 1.3 57.9 + - - +
489B GLN* 3.3 7.2 + - - +
490B SER* 2.8 31.8 + - - -
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Residues in contact with SER 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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451B TYR 3.7 3.4 - - - -
452B VAL* 4.2 20.2 - - - -
464B TRP* 3.2 14.0 + - - -
465B MET* 3.6 15.7 - - - +
466B THR* 3.1 29.5 + - - +
482B VAL* 4.1 0.3 - - - +
483B ASP 2.8 24.2 + - - -
484B LYS 3.8 2.9 - - - -
486B ALA* 1.3 77.1 - - - +
488B ALA* 1.3 57.5 + - - +
490B SER* 3.3 4.9 + - - -
491B PHE 2.8 24.3 + - - -
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Residues in contact with ALA 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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451B TYR* 3.6 34.2 + - + -
484B LYS 2.8 17.9 + - - +
487B SER* 1.3 76.7 - - - +
489B GLN* 1.3 60.7 + - - +
491B PHE* 3.3 14.9 - - - +
492B ILE* 3.5 14.2 + - - +
625B LEU 4.8 2.2 - - - +
626B PHE* 3.7 25.1 - - + -
631B MET* 3.9 7.2 - - + -
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Residues in contact with GLN 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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485B GLY 2.9 18.7 + - - +
486B ALA* 3.7 6.6 - - - +
488B ALA* 1.3 75.4 - - - +
490B SER* 1.3 60.2 + - - +
492B ILE* 3.4 2.8 + - - +
493B GLU* 2.9 68.0 + - - +
625B LEU* 3.9 25.9 - - + +
626B PHE* 4.1 6.2 - - + -
635B ARG* 3.4 24.6 + - - +
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Residues in contact with SER 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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464B TRP* 4.1 23.6 + - - +
466B THR* 5.8 3.1 - - - +
486B ALA 2.8 20.9 + - - -
487B SER* 3.6 5.2 - - - -
489B GLN* 1.3 71.0 - - - +
491B PHE* 1.3 66.5 - - - +
493B GLU* 4.4 5.8 - - - +
494B ARG* 2.9 32.0 + - - +
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Residues in contact with PHE 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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14A G 4.1 19.7 - - - -
15A C 5.3 0.4 - - - -
450B TYR* 3.6 42.2 - + - -
451B TYR* 3.4 22.9 - - + +
464B TRP* 3.3 39.8 - + - +
487B SER 2.8 15.1 + - - +
488B ALA 3.3 9.6 - - - +
490B SER* 1.3 76.7 - - - +
492B ILE* 1.3 88.6 + - + +
494B ARG* 3.4 15.2 - - - +
495B MET* 3.2 37.6 - - + +
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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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488B ALA 3.5 8.9 + - - +
489B GLN 3.4 2.7 + - - +
490B SER 3.2 0.2 - - - -
491B PHE* 1.3 99.5 - - + +
493B GLU* 1.3 62.8 + - + +
495B MET* 2.9 28.2 + - + +
496B THR* 3.1 32.7 + - + +
624B THR 5.6 2.0 - - - +
625B LEU* 3.7 35.4 - - + +
659B TRP* 3.7 27.1 - - + +
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Residues in contact with GLU 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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489B GLN* 2.9 54.2 + - + +
490B SER* 4.3 4.1 - - - +
492B ILE* 1.3 76.3 - - + +
494B ARG* 1.3 61.8 + - - +
495B MET 3.3 0.3 + - - -
496B THR* 3.8 8.5 - - - +
498B PHE* 5.3 0.2 - - - -
506B LYS* 2.7 45.8 + - + +
625B LEU* 4.7 10.3 - - + +
659B TRP* 6.4 0.9 - - + -
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Residues in contact with ARG 494 (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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14A G 4.7 6.5 + - - -
461B ARG 4.8 5.7 + - - -
462B PHE* 4.1 10.1 + - - +
463B ALA 3.9 17.8 + - - -
464B TRP* 3.5 40.9 - - - +
490B SER* 2.9 22.0 + - - +
491B PHE* 3.4 21.7 - - - +
493B GLU* 1.3 75.9 - - - +
495B MET* 1.3 73.5 + - + +
496B THR 5.2 0.2 - - - +
506B LYS* 5.1 0.4 - - - -
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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