Contacts of the helix formed by residues 487 - 498 (chain B) in PDB entry 4BGG
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 487 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404B ILE* 3.9 4.5 - - - -
485B ARG 5.0 2.5 - - - +
486B LEU* 1.3 77.5 - - - +
488B ALA* 1.3 65.5 + - - +
489B LEU* 3.5 8.9 + - - +
490B ARG* 3.1 25.4 + - + +
491B ILE* 3.0 24.9 + - - +
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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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313B ALA* 4.5 4.5 - - - +
316B LEU* 4.3 9.2 - - + -
317B ALA* 3.8 28.5 - - - +
320B HIS* 3.7 27.4 + - + +
404B ILE* 3.5 17.2 - - + +
487B THR* 1.3 75.0 - - - +
489B LEU* 1.3 62.1 + - - +
491B ILE* 3.3 7.4 + - - +
492B LYS* 3.0 23.0 + - - +
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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
----------------------------------------------------------
317B ALA* 4.3 11.1 - - + +
321B ILE* 5.7 10.5 - - + -
487B THR* 3.2 8.5 + - - +
488B ALA* 1.3 78.2 - - - +
490B ARG* 1.3 57.1 + - - +
492B LYS* 3.2 23.7 + - + +
493B LYS* 3.0 61.1 + - + +
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Residues in contact with ARG 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 LEU* 4.2 21.1 - - + -
487B THR* 3.1 26.1 + - + +
489B LEU* 1.3 73.5 - - - +
491B ILE* 1.3 66.8 + - - +
493B LYS* 3.8 18.4 - - - +
494B THR* 2.9 41.6 + - - +
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Residues in contact with ILE 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ALA* 4.1 4.5 - - + -
316B LEU* 6.2 0.4 - - + -
404B ILE* 4.1 17.0 - - + -
407B PHE* 3.5 44.2 - - + -
411B LEU* 5.4 0.2 - - + -
473B LEU* 4.2 17.2 - - + +
477B CYS* 3.8 17.5 - - - -
486B LEU* 3.8 23.6 - - + -
487B THR 3.0 16.3 + - - +
488B ALA* 3.3 8.3 + - - +
490B ARG* 1.3 75.9 - - - +
492B LYS* 1.3 56.7 + - - +
494B THR* 3.4 1.7 + - - -
495B LEU* 2.9 45.3 + - + +
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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
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259B HIS* 5.8 3.0 + - - -
310B LEU* 3.9 17.7 - - + +
313B ALA* 4.2 13.5 - - + +
314B SER* 3.5 38.4 + - - +
317B ALA* 4.5 8.3 - - + +
488B ALA 3.0 13.9 + - - +
489B LEU* 3.4 25.1 - - + +
491B ILE* 1.3 78.9 - - - +
493B LYS* 1.3 58.0 + - + +
495B LEU* 3.4 0.9 + - - -
496B THR* 2.9 38.6 + - - +
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Residues in contact with LYS 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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347A ASN* 6.4 2.0 - - + -
489B LEU* 3.0 52.5 + - + +
490B ARG* 3.3 18.8 + - - +
492B LYS* 1.3 76.7 - - + +
494B THR* 1.3 63.7 + - - +
496B THR* 3.2 8.1 + - - -
497B LYS* 3.0 30.2 + - + +
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Residues in contact with THR 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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469B SER* 5.8 4.3 - - - +
473B LEU* 4.1 29.7 - - + +
486B LEU* 5.7 0.5 - - - +
490B ARG* 2.9 32.7 + - - +
491B ILE 3.8 3.6 - - - -
493B LYS* 1.3 76.5 - - - +
495B LEU* 1.3 62.6 + - - +
497B LYS* 3.4 22.0 + - + +
498B ILE* 3.6 14.0 + - + +
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Residues in contact with LEU 495 (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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306B LEU* 4.4 12.8 - - + +
309B VAL* 3.8 42.0 - - + +
310B LEU* 4.0 18.8 - - + +
313B ALA* 4.1 8.1 - - + -
407B PHE* 4.6 3.6 - - + -
411B LEU* 5.6 0.7 - - + -
470B LEU* 3.5 32.1 - - + -
473B LEU* 3.6 15.3 - - + -
491B ILE* 2.9 35.6 + - + +
492B LYS 3.9 2.9 - - - +
494B THR* 1.3 75.3 - - - +
496B THR* 1.3 62.9 + - - +
498B ILE* 3.2 25.5 + - + +
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Residues in contact with THR 496 (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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307A ARG* 4.1 30.7 + - - +
347A ASN* 3.3 39.3 - - + +
310B LEU* 3.8 16.1 - - - +
492B LYS* 2.9 30.0 + - - +
493B LYS* 3.2 8.4 + - - -
495B LEU* 1.3 77.1 - - - +
497B LYS* 1.3 62.2 + - - +
498B ILE 3.1 8.8 + - - -
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Residues in contact with LYS 497 (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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493B LYS* 3.0 24.2 + - + +
494B THR* 3.5 11.4 - - + +
495B LEU 3.3 0.6 - - - -
496B THR* 1.3 75.0 - - + +
498B ILE* 1.3 60.2 + - + +
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Residues in contact with ILE 498 (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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301A ASP* 5.6 1.7 - - - +
303A VAL* 5.6 7.1 - - - +
307A ARG* 6.0 2.2 - - - -
302B THR* 6.0 0.2 - - + -
306B LEU* 3.8 41.9 - - + +
466B THR* 4.6 15.3 - - + +
469B SER* 3.8 31.6 - - - +
470B LEU* 5.1 2.7 - - + -
473B LEU* 5.9 0.4 - - + -
494B THR* 3.6 17.9 + - + +
495B LEU* 3.2 24.7 + - + +
496B THR 3.1 10.8 + - - -
497B LYS* 1.3 80.2 - - + +
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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