Contacts of the helix formed by residues 488 - 505 (chain B) in PDB entry 3BJI
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 488 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469B HIS* 3.5 14.0 - - - +
486B PHE 3.7 1.4 - - - +
487B LYS* 1.3 82.4 - - - +
489B ARG* 1.3 60.4 + - + +
490B GLU* 2.5 53.6 - - + +
491B LEU* 3.0 26.1 - - + +
492B LYS 3.5 12.8 + - - -
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Residues in contact with ARG 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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469B HIS* 3.8 30.4 + - + +
488B THR* 1.3 72.5 - - - +
490B GLU* 1.3 66.1 + - - +
491B LEU 3.1 0.4 - - - -
492B LYS* 3.2 13.5 + - + +
493B LYS* 3.1 33.9 + - + +
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Residues in contact with GLU 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B THR* 2.5 23.7 - - + +
489B ARG* 1.3 73.3 - - - +
491B LEU* 1.3 55.8 + - + -
493B LYS* 3.3 6.4 + - - +
494B LYS* 2.9 38.3 + - + +
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Residues in contact with LEU 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B ILE* 6.2 1.1 - - + -
486B PHE* 3.8 16.5 - - + -
487B LYS* 4.1 21.1 - - + -
488B THR* 3.0 39.5 - - + +
490B GLU* 1.3 79.5 - - + +
492B LYS* 1.3 64.4 + - - +
494B LYS* 4.3 17.3 - - + -
495B TRP* 3.2 40.8 + - + +
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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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456B ASP* 4.3 14.8 - - - +
469B HIS* 4.3 16.4 - - + +
470B MET 3.8 25.1 - - - +
471B PHE* 3.8 21.8 - - + -
486B PHE* 3.8 19.6 - - + +
488B THR 3.5 3.4 + - - -
489B ARG* 3.2 18.8 + - + +
491B LEU* 1.3 78.5 - - - +
493B LYS* 1.3 63.6 + - + +
495B TRP* 3.8 1.2 - - - +
496B MET* 2.8 36.0 + - - +
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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
----------------------------------------------------------
489B ARG* 3.1 29.4 + - + +
490B GLU* 3.8 4.9 - - - +
492B LYS* 1.3 79.9 - - + +
494B LYS* 1.3 66.2 + - - +
496B MET* 3.2 5.5 + - - +
497B GLU* 2.8 28.3 + - - +
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Residues in contact with LYS 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B ILE* 5.0 10.3 - - + -
490B GLU* 2.9 24.1 + - + +
491B LEU* 4.0 20.2 - - + +
493B LYS* 1.3 76.0 - - - +
495B TRP* 1.3 67.4 + - + +
497B GLU* 3.1 25.8 - - - +
498B GLN* 3.2 14.8 + - - +
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Residues in contact with TRP 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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405B ILE* 3.4 45.9 - - + +
406B ASP 3.8 17.6 + - - -
407B GLY* 3.9 11.5 - - - -
408B GLU 4.9 4.9 + - - -
409B LEU* 4.7 5.4 - - + -
424B ALA* 3.7 29.6 - - + -
426B LEU* 3.9 24.5 - - + -
431B LEU* 4.3 3.4 - - + -
471B PHE* 4.4 1.8 - - + -
486B PHE* 3.7 36.2 - + + -
491B LEU* 3.2 36.1 + - + +
492B LYS 3.8 2.2 - - - +
494B LYS* 1.3 77.4 - - + +
496B MET* 1.3 66.6 + - - +
498B GLN* 3.2 8.0 + - - +
499B PHE* 3.1 50.6 + + - -
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Residues in contact with MET 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B VAL* 3.8 27.8 - - + +
455B ARG 4.1 0.9 - - - -
456B ASP* 3.6 51.4 - - + +
471B PHE* 4.0 26.6 - - + -
492B LYS* 2.8 24.6 + - - +
493B LYS* 3.8 5.2 - - - +
495B TRP* 1.3 75.9 - - - +
497B GLU* 1.3 60.6 + - - +
499B PHE* 3.0 6.2 + - - +
500B GLU* 2.9 45.3 + - + +
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Residues in contact with GLU 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B LYS 2.8 18.6 + - - +
494B LYS* 3.1 19.5 - - - +
496B MET* 1.3 72.5 - - - +
498B GLN* 1.3 77.0 + - - +
500B GLU* 3.2 18.5 + - - +
501B MET* 3.2 28.4 + - - +
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Residues in contact with GLN 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B LYS* 3.0 57.7 - - + +
405B ILE* 4.1 16.4 - - + +
426B LEU* 4.1 8.1 - - + -
494B LYS 3.2 13.1 + - - +
495B TRP* 3.6 9.6 - - - +
497B GLU* 1.3 92.1 + - - +
499B PHE* 1.3 59.8 + - - +
501B MET* 3.0 41.5 + - - +
502B ALA* 2.9 27.4 + - - +
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Residues in contact with PHE 499 (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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426B LEU* 3.9 30.3 - - + -
431B LEU* 3.9 14.8 - - + -
449B LEU* 4.7 11.9 - - + -
454B VAL* 4.7 11.0 - - + -
471B PHE* 3.5 31.4 - + - -
473B LEU* 4.1 30.1 - - + -
484B LEU* 3.9 18.8 - - + -
495B TRP* 3.1 45.0 + + - -
496B MET* 3.0 8.9 + - - +
498B GLN* 1.3 73.4 - - - +
500B GLU* 1.3 68.4 + - - +
502B ALA* 3.1 2.2 + - - +
503B ILE* 3.0 38.9 + - + +
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Residues in contact with GLU 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B VAL* 5.5 5.9 - - + +
496B MET* 2.9 41.7 + - + +
497B GLU* 3.2 15.5 + - - +
499B PHE* 1.3 77.8 - - + +
501B MET* 1.3 56.2 + - + +
503B ILE* 4.1 7.7 - - - +
504B SER* 2.9 30.2 + - - -
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Residues in contact with MET 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B LYS* 4.1 16.6 - - + +
497B GLU* 3.2 20.2 + - - +
498B GLN* 3.0 46.2 - - - +
499B PHE 3.1 0.4 - - - -
500B GLU* 1.3 75.4 - - + +
502B ALA* 1.3 67.3 + - - +
504B SER* 2.9 9.8 + - - +
505B ASN* 2.7 29.6 + - - +
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Residues in contact with ALA 502 (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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404B LYS* 4.1 13.8 - - + +
426B LEU* 4.4 4.0 - - + -
427B LEU 3.8 9.6 - - - +
428B ASP* 3.4 23.7 - - - +
449B LEU* 3.8 17.3 - - + -
498B GLN 2.9 16.8 + - - +
499B PHE* 3.6 10.3 - - - +
501B MET* 1.3 73.5 - - - +
503B ILE* 1.3 61.2 + - - +
505B ASN* 3.2 11.1 + - - +
506B ILE* 3.3 18.6 - - - +
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Residues in contact with ILE 503 (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 LEU* 5.1 15.5 - - + +
452B PHE 4.3 18.4 - - - +
453B GLN* 5.0 1.6 - - - -
454B VAL* 3.3 33.9 - - + -
473B LEU* 5.9 2.0 - - + -
499B PHE* 3.0 23.4 + - + +
500B GLU* 4.1 5.2 - - - +
502B ALA* 1.3 75.7 - - + +
504B SER* 1.3 62.0 + - - +
505B ASN 3.1 0.4 - - - -
506B ILE* 3.1 9.4 + - + +
507B TYR* 2.9 45.2 + - + +
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Residues in contact with SER 504 (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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500B GLU 2.9 20.7 + - - -
501B MET* 2.9 11.4 + - - +
503B ILE* 1.3 76.5 - - - +
505B ASN* 1.3 63.8 + - - +
507B TYR 4.2 6.5 - - - -
508B PRO* 3.2 25.3 - - - +
555B LYS* 4.0 16.3 + - - -
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Residues in contact with ASN 505 (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 ARG* 6.0 0.8 - - - +
404B LYS* 3.4 17.8 - - - +
428B ASP* 2.5 32.4 + - - +
501B MET* 2.7 16.4 + - - +
502B ALA 3.5 9.0 - - - +
503B ILE 3.1 1.0 - - - -
504B SER* 1.3 74.4 - - - +
506B ILE* 1.3 56.2 + - - +
508B PRO* 3.3 3.8 - - - +
520B MET* 3.4 19.1 - - + +
544B TYR* 2.4 37.2 + - - +
555B LYS* 2.9 27.5 + - - -
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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