Contacts of the helix formed by residues 493 - 512 (chain B) in PDB entry 5J3V
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 ASN 493 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B LEU 5.8 1.0 + - - -
452B ALA* 3.7 25.5 - - + +
455B ARG* 4.5 4.7 - - - +
491B ASP* 2.8 13.2 + - - +
492B SER* 1.3 80.1 + - - +
494B LYS* 1.3 65.2 + - - +
495B ARG* 2.9 40.6 + - - +
496B VAL* 3.0 22.5 + - + +
497B GLN* 3.1 24.5 + - - +
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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
----------------------------------------------------------
492B SER 4.9 4.9 - - - +
493B ASN* 1.3 72.4 - - - +
495B ARG* 1.3 69.4 + - + +
497B GLN* 3.0 20.2 + - - +
498B GLU* 3.0 31.5 + - - +
534B GLN* 2.8 39.3 + - + +
537B ASN* 3.5 5.7 + - - +
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Residues in contact with ARG 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B LEU 4.1 3.4 + - - -
318B LEU* 3.4 40.6 + - - +
319B LYS* 5.6 2.6 - - - +
369B THR* 2.6 49.5 + - - +
452B ALA 6.6 0.2 - - - -
453B LEU* 4.9 14.8 - - + -
456B SER* 4.0 10.5 - - - +
493B ASN* 2.9 18.7 + - - +
494B LYS* 1.3 79.6 - - + +
496B VAL* 1.3 61.4 + - + +
498B GLU* 3.6 17.7 + - - +
499B ALA* 3.2 23.2 + - - +
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Residues in contact with VAL 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B ALA* 3.5 28.3 - - + +
455B ARG* 4.0 16.6 - - + +
456B SER* 4.2 10.1 - - - +
459B CYS* 5.1 1.1 - - - -
488B ARG* 3.8 20.2 - - + +
491B ASP* 3.6 28.9 - - + +
493B ASN* 3.0 34.8 + - + +
494B LYS 3.2 0.2 - - - -
495B ARG* 1.3 74.5 - - + +
497B GLN* 1.3 60.4 + - - +
499B ALA* 3.9 0.5 - - - +
500B ALA* 2.9 30.5 + - + +
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Residues in contact with GLN 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B ARG 3.8 7.2 - - - -
489B ILE* 3.4 15.2 + - - +
491B ASP 2.4 34.0 + - - +
492B SER 4.6 3.8 + - - -
493B ASN 3.1 14.4 + - - +
494B LYS* 3.0 17.4 + - - +
496B VAL* 1.3 78.2 - - - +
498B GLU* 1.3 62.4 + - - +
500B ALA* 4.2 0.2 - - - +
501B CYS* 3.0 28.9 + - - +
532B LYS* 4.1 25.6 - - - +
533B TYR* 3.2 30.2 + - - +
537B ASN* 3.4 16.1 + - - +
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Residues in contact with GLU 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B LYS* 3.0 18.5 + - - +
495B ARG* 3.8 18.4 - - - +
497B GLN* 1.3 77.1 - - - +
499B ALA* 1.3 56.9 + - - +
501B CYS* 4.9 0.4 - - - -
502B SER* 3.0 32.1 + - - -
536B LYS* 4.0 25.2 + - - +
537B ASN* 3.3 30.6 - - - +
540B ILE* 3.9 25.5 - - + +
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Residues in contact with ALA 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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456B SER* 3.5 36.6 - - - +
459B CYS* 3.8 3.3 - - + +
460B TRP* 5.0 5.0 + - + +
495B ARG 3.2 14.5 + - - +
496B VAL 4.0 0.9 - - - +
497B GLN 3.4 0.2 - - - -
498B GLU* 1.3 78.8 - - - +
500B ALA* 1.3 58.8 + - - +
502B SER* 3.4 4.9 + - - -
503B ALA* 2.8 31.0 + - - +
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Residues in contact with ALA 500 (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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459B CYS* 3.7 17.9 - - - -
485B LEU* 4.1 10.6 - - + +
488B ARG* 3.5 37.9 - - + +
489B ILE* 4.0 5.3 - - - +
496B VAL 2.9 18.2 + - - +
497B GLN 4.2 0.4 - - - +
499B ALA* 1.3 74.3 - - - +
501B CYS* 1.3 61.1 + - - +
503B ALA* 3.3 2.4 + - - +
504B PHE* 2.9 30.0 + - - +
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Residues in contact with CYS 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B ILE* 4.1 19.3 - - + +
497B GLN 3.0 19.8 + - - +
498B GLU* 4.9 0.2 - - - -
500B ALA* 1.3 77.1 - - - +
502B SER* 1.3 61.3 + - - +
504B PHE* 3.6 2.4 + - - +
505B ALA* 3.3 20.3 + - - +
533B TYR* 3.9 14.6 - - + +
540B ILE* 3.9 12.8 - - + +
541B LEU* 3.7 40.2 - - - -
544B ALA* 3.7 18.4 - - - +
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Residues in contact with SER 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498B GLU 3.0 20.4 + - - -
499B ALA* 3.7 5.2 - - - -
501B CYS* 1.3 75.8 - - - +
503B ALA* 1.3 64.1 + - - +
505B ALA* 3.3 8.7 + - - +
506B THR* 3.3 21.0 + - - -
540B ILE* 3.6 18.5 - - - +
543B ASP* 5.5 1.1 - - - -
22D THR 5.3 0.2 + - - -
26D ARG* 3.5 25.9 - - - +
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Residues in contact with ALA 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B CYS* 3.2 35.7 - - + +
460B TRP* 4.4 1.3 - - - +
463B SER* 3.7 17.5 - - - +
485B LEU* 4.6 10.3 - - + +
499B ALA 2.8 19.3 + - - +
500B ALA* 3.3 4.5 + - - +
502B SER* 1.3 74.0 - - - +
504B PHE* 1.3 64.0 + - - +
506B THR* 3.2 5.6 + - - -
507B LEU* 3.1 21.5 + - - +
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Residues in contact with PHE 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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482B MET* 3.8 24.7 - - + -
485B LEU* 3.9 25.5 - - + +
486B LEU* 3.6 27.6 - - + -
489B ILE* 4.2 15.5 - - + -
500B ALA 2.9 17.7 + - - +
501B CYS 3.8 5.6 - - - +
502B SER 3.2 0.2 - - - -
503B ALA* 1.3 76.0 - - - +
505B ALA* 1.3 59.0 + - - +
507B LEU* 3.2 9.8 + - + +
508B GLU* 2.9 66.9 + - + +
515B LEU* 5.4 2.7 - - + -
522B ILE* 3.6 34.8 - - + -
526B LEU* 5.0 6.1 - - + -
544B ALA* 5.1 4.0 - - + -
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Residues in contact with ALA 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B CYS 3.3 10.9 + - - +
502B SER* 3.3 10.9 + - - +
503B ALA 3.2 0.6 - - - -
504B PHE* 1.3 77.1 - - - +
506B THR* 1.3 63.4 + - - +
508B GLU* 3.4 12.0 + - - -
509B GLU 3.4 15.8 + - - -
540B ILE 5.5 0.2 - - - +
543B ASP* 3.6 27.8 - - - +
544B ALA* 4.3 12.1 - - - +
547B THR* 3.5 12.5 - - - +
26D ARG* 3.7 15.5 + - - +
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Residues in contact with THR 506 (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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463B SER* 3.3 36.0 + - - +
466B ALA* 4.5 4.3 - - + -
502B SER 3.3 7.3 + - - -
503B ALA* 3.2 9.9 + - - -
504B PHE 3.2 0.2 - - - -
505B ALA* 1.3 79.2 - - - +
507B LEU* 1.3 60.3 + - - +
509B GLU* 3.4 13.0 + - - +
510B GLU* 3.6 18.4 + - + +
26D ARG* 3.2 34.6 + - - +
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Residues in contact with LEU 507 (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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463B SER* 6.0 1.6 - - - -
466B ALA* 4.0 25.3 - - + +
469B VAL* 4.9 1.6 - - + -
470B VAL* 4.1 9.6 - - + -
478B LEU* 4.1 24.7 - - + -
481B LEU* 4.0 27.4 - - + -
482B MET* 3.9 27.8 - - + -
485B LEU* 4.1 12.6 - - + -
503B ALA 3.1 12.8 + - - +
504B PHE* 3.2 12.3 + - + +
506B THR* 1.3 76.9 - - - +
508B GLU* 1.3 58.2 + - + +
510B GLU* 3.4 0.9 + - - -
511B ALA* 2.9 32.8 + - + +
515B LEU* 5.3 3.8 - - + -
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Residues in contact with GLU 508 (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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504B PHE* 2.9 48.4 + - + +
505B ALA* 3.6 13.6 - - - +
506B THR 3.2 0.2 - - - -
507B LEU* 1.3 76.9 - - + +
509B GLU* 1.3 63.6 + - - +
512B CYS 3.1 15.4 + - - -
515B LEU* 3.7 21.2 - - + +
522B ILE* 4.3 0.5 - - - +
526B LEU* 4.4 1.4 - - - +
544B ALA* 2.9 23.3 - - - +
547B THR* 3.6 13.3 - - + -
548B LEU* 3.3 36.1 + - - +
551B SER* 2.8 21.1 + - - +
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Residues in contact with GLU 509 (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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505B ALA 3.4 1.9 + - - +
506B THR 3.7 7.9 - - - +
507B LEU 3.3 0.4 - - - -
508B GLU* 1.3 76.8 - - - +
510B GLU* 1.3 63.7 + - + +
512B CYS* 3.2 22.5 - - - -
547B THR* 3.6 18.6 - - + -
551B SER* 4.1 4.5 - - - -
23D LYS* 3.8 13.2 + - - -
26D ARG* 2.7 30.0 + - - +
27D LYS* 3.2 32.0 + - - -
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Residues in contact with GLU 510 (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 ALA* 4.0 31.2 - - + +
467B HIS* 3.8 30.6 + - - +
470B VAL* 3.9 16.8 - - + +
506B THR* 3.7 16.4 - - + +
507B LEU 3.4 5.5 + - - +
508B GLU 3.3 0.2 - - - -
509B GLU* 1.3 82.9 - - + +
511B ALA* 1.3 62.3 + - - +
512B CYS* 4.1 5.5 - - - +
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Residues in contact with ALA 511 (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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470B VAL* 3.7 20.8 - - + +
478B LEU* 4.7 6.1 - - + -
507B LEU* 2.9 17.8 + - + +
510B GLU* 1.3 78.9 - - - +
512B CYS* 1.3 69.9 + - - +
513B THR* 3.1 2.9 + - - -
514B GLU* 3.1 24.3 + - + +
515B LEU* 3.7 31.6 - - + -
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Residues in contact with CYS 512 (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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508B GLU 3.1 9.5 + - - -
509B GLU 3.2 22.0 - - - -
510B GLU 4.1 5.4 - - - -
511B ALA* 1.3 77.5 - - - +
513B THR* 1.3 66.1 + - + +
514B GLU 3.1 4.4 + - - -
515B LEU* 3.6 18.2 + - - +
551B SER* 3.6 37.8 - - - +
552B VAL* 4.1 2.6 - - - +
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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
------------------------------------------------------------
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