Contacts of the helix formed by residues 494 - 513 (chain B) in PDB entry 2PKG
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 494 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492B ASP* 3.3 13.4 - - - +
493B PRO* 1.3 78.1 - - + +
495B TYR* 1.3 74.2 + - - +
496B LEU* 3.0 35.6 + - - +
497B HIS* 2.7 47.5 + - + +
498B ARG* 3.6 5.5 + - - -
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Residues in contact with TYR 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B PRO 3.4 6.5 + - - -
494B ASN* 1.3 75.2 - - - +
496B LEU* 1.3 88.6 + - + +
498B ARG* 2.9 35.9 + - - +
499B MET* 2.9 56.7 + - + +
533B VAL* 3.3 35.4 - - + -
535B ASN* 4.0 17.6 + - + -
536B VAL* 4.0 3.7 - - + +
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Residues in contact with LEU 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B ARG* 4.7 23.4 + - - +
494B ASN* 2.7 33.2 + - - +
495B TYR* 1.3 100.7 - - + +
497B HIS* 1.3 63.8 + - + +
499B MET* 3.3 25.0 + - + +
500B THR* 3.2 21.8 + - - -
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Residues in contact with HIS 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B LEU 5.0 2.4 + - - -
452B VAL* 2.9 54.8 - - + +
459B ARG* 5.2 9.2 - - - -
489B MET* 4.2 12.7 - - + +
492B ASP* 3.0 37.5 - - + +
494B ASN* 2.7 37.9 + - - +
496B LEU* 1.3 74.4 - - + +
498B ARG* 1.3 65.3 + - - +
500B THR* 3.0 18.9 + - - -
501B THR* 2.8 14.8 + - - -
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Residues in contact with ARG 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B MET 3.9 1.7 + - - +
490B SER* 3.1 34.1 - - - +
491B GLY* 4.3 1.1 - - - -
492B ASP 2.8 30.6 + - - +
493B PRO* 3.3 23.6 + - - +
494B ASN 3.6 1.8 + - - -
495B TYR* 2.9 33.7 + - - +
497B HIS* 1.3 77.8 - - - +
499B MET* 1.3 66.0 + - - +
501B THR* 2.9 24.3 + - - -
502B LEU 3.3 0.9 + - - -
528B MET* 3.3 20.9 - - + +
531B ASP* 2.9 39.2 + - - +
532B PRO* 4.4 6.3 - - - +
533B VAL* 3.6 7.9 - - - +
536B VAL* 3.9 4.0 - - + +
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Residues in contact with MET 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B TYR* 2.9 50.2 + - + +
496B LEU* 3.4 30.3 - - + +
497B HIS 3.1 0.2 - - - -
498B ARG* 1.3 76.9 - - - +
500B THR* 1.3 64.5 + - - +
502B LEU* 2.8 23.6 + - - +
503B PHE* 2.9 31.2 + - + -
535B ASN* 3.9 24.7 - - + +
536B VAL* 4.4 11.6 - - + +
539B ASN* 4.0 23.1 - - + +
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Residues in contact with THR 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B LEU* 3.7 43.9 + - + +
459B ARG* 3.8 24.9 + - + +
463B THR* 4.6 6.7 - - - +
489B MET* 4.5 5.2 - - - -
496B LEU 3.2 10.0 + - - -
497B HIS* 3.0 13.1 + - - -
499B MET* 1.3 78.9 - - - +
501B THR* 1.3 52.0 + - - +
503B PHE* 3.1 14.5 + - + +
504B CYS* 2.7 37.4 + - - +
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Residues in contact with THR 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B VAL* 2.9 34.8 - - + +
487B LEU* 4.0 8.7 - - + -
489B MET* 3.4 8.0 - - - +
490B SER* 3.3 33.1 + - - +
497B HIS 2.8 15.4 + - - -
498B ARG* 2.9 17.3 + - - -
499B MET 2.9 0.2 + - - -
500B THR* 1.3 73.8 - - - +
502B LEU* 1.3 63.8 + - - +
504B CYS* 3.2 8.4 + - - +
505B ILE* 3.1 27.0 + - + +
524B THR* 4.9 2.0 - - + -
528B MET* 4.4 2.0 - - + -
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Residues in contact with LEU 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498B ARG 3.3 3.3 + - - +
499B MET* 2.8 12.4 + - - +
501B THR* 1.3 74.8 - - - +
503B PHE* 1.3 65.1 + - + +
504B CYS 2.9 0.9 + - - -
505B ILE* 2.9 9.3 + - + +
506B ASN* 2.7 34.1 + - - +
525B VAL* 4.0 33.9 - - + -
528B MET* 3.5 40.2 - - + -
536B VAL* 3.6 15.5 - - + +
539B ASN* 3.9 8.1 - - + -
540B VAL* 3.6 32.8 - - + +
543B SER* 3.7 12.6 - - - +
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Residues in contact with PHE 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B TYR* 5.6 8.7 - + - -
460B GLU* 5.0 17.0 - - - +
463B THR* 3.6 18.7 - - + +
499B MET* 2.9 32.8 + - + -
500B THR* 3.3 17.9 - - + +
502B LEU* 1.3 81.0 - - + +
504B CYS* 1.3 61.6 + - - +
506B ASN* 3.5 26.9 - - - +
507B VAL* 3.5 7.8 + - - +
539B ASN* 3.0 42.4 - - + -
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Residues in contact with CYS 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B LEU* 4.0 18.8 - - - -
463B THR* 3.7 16.8 - - - -
466B LEU* 3.6 27.4 - - - -
486B VAL* 3.8 18.4 - - + -
489B MET* 5.8 2.2 - - - -
500B THR* 2.7 20.9 + - - +
501B THR* 3.4 9.2 - - - +
502B LEU 3.0 0.4 - - - -
503B PHE* 1.3 71.5 - - - +
505B ILE* 1.3 67.8 + - - +
507B VAL* 2.7 15.2 + - - +
508B LEU* 2.8 26.1 + - + +
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Residues in contact with ILE 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B VAL* 4.5 4.5 - - + -
487B LEU* 3.6 31.4 - - + -
501B THR* 3.1 16.4 + - + +
502B LEU* 2.9 9.6 + - + +
504B CYS* 1.3 76.4 - - - +
506B ASN* 1.3 68.5 + - - +
507B VAL 2.7 2.1 + - - -
508B LEU* 3.0 5.5 + - - +
509B SER* 2.9 24.1 + - - -
521B MET* 3.5 40.8 - - + +
524B THR* 4.3 7.6 - - + -
525B VAL* 3.4 34.3 - - + -
547B ILE* 4.2 12.3 - - + -
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Residues in contact with ASN 506 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B LEU 2.7 22.2 + - - +
503B PHE* 3.5 24.2 - - - +
505B ILE* 1.3 74.8 - - - +
507B VAL* 1.3 61.2 + - + +
509B SER* 3.5 13.4 + - - -
510B GLU* 3.6 9.5 - - - +
539B ASN* 5.7 0.2 - - - +
542B LYS* 5.1 1.4 - - - +
543B SER* 2.9 52.2 + - - +
546B LYS* 3.6 25.9 - - + +
547B ILE* 4.3 6.5 - - - +
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Residues in contact with VAL 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B THR* 4.9 14.1 - - + +
464B SER* 5.2 5.8 - - - -
467B LYS* 3.5 37.2 - - + +
503B PHE 3.9 10.3 - - - +
504B CYS 2.7 14.3 + - - +
506B ASN* 1.3 76.9 - - + +
508B LEU* 1.3 67.7 + - + +
509B SER 3.1 1.6 - - - -
510B GLU* 3.0 38.0 + - - +
511B VAL* 4.0 3.6 + - - +
546B LYS* 6.2 0.2 - - - -
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Residues in contact with LEU 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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463B THR* 5.7 0.7 - - + -
466B LEU* 4.2 25.4 - - + -
467B LYS 4.9 2.5 - - - +
470B VAL* 3.9 28.5 - - + -
478B ALA* 5.2 1.3 - - + -
482B ILE* 4.5 14.6 - - + -
483B ILE* 4.6 10.5 - - + -
486B VAL* 4.9 6.5 - - + -
504B CYS* 2.8 53.7 + - + +
505B ILE* 3.9 3.4 - - - +
507B VAL* 1.3 75.1 - - + +
509B SER* 1.3 65.7 + - - +
511B VAL* 3.0 8.1 + - - +
512B CYS* 2.9 34.9 + - - -
521B MET* 4.0 15.9 - - - -
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Residues in contact with SER 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 ILE 2.9 15.6 + - - -
506B ASN 3.5 11.3 + - - -
508B LEU* 1.3 75.7 - - - +
510B GLU* 1.3 70.6 + - - +
511B VAL 2.4 15.2 + - - -
512B CYS* 2.9 10.8 + - - +
513B GLY 3.7 7.1 + - - -
517B THR* 3.9 10.6 + - - -
521B MET* 3.4 17.4 - - - +
546B LYS* 5.1 1.0 - - - +
547B ILE* 3.5 24.1 - - - +
550B ILE* 3.0 27.1 - - - +
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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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467B LYS* 4.5 11.7 + - - +
506B ASN 3.6 11.9 - - - +
507B VAL* 3.0 36.2 + - + +
509B SER* 1.3 83.8 + - - +
511B VAL* 1.3 69.6 + - + +
546B LYS* 3.1 34.2 + - - -
550B ILE* 3.8 9.4 - - + -
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Residues in contact with VAL 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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467B LYS* 4.1 34.3 - - + +
470B VAL* 3.9 34.2 - - + +
471B GLU* 4.7 10.5 - - + +
475B LYS* 4.1 15.6 + - - +
507B VAL 4.6 2.5 - - - +
508B LEU* 3.5 12.3 - - - +
509B SER 2.4 14.6 + - - -
510B GLU* 1.3 80.3 - - + +
512B CYS* 1.3 60.3 + - - +
513B GLY 3.4 2.6 + - - +
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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
----------------------------------------------------------
470B VAL* 5.1 0.9 - - - -
475B LYS* 3.4 21.8 - - - +
478B ALA* 4.2 21.5 - - - -
483B ILE* 4.2 16.8 - - - -
508B LEU* 2.9 37.5 + - - +
509B SER* 2.9 2.0 + - - -
511B VAL* 1.3 83.1 - - - +
513B GLY* 1.3 64.5 + - - +
516B ILE* 3.3 35.1 - - + +
517B THR* 4.1 8.5 - - - +
521B MET* 4.9 1.8 - - - -
154C GLU* 5.6 0.5 - - - +
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Residues in contact with GLY 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B LYS* 5.0 7.6 - - - -
509B SER 3.7 6.8 + - - -
511B VAL 3.4 3.0 - - - -
512B CYS* 1.3 79.5 - - - +
514B GLN* 1.3 67.3 + - - -
515B ASP* 3.4 2.7 - - - -
516B ILE 2.9 15.1 + - - -
517B THR* 3.1 12.8 + - - -
550B ILE* 4.5 3.1 - - - -
154C GLU* 5.7 3.8 - - - -
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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