Contacts of the helix formed by residues 533 - 548 (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 VAL 533 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495B TYR* 3.3 49.1 - - + -
498B ARG* 3.6 9.0 - - - +
531B ASP* 2.7 20.9 + - - +
532B PRO* 1.3 77.4 - - + +
534B ALA* 1.3 69.5 + - - +
535B ASN* 3.7 17.0 - - + +
536B VAL* 3.2 19.8 + - + +
537B ARG* 3.4 3.5 + - - -
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Residues in contact with ALA 534 (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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532B PRO 3.7 3.8 + - - -
533B VAL* 1.3 68.2 - - - +
535B ASN* 1.3 59.9 + - - +
536B VAL 2.5 6.3 + - - -
537B ARG* 2.5 52.3 + - - +
538B PHE* 3.0 14.0 + - + -
572B ASP* 3.6 31.9 - - + +
575B VAL* 4.6 1.6 - - + -
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Residues in contact with ASN 535 (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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495B TYR* 4.0 12.6 + - - -
499B MET* 3.9 26.3 - - + +
533B VAL* 3.9 14.0 - - + +
534B ALA* 1.3 80.3 + - - +
536B VAL* 1.3 56.1 + - - +
538B PHE* 3.4 27.3 - - + -
539B ASN* 2.9 35.3 + - - +
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Residues in contact with VAL 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B TYR* 4.0 17.7 - - + +
498B ARG* 3.9 9.9 - - + +
499B MET* 4.4 9.0 - - + -
502B LEU* 3.6 7.3 - - + +
528B MET* 4.2 28.0 - - + +
531B ASP* 3.3 44.2 - - + +
533B VAL* 3.3 19.5 - - + +
534B ALA 2.5 4.8 + - - -
535B ASN* 1.3 74.7 - - - +
537B ARG* 1.3 49.9 + - - +
539B ASN* 3.0 6.4 + - - +
540B VAL* 2.7 32.9 + - - +
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Residues in contact with ARG 537 (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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528B MET 4.0 1.3 - - - +
529B ALA 2.9 34.3 - - - +
530B GLY* 4.2 3.7 + - - -
531B ASP 3.2 31.2 + - - +
532B PRO* 3.9 9.2 + - - +
533B VAL 3.9 3.0 + - - -
534B ALA* 2.5 37.8 + - - +
536B VAL* 1.3 71.7 - - - +
538B PHE* 1.3 67.0 + - - +
539B ASN 2.8 1.3 - - - -
540B VAL* 2.6 29.3 + - + +
541B ALA* 3.1 6.4 + - - +
567B LEU* 5.0 3.7 - - + +
570B ASP* 3.1 39.5 + - - +
572B ASP* 4.8 4.8 - - - +
575B VAL* 4.4 9.5 - - + +
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Residues in contact with PHE 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B ALA* 3.0 8.0 + - + -
535B ASN* 3.4 46.7 - - - -
537B ARG* 1.3 79.1 - - - +
539B ASN* 1.3 76.7 - - - +
541B ALA* 3.7 4.6 - - - +
542B LYS* 3.0 54.9 + - + +
574B ASP* 3.8 17.7 - - + +
575B VAL* 3.5 41.3 - - + +
578B PHE* 3.7 17.0 - + - +
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Residues in contact with ASN 539 (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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499B MET* 4.0 13.0 - - + -
502B LEU* 3.9 9.0 - - + -
503B PHE* 3.0 38.3 - - + -
535B ASN* 2.9 22.0 + - - +
536B VAL* 3.0 5.8 + - - +
537B ARG 2.8 1.8 - - - -
538B PHE* 1.3 103.5 - - - +
540B VAL* 1.3 54.7 + - - -
541B ALA 3.1 1.8 - - - -
542B LYS* 3.4 21.3 + - - +
543B SER* 2.7 32.6 + - - -
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Residues in contact with VAL 540 (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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502B LEU* 3.6 15.0 - - + -
525B VAL* 2.9 39.3 - - + +
526B LEU* 5.0 0.2 - - - -
528B MET 4.6 2.9 - - - +
529B ALA* 3.9 27.6 - - + +
536B VAL 2.7 13.6 + - - +
537B ARG* 2.6 39.0 + - + +
539B ASN* 1.3 72.1 - - - +
541B ALA* 1.3 69.0 + - - +
543B SER* 3.2 5.5 + - - -
544B LEU* 3.2 24.2 + - + +
567B LEU* 4.5 7.2 - - + -
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Residues in contact with ALA 541 (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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537B ARG 3.1 5.5 + - - +
538B PHE* 3.7 11.2 - - - +
540B VAL* 1.3 79.1 - - - +
542B LYS* 1.3 54.8 + - - +
543B SER 2.6 15.5 + - - -
544B LEU* 2.6 26.7 + - - +
545B GLN* 3.0 9.9 + - - +
564B LEU* 5.5 2.0 - - + -
567B LEU* 4.6 11.4 - - + -
575B VAL* 5.0 1.1 - - + +
578B PHE 4.3 4.0 - - - +
579B ALA* 4.0 32.5 - - + +
582B ALA* 4.5 6.1 - - + +
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Residues in contact with LYS 542 (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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506B ASN* 5.1 2.2 - - - +
538B PHE* 3.0 53.3 - - + +
539B ASN* 3.6 21.2 + - - +
541B ALA* 1.3 74.4 - - - +
543B SER* 1.3 56.1 + - - +
545B GLN* 3.1 17.1 - - - +
546B LYS* 3.0 24.6 + - - +
578B PHE* 3.6 42.2 - - + +
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Residues in contact with SER 543 (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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502B LEU* 3.7 15.5 - - - +
503B PHE* 5.3 0.2 - - - -
506B ASN* 2.9 36.2 + - - +
525B VAL* 4.1 14.8 - - - -
539B ASN* 2.7 19.7 + - - -
540B VAL* 3.2 10.8 - - - -
541B ALA 2.6 4.6 + - - -
542B LYS* 1.3 71.5 - - - +
544B LEU* 1.3 54.2 + - - -
545B GLN 3.0 1.8 - - - -
546B LYS* 3.1 2.5 + - - +
547B ILE* 2.8 39.9 + - - +
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Residues in contact with LEU 544 (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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522B LEU* 3.7 30.1 - - + -
525B VAL* 3.9 15.3 - - + -
526B LEU* 4.0 19.3 - - + -
540B VAL* 3.6 22.2 - - + +
541B ALA* 2.6 14.8 + - - +
543B SER* 1.3 69.3 - - - +
545B GLN* 1.3 58.7 + - - +
547B ILE* 4.2 6.5 - - + -
548B GLY* 2.6 35.3 + - - -
551B LEU* 5.9 0.2 - - + -
560B VAL* 4.3 14.2 - - + +
563B ILE 5.0 4.7 - - - +
564B LEU* 4.3 33.9 - - + -
567B LEU* 5.0 4.5 - - + -
586B LEU* 4.6 3.9 - - - +
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Residues in contact with GLN 545 (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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541B ALA 3.0 4.2 + - - -
542B LYS* 3.1 19.6 - - - +
544B LEU* 1.3 83.0 - - - +
546B LYS* 1.3 65.1 + - - +
548B GLY* 2.8 6.2 + - - -
549B PRO* 3.2 13.0 - - - +
578B PHE* 4.9 4.9 - - - +
581B GLU* 4.0 17.4 + - - +
582B ALA* 3.8 39.1 + - + +
585B VAL* 4.2 25.5 - - + +
586B LEU* 4.4 7.0 - - + +
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Residues in contact with LYS 546 (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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506B ASN* 3.6 32.3 - - + +
507B VAL* 6.2 0.7 - - - -
509B SER* 5.1 1.3 + - - +
510B GLU* 3.1 36.6 + - - -
542B LYS 3.0 10.1 + - - +
543B SER* 3.1 11.2 + - - +
545B GLN* 1.3 84.0 - - - +
547B ILE* 1.3 60.8 + - + +
548B GLY 3.1 2.6 + - - -
549B PRO* 3.7 9.9 - - - +
550B ILE* 5.1 4.5 - - - +
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Residues in contact with ILE 547 (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* 4.2 14.8 - - + -
506B ASN* 4.3 12.3 - - - +
509B SER* 3.5 34.8 - - - +
517B THR* 4.3 15.7 - - + +
522B LEU* 4.0 38.8 - - + +
525B VAL* 4.5 13.0 - - + -
543B SER* 2.8 24.0 + - - +
544B LEU* 4.2 9.9 - - + +
546B LYS* 1.3 70.8 - - - +
548B GLY* 1.3 69.8 + - - +
549B PRO 3.6 0.2 - - - -
550B ILE* 3.6 13.4 + - + +
551B LEU* 3.7 16.4 + - + +
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Residues in contact with GLY 548 (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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544B LEU 2.6 24.5 + - - -
545B GLN 2.8 5.4 + - - -
546B LYS 3.0 0.6 - - - -
547B ILE* 1.3 79.0 - - - +
549B PRO* 1.3 68.5 - - - +
551B LEU* 2.8 23.8 + - - +
556B LEU* 4.4 16.3 - - - +
560B VAL* 6.3 1.6 - - - -
586B LEU* 4.3 8.5 - - - -
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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
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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