Contacts of the helix formed by residues 533 - 549 (chain B) in PDB entry 1B3U
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 ALA 533 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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531B PRO 3.1 5.3 + - - -
532B VAL* 1.3 67.1 - - - +
534B ASN* 1.3 65.6 + - - +
535B VAL 3.0 2.5 - - - -
536B ARG* 3.2 30.6 - - + +
537B PHE* 3.0 29.8 + - - +
570B GLN* 6.2 0.4 - - + -
572B VAL* 3.6 35.9 - - + -
574B VAL* 4.9 4.5 - - + +
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Residues in contact with ASN 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B TYR* 3.9 9.9 + - + -
498B MET* 3.1 39.5 - - - +
532B VAL* 3.0 17.0 - - + +
533B ALA* 1.3 78.2 - - - +
535B VAL* 1.3 59.7 + - - +
537B PHE* 3.1 40.9 - - - -
538B ASN* 3.5 15.2 - - - +
572B VAL* 5.8 0.2 - - - +
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Residues in contact with VAL 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B TYR* 4.2 15.3 - - + +
497B ARG* 4.6 6.5 - - + +
498B MET* 3.9 21.3 - - + -
501B LEU* 3.8 16.3 - - + +
527B MET* 4.6 11.0 - - + +
530B ASP* 3.0 40.6 - - + +
532B VAL* 2.9 17.6 + - + +
534B ASN* 1.3 77.1 - - - +
536B ARG* 1.3 60.4 + - - +
538B ASN* 2.9 22.2 + - - +
539B VAL* 3.0 16.8 + - + +
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Residues in contact with ARG 536 (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 ALA 3.1 28.5 - - - +
529B GLY* 4.8 1.5 - - - -
530B ASP* 2.9 32.4 + - + +
531B PRO* 2.7 21.1 + - - +
532B VAL 3.2 0.8 + - - -
533B ALA* 3.1 33.2 + - - +
535B VAL* 1.3 78.2 - - - +
537B PHE* 1.3 58.5 + - - +
539B VAL* 3.0 30.3 + - - +
540B ALA 3.3 4.0 + - - -
566B LEU* 4.2 6.3 - - + +
570B GLN* 2.7 48.0 + - - +
572B VAL* 5.5 0.4 - - - +
574B VAL* 3.5 19.9 - - + +
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Residues in contact with PHE 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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533B ALA 3.0 25.8 + - - +
534B ASN* 3.1 41.5 - - - -
536B ARG* 1.3 77.0 - - - +
538B ASN* 1.3 73.8 + - - +
539B VAL 3.2 0.2 - - - -
540B ALA* 3.6 7.6 + - - +
541B LYS* 3.0 32.8 + - + +
572B VAL* 4.9 9.0 - - + -
573B ASP* 3.8 21.8 - - + +
574B VAL* 3.6 29.8 - - - +
577B PHE* 3.3 30.4 - + + -
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Residues in contact with ASN 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498B MET* 4.5 7.3 - - + +
501B LEU* 4.0 21.8 - - + +
502B PHE* 2.9 47.4 - - - -
505B ASN* 5.4 0.4 + - - -
534B ASN 3.5 12.5 - - - +
535B VAL* 2.9 14.6 + - - +
537B PHE* 1.3 87.9 - - + +
539B VAL* 1.3 63.0 + - - +
541B LYS* 3.4 20.2 + - - +
542B SER* 3.1 27.0 + - - -
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Residues in contact with VAL 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B LEU* 4.1 11.7 - - + -
524B VAL* 3.8 23.8 - - + +
527B MET* 3.8 33.9 - - + +
528B ALA* 4.1 9.4 - - + +
535B VAL 3.0 19.1 + - - +
536B ARG* 3.0 16.1 + - - +
538B ASN* 1.3 74.8 - - - +
540B ALA* 1.3 60.9 + - - +
542B SER* 2.9 8.2 + - - -
543B LEU* 2.8 41.5 + - + +
562B ILE* 5.4 0.2 - - + -
566B LEU* 4.4 10.1 - - + -
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Residues in contact with ALA 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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536B ARG 3.3 3.4 + - - +
537B PHE* 3.8 11.2 - - - +
539B VAL* 1.3 80.9 - - - +
541B LYS* 1.3 62.0 + - - +
543B LEU* 3.5 0.9 + - - +
544B GLN* 3.1 24.1 + - - +
563B LEU* 4.1 13.9 - - + -
566B LEU* 4.2 13.7 - - + +
574B VAL* 5.7 0.2 - - + -
577B PHE* 3.9 7.4 - - + +
578B ALA* 3.7 34.1 - - + +
581B ALA* 3.7 7.1 - - - +
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Residues in contact with LYS 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B ASN* 4.9 4.3 - - - +
537B PHE* 3.0 31.9 - - + +
538B ASN* 3.6 24.7 - - - +
539B VAL 3.1 0.6 - - - -
540B ALA* 1.3 77.9 - - - +
542B SER* 1.3 57.6 + - - +
544B GLN* 3.5 10.7 + - - +
545B LYS* 3.0 26.9 + - - +
577B PHE* 3.8 37.8 - - + +
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Residues in contact with SER 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B LEU* 3.7 22.1 + - - +
504B ILE* 5.7 0.4 - - - -
505B ASN* 2.4 41.8 + - - +
524B VAL* 4.6 9.9 - - - -
538B ASN* 3.1 13.2 + - - -
539B VAL* 2.9 10.8 + - - -
541B LYS* 1.3 74.1 - - - +
543B LEU* 1.3 56.3 + - - +
545B LYS* 3.0 0.8 + - - -
546B ILE* 2.7 43.4 + - - +
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Residues in contact with LEU 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B LEU* 4.1 23.3 - - + -
524B VAL* 3.8 20.9 - - + -
525B LEU* 4.3 7.0 - - + -
539B VAL* 2.8 30.9 + - + +
540B ALA 3.8 4.3 - - - +
542B SER* 1.3 76.7 - - - +
544B GLN* 1.3 55.7 + - - +
546B ILE* 4.1 7.2 - - + -
547B GLY* 2.6 32.9 + - - -
559B VAL* 4.2 20.3 - - + +
562B ILE* 4.2 18.2 - - + -
563B LEU* 3.8 34.1 - - + -
566B LEU* 5.3 0.2 - - + -
585B LEU* 4.0 6.1 - - - +
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Residues in contact with GLN 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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540B ALA 3.1 17.3 + - - +
541B LYS* 3.7 8.9 - - - +
543B LEU* 1.3 77.0 - - - +
545B LYS* 1.3 60.9 - - - +
548B PRO* 3.3 17.0 - - - +
577B PHE 4.6 2.2 + - - -
580B GLU* 3.1 26.9 + - - +
581B ALA* 3.0 34.7 - - + +
584B VAL* 4.0 18.8 - - + +
585B LEU* 3.4 24.1 - - + +
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Residues in contact with LYS 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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505B ASN* 3.3 38.5 + - + +
506B VAL* 5.5 2.7 - - - +
508B SER* 4.8 0.7 + - - +
509B GLU* 2.7 43.2 + - - +
541B LYS 3.0 17.7 + - - +
542B SER* 3.0 7.6 + - - +
544B GLN* 1.3 80.9 - - - +
546B ILE* 1.3 61.0 + - + +
548B PRO* 3.6 13.2 - - - +
549B ILE* 4.6 5.5 - - - +
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Residues in contact with ILE 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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504B ILE* 4.0 14.4 - - + +
505B ASN* 4.3 11.4 - - - +
508B SER* 3.0 36.8 - - - +
516B THR* 4.4 16.8 - - + -
521B LEU* 4.3 24.0 - - + -
524B VAL* 4.4 20.0 - - + -
542B SER* 2.7 25.6 + - - +
543B LEU* 4.1 11.0 - - + -
545B LYS* 1.3 71.7 - - - +
547B GLY* 1.3 70.2 + - - +
548B PRO* 3.3 3.6 - - - -
549B ILE* 2.9 24.5 + - + +
550B LEU* 3.7 8.7 - - + +
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Residues in contact with GLY 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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543B LEU* 2.6 26.2 + - - -
546B ILE* 1.3 73.5 - - - +
548B PRO* 1.3 60.9 - - - +
549B ILE 2.9 5.9 + - - -
550B LEU* 3.2 33.8 + - - +
555B LEU* 3.8 22.6 - - - +
559B VAL* 5.5 2.0 - - - -
585B LEU* 4.6 3.6 - - - -
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Residues in contact with PRO 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 GLN 3.3 19.3 - - - +
545B LYS 3.6 12.1 - - - +
546B ILE 3.3 2.5 - - - -
547B GLY* 1.3 88.7 - - - +
549B ILE* 1.3 62.5 + - + +
550B LEU 3.5 4.7 - - - +
555B LEU* 5.7 3.6 - - + -
585B LEU* 4.3 10.9 - - + -
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Residues in contact with ILE 549 (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 SER* 3.4 46.4 - - - +
509B GLU* 3.6 11.9 - - + +
512B GLY* 4.1 8.1 - - - +
513B GLN* 3.0 47.5 - - - +
516B THR* 4.4 8.3 - - + +
545B LYS 4.6 5.2 - - - +
546B ILE* 2.9 19.3 + - + +
548B PRO* 1.3 79.5 - - + +
550B LEU* 1.3 62.3 + - + +
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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