Contacts of the helix formed by residues 598 - 612 (chain A) in PDB entry 1B0P
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 ILE 598 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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555A LEU* 4.8 10.8 - - + -
591A TYR* 5.2 10.8 - - + -
593A LYS* 4.0 22.0 - - + +
594A LYS* 3.3 30.1 - - - +
595A GLY* 5.3 0.2 - - - -
596A GLU 4.3 1.0 - - - +
597A LYS* 1.3 79.6 - - + +
599A VAL* 1.3 65.4 + - - +
601A MET* 2.8 26.2 + - + +
602A ASN* 2.9 26.7 + - - +
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Residues in contact with VAL 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A ILE* 4.0 9.8 - - + +
588A HIS* 3.3 54.3 - - + +
591A TYR* 5.4 8.5 - - + +
594A LYS* 5.2 9.9 - - + -
595A GLY 4.8 5.2 - - - +
596A GLU* 3.7 36.5 - - - +
598A ILE* 1.3 77.5 - - - +
600A LYS* 1.3 57.8 + - - +
602A ASN* 3.0 11.9 + - - +
603A THR* 2.9 32.1 + - - +
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Residues in contact with LYS 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A GLU* 3.4 22.1 + - - +
597A LYS* 2.8 16.3 + - + +
599A VAL* 1.3 79.4 - - - +
601A MET* 1.3 58.4 + - + -
603A THR* 3.3 13.4 + - - +
604A ASP* 2.9 55.2 + - - +
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Residues in contact with MET 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553A VAL* 3.6 18.4 - - - +
554A GLY* 3.4 29.4 - - - +
555A LEU* 3.5 27.6 - - + +
597A LYS* 2.9 44.2 + - + +
598A ILE* 2.8 23.6 + - + +
600A LYS* 1.3 73.4 - - + +
602A ASN* 1.3 57.8 + - - +
604A ASP* 3.2 11.7 + - - +
605A ALA 2.9 23.7 + - - -
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Residues in contact with ASN 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555A LEU* 3.8 21.7 - - - +
561A MET* 4.0 17.9 - - + +
587A ILE* 3.5 20.0 - - + -
591A TYR* 3.1 45.6 + - - -
598A ILE* 2.9 30.7 + - - +
599A VAL 3.3 8.3 - - - +
601A MET* 1.3 75.8 - - - +
603A THR* 1.3 64.0 + - - +
604A ASP 3.1 1.1 - - - -
605A ALA* 3.4 3.0 + - - +
606A VAL* 3.1 29.1 + - - +
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Residues in contact with THR 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584A LYS* 5.0 19.6 - - + +
587A ILE* 4.4 7.4 - - - +
588A HIS* 4.5 11.0 + - + -
599A VAL* 2.9 23.8 + - - +
600A LYS* 3.3 19.3 + - - +
602A ASN* 1.3 77.4 - - - +
604A ASP* 1.3 61.8 + - - +
606A VAL* 3.9 8.1 - - + +
607A ASP* 2.7 40.3 + - - +
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Residues in contact with ASP 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553A VAL* 3.7 23.1 - - + +
600A LYS* 2.9 50.9 + - - +
601A MET* 3.3 10.1 - - - +
602A ASN 3.1 0.2 - - - -
603A THR* 1.3 78.2 - - - +
605A ALA* 1.3 60.4 + - - +
607A ASP* 3.1 5.2 + - - +
608A GLN* 2.8 29.8 + - - +
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Residues in contact with ALA 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549A ILE* 4.3 3.8 - - - +
553A VAL* 3.8 13.4 - - + +
555A LEU* 3.3 32.8 - - + -
561A MET* 4.5 9.0 - - + -
562A ILE* 4.1 19.0 - - + +
601A MET 2.9 7.5 + - - +
602A ASN* 3.7 5.2 - - - +
604A ASP* 1.3 74.6 - - - +
606A VAL* 1.3 63.2 + - - +
608A GLN* 3.2 2.7 + - - +
609A ALA* 2.8 27.1 + - - +
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Residues in contact with VAL 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561A MET* 3.5 32.8 - - + -
565A THR* 3.6 20.1 - - + +
580A VAL* 4.0 27.4 - - + +
583A LEU* 4.2 7.4 - - + -
584A LYS* 5.8 4.7 - - + -
587A ILE* 3.5 13.7 - - + -
602A ASN 3.1 18.0 + - - +
603A THR* 3.9 8.1 - - + +
604A ASP 3.2 0.2 - - - -
605A ALA* 1.3 76.9 - - - +
607A ASP* 1.3 63.1 + - - +
609A ALA* 3.5 2.4 - - - +
610A VAL* 3.1 28.7 + - + +
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Residues in contact with ASP 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580A VAL* 5.4 5.4 - - - +
603A THR* 2.7 33.9 + - - +
604A ASP* 3.1 4.9 + - - +
606A VAL* 1.3 81.6 - - - +
608A GLN* 1.3 63.5 + - - +
610A VAL* 3.8 8.3 + - - +
611A THR* 2.8 26.9 + - - -
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Residues in contact with GLN 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549A ILE* 3.6 37.8 - - + +
552A ASP* 3.4 36.8 + - - +
553A VAL* 3.1 20.3 - - + +
604A ASP 2.8 20.3 + - - +
607A ASP* 1.3 73.5 - - - +
609A ALA* 1.3 59.4 + - - +
611A THR* 3.7 5.5 + - - -
612A SER* 3.0 29.7 + - - +
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Residues in contact with ALA 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544A ILE* 4.0 6.4 - - + +
549A ILE* 4.4 4.9 - - - +
562A ILE* 3.9 26.9 - - + -
565A THR* 3.7 17.5 - - + -
605A ALA 2.8 17.6 + - - +
606A VAL 3.5 4.5 - - - +
608A GLN* 1.3 75.5 - - - +
610A VAL* 1.3 65.4 + - - +
612A SER* 3.1 3.6 + - - -
613A LEU* 3.0 31.7 + - + +
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Residues in contact with VAL 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565A THR* 3.5 23.3 - - + -
569A LYS* 2.9 56.4 + - + +
576A PHE* 6.1 1.3 - - + -
580A VAL* 4.7 17.0 - - + -
606A VAL* 3.1 16.2 + - + +
607A ASP* 3.8 8.7 + - - +
609A ALA* 1.3 75.7 - - - +
611A THR* 1.3 63.4 + - - +
613A LEU* 3.5 4.7 + - - -
614A GLN* 3.6 0.7 + - - -
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Residues in contact with THR 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607A ASP 2.8 18.2 + - - -
608A GLN* 3.9 5.5 - - - -
609A ALA 3.2 0.6 - - - -
610A VAL* 1.3 78.6 - - - +
612A SER* 1.3 60.2 + - - +
613A LEU 3.3 0.2 - - - -
614A GLN* 3.2 20.8 + - - +
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Residues in contact with SER 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A ASN 4.2 12.6 - - - +
544A ILE* 4.5 5.9 - - - +
549A ILE* 4.0 21.9 - - - +
608A GLN* 3.0 20.6 + - - +
609A ALA 3.1 5.0 + - - -
611A THR* 1.3 77.7 - - - +
613A LEU* 1.3 61.0 + - - +
614A GLN* 3.1 12.6 + - - +
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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
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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