Contacts of the helix formed by residues 546 - 559 (chain A) in PDB entry 3I5H
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 SER 546 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544A LYS 3.3 7.0 + - - -
545A ALA* 1.3 75.9 - - - +
547A ASP* 1.3 77.2 + - - +
548A THR* 3.0 11.6 + - - -
549A SER* 2.5 35.4 + - - -
550A PHE 3.1 4.3 + - - -
597A LEU* 3.7 9.0 - - - +
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Residues in contact with ASP 547 (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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546A SER* 1.3 78.9 + - - +
548A THR* 1.3 62.6 + - - +
550A PHE* 3.2 9.7 + - - +
551A LYS* 3.1 21.3 + - - +
579A HIS* 6.2 1.8 - - + -
593A ILE* 4.1 15.6 - - + +
594A ALA* 2.4 37.5 - - - +
595A GLY* 4.3 1.4 - - - -
597A LEU* 4.3 17.8 + - - +
598A ASP* 4.9 3.3 - - - +
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Residues in contact with THR 548 (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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546A SER* 3.0 8.3 + - - -
547A ASP* 1.3 75.1 - - - +
549A SER* 1.3 63.1 + - - +
550A PHE 2.9 6.5 + - - -
551A LYS* 3.1 15.3 + - + +
552A ASN* 2.9 44.5 + - - +
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Residues in contact with SER 549 (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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539A GLU* 2.7 32.4 + - - +
544A LYS 5.1 1.6 - - - -
545A ALA* 3.4 3.0 - - - -
546A SER* 2.5 44.5 + - - +
548A THR* 1.3 74.1 - - - +
550A PHE* 1.3 57.5 + - - +
552A ASN* 3.9 10.0 - - - +
553A LYS* 3.8 14.2 + - - +
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Residues in contact with PHE 550 (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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532A ILE* 4.4 5.2 - - + -
535A ILE* 3.8 11.7 - - + -
536A LEU* 3.0 61.0 - - + -
539A GLU* 3.9 27.8 - - + -
546A SER 3.1 7.9 + - - +
547A ASP* 3.4 10.5 - - - +
548A THR 2.9 0.6 - - - -
549A SER* 1.3 76.1 - - - +
551A LYS* 1.3 66.1 + - - +
552A ASN 3.3 0.2 - - - -
553A LYS* 3.1 5.9 + - - +
554A LEU* 3.0 39.8 + - + +
593A ILE* 3.2 50.3 - - + -
596A TRP* 4.3 4.7 - + + -
597A LEU* 4.8 7.2 - - + -
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Residues in contact with LYS 551 (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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547A ASP 3.1 9.2 + - - +
548A THR* 3.1 15.5 + - + +
550A PHE* 1.3 77.3 - - - +
552A ASN* 1.3 75.4 + - - +
554A LEU* 2.7 16.5 + - - +
555A TYR* 2.7 73.9 + - + +
567A LYS* 4.2 7.0 - - - +
577A GLU* 4.0 17.8 + - - -
579A HIS* 4.7 19.6 - - + -
593A ILE* 5.4 4.5 - - + -
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Residues in contact with ASN 552 (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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548A THR* 2.9 38.8 + - - +
549A SER* 3.9 9.2 - - - +
551A LYS* 1.3 87.4 - - - +
553A LYS* 1.3 54.5 + - - +
555A TYR* 2.8 8.7 + - - -
556A ASP* 2.5 49.3 + - - +
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Residues in contact with LYS 553 (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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535A ILE* 4.0 25.1 - - + +
538A GLU* 4.7 15.9 + - + +
539A GLU* 2.8 38.9 + - - +
542A PHE* 5.2 8.1 - - - -
549A SER 3.8 9.5 + - - +
550A PHE* 3.1 10.8 + - - +
552A ASN* 1.3 78.9 - - - +
554A LEU* 1.3 58.1 + - - +
556A ASP* 3.4 11.9 + - + +
557A ASN* 3.0 46.4 + - - +
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Residues in contact with LEU 554 (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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532A ILE* 4.3 19.7 - - + +
535A ILE* 3.9 34.8 - - + -
550A PHE* 3.0 50.1 + - + +
551A LYS* 2.7 17.6 + - - +
553A LYS* 1.3 69.0 - - - +
555A TYR* 1.3 72.7 - - + +
557A ASN 3.2 2.8 + - - -
558A HIS* 2.9 30.1 + - + +
565A PHE* 4.3 12.1 - - + -
579A HIS* 6.2 0.4 - - + -
580A PHE* 4.5 18.2 - - + -
593A ILE* 4.3 12.6 - - + -
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Residues in contact with TYR 555 (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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551A LYS* 2.7 58.0 + - + +
552A ASN* 3.3 11.4 - - - +
554A LEU* 1.3 77.7 - - + +
556A ASP* 1.3 69.3 + - - +
559A LEU* 3.1 42.7 + - + +
565A PHE* 4.1 19.1 - + - -
567A LYS* 3.1 44.9 + - + +
578A ALA 4.8 0.5 + - - -
579A HIS* 2.5 36.6 + - + -
580A PHE* 4.5 0.2 - - + -
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Residues in contact with ASP 556 (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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552A ASN* 2.5 34.0 + - - +
553A LYS* 3.4 13.1 + - + +
555A TYR* 1.3 78.7 - - - +
557A ASN* 1.3 64.1 + - + +
558A HIS 3.3 0.3 + - - -
559A LEU 4.7 0.5 + - - -
561A LYS* 3.5 22.5 + - - -
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Residues in contact with ASN 557 (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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530A MET* 4.4 24.9 - - - +
535A ILE* 4.1 12.6 - - + +
553A LYS* 3.0 33.8 + - - +
556A ASP* 1.3 81.1 - - - +
558A HIS* 1.3 89.3 + - + +
561A LYS* 3.8 19.0 + - - +
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Residues in contact with HIS 558 (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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525A LEU* 3.6 23.7 - - + +
528A LYS* 3.4 19.5 - - - -
530A MET* 2.7 30.2 + - + -
531A GLY* 4.5 3.8 - - - -
532A ILE* 5.5 2.5 - - + -
535A ILE* 3.7 11.7 - - + +
554A LEU* 2.9 21.8 + - + +
555A TYR 3.2 1.2 + - - -
556A ASP 3.3 0.4 + - - -
557A ASN* 1.3 105.1 + - + +
559A LEU* 1.3 71.2 + - - +
560A GLY 3.7 1.1 - - - -
561A LYS* 3.1 9.0 + - - +
562A ASN* 3.1 25.9 + - + +
565A PHE* 3.7 28.7 - + + -
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Residues in contact with LEU 559 (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 TYR* 3.1 44.3 + - + +
556A ASP 4.7 0.4 + - - -
558A HIS* 1.3 79.8 - - - +
560A GLY* 1.3 66.8 + - - +
561A LYS* 5.0 0.4 - - - +
562A ASN 3.7 3.8 + - - +
565A PHE* 3.6 35.7 - - + +
566A GLY* 5.4 1.6 - - - -
567A LYS* 4.3 28.7 - - + +
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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