Contacts of the helix formed by residues 543 - 556 (chain C) in PDB entry 2W4V
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 ASP 543 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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541C LYS 4.5 2.5 - - - +
542C ALA* 1.3 78.4 - - - +
544C ASP* 1.3 84.8 + - - +
545C LYS* 2.9 18.9 + - + +
546C SER* 3.2 8.2 + - - +
547C PHE* 2.3 39.1 + - - -
595C LEU* 5.5 4.5 - - - -
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Residues in contact with ASP 544 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543C ASP* 1.3 90.1 + - - +
545C LYS* 1.3 55.7 + - - -
547C PHE* 4.3 5.4 - - - -
548C GLN* 3.3 21.3 + - - +
577C HIS* 4.5 2.6 + - - -
591C ILE* 2.6 24.4 - - - +
592C THR* 2.5 45.5 - - - +
593C GLY 3.3 6.3 + - - +
594C TRP 4.8 0.2 + - - -
595C LEU* 5.6 5.0 - - + +
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Residues in contact with LYS 545 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543C ASP* 3.0 8.7 + - + +
544C ASP* 1.3 78.6 - - - +
546C SER* 1.3 60.1 + - - +
547C PHE 3.1 1.6 - - - -
548C GLN* 3.7 4.4 - - + +
549C ASP* 2.3 67.7 + - - +
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Residues in contact with SER 546 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536C GLU* 3.5 7.0 + - - +
542C ALA* 3.7 10.0 - - - +
543C ASP* 3.2 25.3 + - - +
545C LYS* 1.3 80.3 - - - +
547C PHE* 1.3 62.3 + - - +
549C ASP* 4.2 5.1 - - - +
550C LYS* 2.9 31.7 + - - +
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Residues in contact with PHE 547 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532C ILE* 5.3 0.9 - - - +
533C LEU* 3.4 28.2 - - + +
536C GLU* 1.8 77.4 - - + -
537C CYS* 3.9 1.6 - - - -
542C ALA* 2.9 26.5 - - + -
543C ASP* 2.3 39.5 - - - +
544C ASP* 4.0 6.7 - - - +
545C LYS 3.1 0.2 - - - -
546C SER* 1.3 83.0 + - - +
548C GLN* 1.3 62.6 + - - +
550C LYS* 3.4 2.8 + - - +
551C LEU* 3.2 29.2 + - - +
591C ILE* 5.7 4.9 - - + +
594C TRP* 6.4 0.4 - - + -
595C LEU* 4.0 25.4 - - + -
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Residues in contact with GLN 548 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544C ASP* 3.3 19.7 + - - +
545C LYS* 3.3 6.8 + - + +
547C PHE* 1.3 80.2 - - - +
549C ASP* 1.3 73.8 + - - +
551C LEU* 3.4 21.0 + - + +
552C TYR* 3.5 12.0 + - - +
562C PHE* 6.1 2.4 - - - -
577C HIS* 3.8 27.5 + - + +
578C PHE* 5.9 0.6 - - + +
591C ILE* 3.4 31.1 - - + +
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Residues in contact with ASP 549 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545C LYS* 2.3 60.6 + - - +
546C SER* 4.2 4.8 - - - +
548C GLN* 1.3 80.1 - - - +
550C LYS* 1.3 58.7 + - - +
551C LEU 2.9 6.1 + - - -
552C TYR* 3.2 5.9 + - - +
553C GLN* 2.9 30.6 + - - +
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Residues in contact with LYS 550 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532C ILE* 3.7 29.9 + - + +
535C GLU* 4.4 12.7 + - - +
536C GLU* 2.5 42.9 + - - +
539C PHE* 5.4 2.4 - - - -
546C SER 2.9 20.4 + - - +
547C PHE* 3.7 4.9 - - - +
549C ASP* 1.3 76.1 - - - +
551C LEU* 1.3 60.8 + - - +
553C GLN* 3.5 19.6 - - + +
554C ASN* 3.6 10.4 + - - +
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Residues in contact with LEU 551 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529C ILE* 4.3 23.1 - - + +
532C ILE* 4.1 31.0 - - + -
533C LEU* 5.8 8.7 - - + -
547C PHE 3.2 15.3 + - - +
548C GLN* 3.4 16.2 - - + +
549C ASP 2.9 1.4 + - - -
550C LYS* 1.3 74.4 - - - +
552C TYR* 1.3 66.5 + - - +
553C GLN 3.1 0.7 - - - -
554C ASN* 2.9 13.3 + - - +
555C HIS* 3.0 25.1 + - - +
562C PHE* 4.9 16.8 - - + -
578C PHE* 5.0 13.2 - - + -
591C ILE* 5.0 16.8 - - + -
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Residues in contact with TYR 552 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548C GLN* 3.5 12.8 + - - +
549C ASP* 3.2 7.9 + - - +
551C LEU* 1.3 77.3 - - - +
553C GLN* 1.3 69.2 + - - +
554C ASN 2.8 1.6 + - - -
556C MET* 1.5 113.2 + - + +
562C PHE* 4.2 4.6 - - + -
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Residues in contact with GLN 553 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549C ASP 2.9 18.4 + - - +
550C LYS* 3.5 17.0 - - + +
552C TYR* 1.3 82.7 - - - +
554C ASN* 1.3 63.0 + - - +
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Residues in contact with ASN 554 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527C MET* 3.1 38.4 + - - +
532C ILE* 4.0 7.5 - - + +
550C LYS 3.6 9.8 + - - +
551C LEU* 2.9 9.5 + - - +
552C TYR 2.8 0.6 + - - -
553C GLN* 1.3 86.6 - - - +
555C HIS* 1.3 92.1 + - - +
556C MET 3.8 0.4 - - - -
558C LYS* 3.6 29.6 - - - +
559C ASN* 4.4 0.2 + - - -
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Residues in contact with HIS 555 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521C ASP 5.4 0.2 + - - -
522C LEU* 3.1 28.0 + - + +
527C MET* 3.7 11.1 - - - +
528C GLY* 3.7 20.4 + - - -
529C ILE* 4.0 6.9 - - + +
532C ILE* 4.7 1.6 - - + -
551C LEU* 3.0 19.8 + - - +
554C ASN* 1.3 106.8 + - - +
556C MET* 1.3 67.9 + - - +
557C GLY 3.0 4.5 + - - -
558C LYS* 3.1 10.5 + - - -
559C ASN* 2.6 44.7 + - - +
562C PHE* 3.9 27.1 - + + -
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Residues in contact with MET 556 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552C TYR* 1.5 148.4 + - + +
553C GLN 5.7 0.2 - - - +
554C ASN 5.3 0.3 - - - -
555C HIS* 1.3 74.5 - - - +
557C GLY* 1.3 58.7 + - - +
558C LYS* 3.1 6.6 + - - +
562C PHE* 2.3 42.8 - - + +
564C LYS* 4.3 30.1 - - + +
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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