Contacts of the helix formed by residues 574 - 588 (chain C) in PDB entry 1WSU
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 ARG 574 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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561C GLY* 2.7 42.4 + - - +
562C VAL 3.0 13.0 + - - +
563C LEU* 4.3 0.2 - - - +
564C VAL* 3.9 25.6 - - + -
572C TRP 3.5 2.9 + - - -
573C HIS* 1.3 71.8 - - - +
575C GLN* 1.3 72.2 + - - +
577C LEU* 3.3 9.9 + - + +
578C GLY* 2.7 30.7 + - - -
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Residues in contact with GLN 575 (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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561C GLY 5.4 0.2 - - - +
573C HIS* 3.3 25.5 + - + +
574C ARG* 1.3 100.4 + - - +
576C ALA* 1.3 55.6 + - - +
578C GLY* 2.9 12.4 + - - -
579C GLU* 2.3 30.5 + - - +
575D GLN* 6.2 0.4 - - - +
579D GLU* 3.3 24.7 - - + +
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Residues in contact with ALA 576 (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 ARG 5.3 1.1 - - - +
530C ARG* 3.9 42.4 - - + +
531C TRP* 2.7 22.2 + - + +
572C TRP* 4.7 1.6 - - + -
573C HIS* 3.3 23.4 + - + +
575C GLN* 1.3 78.7 - - - +
577C LEU* 1.3 58.0 + - - +
579C GLU* 2.7 21.5 - - - +
580C ALA* 2.9 7.8 - - - +
530D ARG* 5.8 0.4 - - - +
579D GLU* 4.9 0.6 + - - -
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Residues in contact with LEU 577 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564C VAL* 3.8 38.8 - - + -
566C ILE* 4.4 7.6 - - + -
572C TRP* 4.0 15.0 - - + -
573C HIS 2.8 17.4 + - - +
574C ARG* 3.5 8.5 - - + +
576C ALA* 1.3 76.7 - - - +
578C GLY* 1.3 58.2 + - - +
580C ALA* 3.5 1.9 - - + +
581C ARG* 2.9 38.9 + - + +
612C LEU* 3.7 30.5 - - + -
615C TYR* 3.9 21.5 - - + +
616C LEU* 4.8 8.1 - - + -
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Residues in contact with GLY 578 (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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574C ARG 2.7 15.0 + - - -
575C GLN* 2.9 8.0 + - - -
577C LEU* 1.3 77.3 - - - +
579C GLU* 1.3 57.0 + - - -
580C ALA 3.0 0.2 - - - -
581C ARG* 2.9 25.8 + - - +
582C GLU* 3.0 10.7 + - - +
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Residues in contact with GLU 579 (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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530C ARG* 2.8 29.5 + - - +
531C TRP* 3.3 17.3 - - + -
575C GLN* 2.3 32.1 + - - +
576C ALA* 2.7 22.4 - - - +
578C GLY* 1.3 71.0 - - - -
580C ALA* 1.3 56.2 + - - +
582C GLU* 3.6 24.1 - - - +
583C VAL* 3.0 32.2 + - + +
527D ARG* 4.4 26.6 - - + +
530D ARG* 4.4 5.0 + - - +
579D GLU* 4.5 7.4 - - - +
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Residues in contact with ALA 580 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531C TRP* 3.1 27.6 - - + +
572C TRP* 3.9 14.8 - - + -
576C ALA 2.9 22.4 + - - +
577C LEU* 3.5 6.3 - - + +
578C GLY 3.0 0.6 - - - -
579C GLU* 1.3 78.3 + - - +
581C ARG* 1.3 62.3 + - - +
583C VAL* 3.4 4.3 + - - +
584C ILE* 3.2 27.7 + - - +
602C LEU* 3.9 10.6 - - + +
612C LEU* 4.8 6.3 - - + -
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Residues in contact with ARG 581 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577C LEU* 2.9 23.5 + - + +
578C GLY* 2.9 12.7 + - - +
580C ALA* 1.3 75.8 - - - +
582C GLU* 1.3 59.9 + - - +
583C VAL 3.2 0.4 - - - -
584C ILE* 3.3 4.0 + - - +
585C LYS* 3.0 31.4 + - - +
615C TYR* 5.0 5.1 + - - -
616C LEU* 4.1 12.0 - - + +
619C VAL* 3.8 17.4 - - - +
621C PHE* 3.2 66.3 - - + +
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Residues in contact with GLU 582 (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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578C GLY 3.0 6.4 + - - +
579C GLU* 3.6 24.8 - - - +
581C ARG* 1.3 77.7 - - - +
583C VAL* 1.3 58.5 + - + +
585C LYS* 3.5 11.1 + - + +
586C ASN* 3.1 28.3 + - + +
520D LYS* 4.0 13.2 + - - -
524D ASP* 4.0 10.6 - - - +
527D ARG* 2.9 33.5 + - - -
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Residues in contact with VAL 583 (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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531C TRP* 3.8 12.6 - - + -
579C GLU* 3.0 24.3 + - + +
580C ALA 3.5 8.1 - - - +
581C ARG 3.2 0.2 - - - -
582C GLU* 1.3 76.0 - - + +
584C ILE* 1.3 65.0 + - + +
586C ASN* 3.4 6.0 + - - +
587C LEU* 3.2 21.3 + - - +
601C ALA* 3.6 33.2 - - + +
602C LEU* 3.9 16.2 - - + -
527D ARG* 6.3 0.7 - - + -
528D VAL* 3.7 29.2 - - + -
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Residues in contact with ILE 584 (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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580C ALA 3.2 16.5 + - - +
581C ARG* 3.6 6.5 - - - +
583C VAL* 1.3 78.0 - - + +
585C LYS* 1.3 58.4 + - - +
587C LEU* 3.1 9.7 + - + +
588C ALA* 3.0 26.9 + - - +
593C PHE* 3.5 28.5 - - + -
598C ALA* 4.4 14.6 - - + +
602C LEU* 4.0 26.5 - - + -
612C LEU* 5.1 2.0 - - + -
613C LEU* 4.0 17.3 - - + -
616C LEU* 4.3 16.8 - - + -
621C PHE* 4.1 17.5 - - + -
622C THR* 4.5 3.6 - - + -
631C VAL* 4.5 3.8 - - + -
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Residues in contact with LYS 585 (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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581C ARG* 3.0 21.9 + - - +
582C GLU* 3.7 9.9 - - + +
584C ILE* 1.3 77.7 - - - +
586C ASN* 1.3 59.4 + - - +
587C LEU 3.1 1.0 + - - -
588C ALA* 3.6 2.6 + - - +
589C SER* 3.0 22.6 + - - -
621C PHE* 4.0 26.0 - - + -
631C VAL* 4.1 23.0 - - + +
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Residues in contact with ASN 586 (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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582C GLU* 3.1 17.9 + - + +
583C VAL* 3.4 7.2 + - - +
584C ILE 3.3 0.2 - - - -
585C LYS* 1.3 77.8 - - - +
587C LEU* 1.3 58.9 + - - +
589C SER* 3.1 22.5 + - - -
590C THR* 5.4 1.6 - - - +
524D ASP* 4.8 18.2 + - - +
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Residues in contact with LEU 587 (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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583C VAL 3.2 11.4 + - - +
584C ILE* 3.1 14.6 + - + +
585C LYS 3.1 0.2 - - - -
586C ASN* 1.3 75.7 - - - +
588C ALA* 1.3 59.7 + - - +
589C SER 2.9 10.2 + - - -
590C THR* 3.3 31.6 + - + +
591C GLY 4.2 1.2 - - - +
592C PRO 5.1 1.0 - - - +
593C PHE* 4.1 27.1 - - + -
597C GLU* 4.0 37.9 - - + +
598C ALA* 4.1 14.6 - - + -
601C ALA* 4.5 15.7 - - + -
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Residues in contact with ALA 588 (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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584C ILE 3.0 6.2 + - - +
585C LYS 3.6 1.8 + - - +
587C LEU* 1.3 73.6 - - - +
589C SER* 1.3 63.9 + - - +
590C THR 3.2 0.9 - - - -
591C GLY* 3.0 26.1 + - - +
593C PHE* 3.8 22.7 - - + -
630C VAL* 4.9 3.9 - - + +
631C VAL* 3.5 40.4 - - + +
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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