Contacts of the helix formed by residues 574 - 587 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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560D GLU 3.0 27.5 + - - -
561D GLY* 2.9 29.7 + - - +
562D VAL* 2.7 36.4 + - - +
564D VAL* 4.5 12.3 - - + +
572D TRP 3.6 0.8 + - - -
573D HIS* 1.3 79.5 - - + +
575D GLN* 1.3 80.3 + - - +
577D LEU* 3.5 6.1 + - - +
578D GLY* 3.4 14.2 + - - -
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Residues in contact with GLN 575 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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575C GLN* 6.2 0.5 - - - +
527D ARG* 4.5 12.1 - - - +
573D HIS* 3.0 22.3 + - + +
574D ARG* 1.3 89.9 - - - +
576D ALA* 1.3 58.3 + - - +
577D LEU 3.0 2.2 - - - -
578D GLY* 2.7 24.5 + - - +
579D GLU* 2.9 23.6 + - + +
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Residues in contact with ALA 576 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526D TYR 5.1 0.2 - - - +
527D ARG 5.6 0.7 - - - +
530D ARG* 3.6 52.5 - - + +
531D TRP* 3.2 10.6 + - - -
572D TRP* 4.1 7.4 - - + -
573D HIS* 3.2 22.9 + - + +
575D GLN* 1.3 76.6 - - - +
577D LEU* 1.3 56.7 + - - +
579D GLU* 3.5 2.8 + - - +
580D ALA* 2.9 25.6 + - - +
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Residues in contact with LEU 577 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564D VAL* 3.9 24.9 - - + -
566D ILE* 5.3 2.0 - - + -
572D TRP* 4.2 14.5 - - + -
573D HIS 3.3 7.8 + - - +
574D ARG* 3.6 10.1 - - - +
575D GLN 3.0 0.4 - - - -
576D ALA* 1.3 76.5 - - - +
578D GLY* 1.3 65.3 + - - +
580D ALA* 3.2 2.0 + - + +
581D ARG* 2.7 62.1 + - + +
612D LEU* 3.4 33.9 - - + -
615D TYR* 3.5 28.3 - - + +
616D LEU* 4.2 5.4 - - + -
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Residues in contact with GLY 578 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574D ARG 3.4 6.6 + - - -
575D GLN* 2.7 15.9 + - - -
577D LEU* 1.3 73.5 - - - +
579D GLU* 1.3 54.9 + - - -
581D ARG* 3.1 17.1 + - - +
582D GLU* 2.9 27.9 + - - +
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Residues in contact with GLU 579 (chain D).
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* 4.2 23.0 - - - +
573C HIS* 5.5 0.9 - - - -
575C GLN* 3.3 34.8 - - + +
576C ALA 4.9 0.3 + - - -
579C GLU* 4.5 7.9 - - - +
530D ARG* 2.8 34.7 + - - -
531D TRP* 4.1 9.2 - - + +
575D GLN* 2.9 20.5 + - + +
576D ALA* 3.9 6.5 - - - +
578D GLY* 1.3 72.1 - - - +
580D ALA* 1.3 65.6 + - - +
582D GLU* 3.0 10.2 + - - +
583D VAL* 3.0 26.5 + - - +
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Residues in contact with ALA 580 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531D TRP* 3.7 11.1 - - + +
572D TRP* 3.6 24.0 - - + -
576D ALA 2.9 18.5 + - - +
577D LEU* 3.6 4.7 - - - +
579D GLU* 1.3 77.1 - - - +
581D ARG* 1.3 58.2 + - - +
583D VAL* 3.3 2.6 + - - +
584D ILE* 2.9 35.3 + - - +
602D LEU* 3.9 12.0 - - + +
612D LEU* 3.8 17.5 - - + -
616D LEU* 5.8 0.2 - - - -
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Residues in contact with ARG 581 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577D LEU* 2.7 61.4 + - + +
578D GLY* 3.2 15.0 - - - +
580D ALA* 1.3 78.4 - - - +
582D GLU* 1.3 57.2 + - - +
584D ILE* 4.3 1.1 - - - -
585D LYS* 3.0 26.0 + - - +
615D TYR* 5.7 1.4 - - - -
616D LEU* 4.1 17.4 - - + +
619D VAL* 5.9 4.3 - - - +
621D PHE* 3.2 49.3 - - + +
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Residues in contact with GLU 582 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523C GLU* 4.9 2.1 - - - +
527C ARG* 3.0 39.3 + - - +
578D GLY 2.9 12.3 + - - +
579D GLU* 3.0 12.5 + - - +
581D ARG* 1.3 77.7 - - - +
583D VAL* 1.3 64.7 + - - +
585D LYS* 3.2 33.1 + - - +
586D ASN* 3.1 20.6 + - - +
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Residues in contact with VAL 583 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524C ASP* 3.9 19.9 - - + +
527C ARG* 3.8 18.6 - - - +
528C VAL* 4.2 9.2 - - + -
531D TRP* 3.8 23.1 - - + -
579D GLU 3.0 14.4 + - - +
580D ALA 3.7 0.2 - - - +
582D GLU* 1.3 76.5 - - - +
584D ILE* 1.3 62.8 + - - +
586D ASN* 3.3 3.6 + - - +
587D LEU* 3.1 21.3 + - - +
601D ALA* 3.2 35.2 - - + +
602D LEU* 3.5 16.2 - - + -
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Residues in contact with ILE 584 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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580D ALA 2.9 29.1 + - - +
581D ARG 3.8 4.5 - - - +
582D GLU 3.2 0.2 - - - -
583D VAL* 1.3 76.0 - - - +
585D LYS* 1.3 63.1 + - - +
586D ASN 3.5 0.2 + - - -
587D LEU* 3.5 21.2 + - + +
588D ALA* 3.8 1.4 + - - +
593D PHE* 4.1 10.4 - - + -
598D ALA* 4.5 22.7 - - + +
601D ALA* 5.0 1.6 - - + -
602D LEU* 4.2 25.6 - - + -
609D VAL* 6.3 0.4 - - + -
612D LEU* 5.1 1.1 - - + -
613D LEU* 4.6 9.9 - - + -
616D LEU* 4.3 14.1 - - + -
621D PHE* 3.7 20.4 - - + -
622D THR* 3.9 10.3 - - + -
631D VAL* 3.3 20.7 - - + +
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Residues in contact with LYS 585 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581D ARG* 3.0 20.2 + - - +
582D GLU* 3.4 34.9 + - - +
583D VAL 3.2 0.4 - - - -
584D ILE* 1.3 77.2 - - - +
586D ASN* 1.3 63.4 + - - +
588D ALA* 3.6 14.2 + - - +
621D PHE* 4.4 14.1 - - + -
631D VAL* 4.3 22.0 - - + +
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Residues in contact with ASN 586 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517C LYS* 4.1 17.5 + - - +
520C LYS* 3.0 33.5 - - + +
521C ASP* 3.6 24.7 + - - +
524C ASP* 2.8 34.2 + - - +
527C ARG* 5.7 0.4 - - - +
582D GLU 3.1 10.4 + - - +
583D VAL 3.5 3.5 + - - +
584D ILE 3.2 0.4 - - - -
585D LYS* 1.3 72.9 - - - +
587D LEU* 1.3 57.1 + - - +
588D ALA 2.6 24.5 + - - -
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Residues in contact with LEU 587 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517C LYS* 5.7 2.0 + - - +
583D VAL 3.1 10.8 + - - +
584D ILE* 3.6 15.0 - - + +
586D ASN* 1.3 79.9 - - - +
588D ALA* 1.3 55.8 + - - +
591D GLY 3.8 8.5 + - - +
592D PRO 4.7 1.3 - - - +
593D PHE* 3.4 42.8 - - + +
597D GLU* 4.3 19.1 - - + +
598D ALA* 3.5 31.4 - - + +
601D ALA* 3.8 13.5 - - + -
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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