Contacts of the helix formed by residues 594 - 602 (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 GLY 594 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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593D PHE* 1.3 86.2 - - - +
595D LEU* 1.3 60.8 + - - -
596D ALA* 3.2 3.4 - - - -
597D GLU* 2.7 23.3 + - - -
598D ALA* 3.1 21.3 + - - +
627D ASP 5.0 2.7 - - - -
628D LYS* 3.6 17.5 - - - -
629D ARG* 6.3 1.3 - - - -
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Residues in contact with LEU 595 (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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594D GLY* 1.3 71.7 - - - -
596D ALA* 1.3 57.6 + - - +
598D ALA* 3.7 3.4 - - - +
599D ARG* 2.9 30.8 + - + +
606D ARG* 3.7 44.9 - - + +
609D VAL* 3.7 14.1 - - + -
610D LEU* 4.0 26.0 - - + +
613D LEU* 3.3 29.8 - - + -
627D ASP 5.5 1.2 + - - -
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Residues in contact with ALA 596 (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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594D GLY* 3.2 0.8 - - - -
595D LEU* 1.3 77.4 - - - +
597D GLU* 1.3 67.4 + - + +
599D ARG* 3.3 9.4 + - - +
600D ASP* 3.0 33.4 + - - +
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Residues in contact with GLU 597 (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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587D LEU* 4.1 13.0 - - + +
592D PRO 4.1 4.9 - - - +
593D PHE* 3.5 17.6 - - + +
594D GLY* 2.7 29.8 + - - +
595D LEU 3.4 0.4 - - - -
596D ALA* 1.3 79.2 - - + +
598D ALA* 1.3 58.6 + - - +
600D ASP* 3.3 8.0 + - - +
601D ALA* 2.8 27.7 + - - +
628D LYS* 3.1 20.8 + - - -
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Residues in contact with ALA 598 (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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584D ILE* 4.5 9.7 - - + +
587D LEU* 3.5 22.6 - - + +
593D PHE* 3.9 12.6 - - + -
594D GLY 3.1 17.8 + - - +
595D LEU 3.7 4.0 - - - +
597D GLU* 1.3 75.8 - - - +
599D ARG* 1.3 63.4 + - - +
600D ASP 3.1 0.4 - - - -
601D ALA* 3.1 12.0 + - - +
602D LEU* 3.1 19.6 + - - +
609D VAL* 4.5 4.5 - - + -
613D LEU* 4.1 16.2 - - + -
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Residues in contact with ARG 599 (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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595D LEU* 2.9 19.5 + - - +
596D ALA* 3.3 9.5 + - - +
598D ALA* 1.3 76.7 - - - +
600D ASP* 1.3 53.3 + - - +
602D LEU 3.7 0.2 - - - -
603D GLY* 2.7 10.4 + - - -
604D SER 2.7 60.4 + - - +
605D SER* 3.7 9.0 - - - +
606D ARG* 3.1 47.5 - - - +
609D VAL* 3.6 23.5 - - + +
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Residues in contact with ASP 600 (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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528C VAL* 5.6 1.2 - - - +
596D ALA* 3.0 24.1 + - - +
597D GLU* 3.6 6.9 - - - +
599D ARG* 1.3 74.9 - - - +
601D ALA* 1.3 67.3 + - - +
602D LEU 3.1 1.8 - - - -
603D GLY* 3.0 14.0 + - - +
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Residues in contact with ALA 601 (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* 5.7 0.2 - - - +
528C VAL* 3.5 13.9 - - - +
583D VAL* 3.2 30.2 - - + +
584D ILE* 5.0 2.2 - - + -
587D LEU* 3.8 26.7 - - + -
597D GLU 2.8 15.2 + - - +
598D ALA* 3.1 11.9 + - - +
600D ASP* 1.3 78.3 - - - +
602D LEU* 1.3 57.6 + - + +
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Residues in contact with LEU 602 (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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528C VAL* 3.7 9.6 - - - +
531D TRP* 3.5 54.1 - - + -
572D TRP* 4.9 3.4 - - + -
580D ALA* 3.9 12.1 - - + +
583D VAL* 3.5 30.3 - - + -
584D ILE* 4.2 15.9 - - + -
598D ALA 3.1 12.9 + - - +
601D ALA* 1.3 76.9 - - - +
603D GLY* 1.3 67.1 + - - +
604D SER* 3.3 10.9 + - - -
609D VAL* 4.5 15.9 - - + -
612D LEU* 3.9 28.3 - - + -
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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