Contacts of the helix formed by residues 560 - 566 (chain Z) in PDB entry 5WTI
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 560 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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559Z SER* 1.3 72.4 - - - +
561Z ILE* 1.3 63.5 + - - -
562Z GLU 3.3 0.7 - - - -
563Z SER* 2.7 27.0 + - - -
804Z LEU 3.4 19.7 - - - -
806Z TYR* 3.9 14.6 - - - -
817Z ALA* 4.1 6.4 - - - +
819Z ASN 3.2 12.7 + - - -
821Z ALA* 3.2 8.8 - - - +
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Residues in contact with ILE 561 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473Z ILE* 3.7 21.8 - - + -
475Z PHE* 3.5 47.1 - - + -
519Z THR* 5.0 7.0 - - + +
559Z SER 4.1 0.6 + - - -
560Z GLY* 1.3 71.3 - - - -
562Z GLU* 1.3 68.3 + - - +
564Z LEU* 3.0 32.5 + - + +
565Z GLU 4.7 0.2 + - - -
804Z LEU* 3.7 40.2 - - + -
806Z TYR* 4.1 8.6 + - - +
821Z ALA* 4.9 0.2 - - - -
866Z TYR* 4.0 18.4 - - + -
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Residues in contact with GLU 562 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475Z PHE* 4.7 18.8 - - + -
558Z LYS* 4.4 16.4 - - + +
559Z SER 3.4 20.1 - - - +
560Z GLY 3.3 0.8 - - - -
561Z ILE* 1.3 82.1 + - + +
563Z SER* 1.3 59.7 + - - +
564Z LEU 3.2 0.9 + - - -
565Z GLU* 3.5 17.5 + - - +
566Z ILE* 5.0 1.9 + - - +
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Residues in contact with SER 563 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557Z LEU* 3.8 17.2 - - - +
558Z LYS* 3.5 32.3 - - - +
560Z GLY 2.7 14.8 + - - -
561Z ILE 3.0 0.2 + - - -
562Z GLU* 1.3 73.6 - - - +
564Z LEU* 1.3 56.6 + - - +
565Z GLU 3.1 7.1 + - - -
566Z ILE* 3.3 11.3 + - - +
569Z ARG* 2.5 25.1 + - - -
820Z PRO* 3.4 1.1 - - - +
821Z ALA 2.7 31.9 + - - -
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Residues in contact with LEU 564 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519Z THR* 5.9 0.7 - - + -
521Z SER* 3.4 23.4 + - - +
523Z VAL* 4.1 1.7 - - - +
561Z ILE* 3.0 31.7 + - + +
563Z SER* 1.3 78.0 + - - +
565Z GLU* 1.3 58.5 + - - +
566Z ILE 3.4 0.7 - - - -
569Z ARG* 4.3 0.7 - - - +
804Z LEU* 4.1 9.9 - - + -
821Z ALA* 3.6 20.4 - - + -
822Z CYS 3.4 32.1 - - - +
823Z GLN* 3.1 30.3 + - + +
866Z TYR 3.4 24.9 - - - +
868Z LEU* 3.7 14.8 - - + -
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Residues in contact with GLU 565 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519Z THR* 5.5 2.3 + - - -
520Z GLU 4.5 11.4 - - - +
521Z SER* 4.3 2.9 - - - -
522Z PRO* 3.5 24.7 - - + +
548Z TRP* 3.1 25.5 - - - -
562Z GLU 3.5 12.7 + - - +
563Z SER 3.1 1.8 - - - -
564Z LEU* 1.3 78.8 - - - +
566Z ILE* 1.3 68.8 + - + +
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Residues in contact with ILE 566 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548Z TRP* 3.8 5.6 - - + -
552Z SER* 4.3 13.0 - - - +
555Z LYS* 3.8 50.9 - - + +
556Z LYS 4.6 5.8 - - - +
557Z LEU* 3.4 38.6 - - + -
558Z LYS 5.7 0.2 - - - +
562Z GLU 5.5 1.8 - - - +
563Z SER* 3.3 11.0 - - - +
564Z LEU 3.4 0.6 - - - -
565Z GLU* 1.3 88.9 - - + +
567Z GLY* 1.3 67.0 + - - +
569Z ARG* 3.0 21.1 + - - +
823Z GLN* 3.5 1.7 + - - -
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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