Contacts of the helix formed by residues 551 - 558 (chain Z) in PDB entry 5GJQ
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 LYS 551 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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549Z GLU* 4.5 2.4 - - - +
550Z LEU* 1.3 86.1 + - - +
552Z ASP* 1.3 63.0 + - - +
553Z THR* 2.9 24.5 + - - +
554Z TYR* 3.6 5.5 + - + +
555Z ALA* 3.6 13.9 + - - +
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Residues in contact with ASP 552 (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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550Z LEU 3.6 1.0 + - - -
551Z LYS* 1.3 71.1 - - - +
553Z THR* 1.3 57.7 + - - +
555Z ALA* 3.1 14.2 - - + +
556Z ARG* 2.9 31.2 + - - +
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Residues in contact with THR 553 (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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551Z LYS* 2.9 17.4 - - - +
552Z ASP* 1.3 74.0 - - - +
554Z TYR* 1.3 52.6 + - - -
555Z ALA 3.1 0.2 - - - -
556Z ARG* 2.7 9.0 + - - +
557Z TRP* 2.7 37.3 + - - +
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Residues in contact with TYR 554 (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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508Z SER* 5.6 9.0 - - - -
516Z GLY* 5.8 3.8 - - - -
542Z ILE* 5.4 4.5 - - - +
549Z GLU* 3.7 31.6 - - + -
551Z LYS* 3.6 4.9 + - + +
553Z THR* 1.3 74.1 - - - +
555Z ALA* 1.3 66.5 + - - +
557Z TRP* 4.4 8.3 - - - -
558Z LEU* 3.6 18.0 - - - +
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Residues in contact with ALA 555 (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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542Z ILE* 5.7 1.7 - - - +
549Z GLU* 5.3 1.2 - - - +
551Z LYS 3.6 6.4 + - - +
552Z ASP* 3.1 24.7 - - + +
554Z TYR* 1.3 80.0 - - - +
556Z ARG* 1.3 58.3 + - + +
558Z LEU* 3.9 2.1 - - - +
559Z PRO* 3.0 26.0 - - - +
579Z ALA 4.0 4.8 - - - +
583Z VAL* 4.5 21.1 - - + -
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Residues in contact with ARG 556 (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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552Z ASP 2.9 14.5 + - - +
553Z THR* 2.7 10.1 + - - +
555Z ALA* 1.3 69.6 - - + +
557Z TRP* 1.3 65.7 + - - +
558Z LEU 3.1 1.6 - - - -
559Z PRO* 3.0 17.5 - - + +
560Z LEU* 3.1 19.7 + - + +
587Z PHE* 6.5 0.9 - - + -
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Residues in contact with TRP 557 (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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516Z GLY* 3.0 38.8 - - - +
517Z VAL* 4.3 1.3 - - - +
519Z ALA* 3.2 17.0 - - + +
520Z LEU* 3.9 10.1 + - + +
553Z THR 2.7 22.5 + - - +
554Z TYR* 4.5 3.6 - - - -
556Z ARG* 1.3 73.6 - - - +
558Z LEU* 1.3 59.5 + - - +
560Z LEU* 4.5 0.7 - - - +
561Z GLY* 3.5 10.0 + - - -
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Residues in contact with LEU 558 (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 ALA* 4.0 12.5 - - + +
538Z ILE* 4.9 12.6 - - + +
541Z THR* 6.2 1.8 - - - -
542Z ILE* 4.3 22.9 - - + +
554Z TYR 3.6 18.1 + - - +
555Z ALA 3.6 2.6 + - - +
556Z ARG 3.1 0.6 - - - -
557Z TRP* 1.3 76.8 - - - +
559Z PRO* 1.4 70.8 - - - +
561Z GLY* 3.1 6.9 + - - -
562Z LEU* 3.4 7.4 + - - +
579Z ALA* 3.9 8.5 - - + +
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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