Contacts of the helix formed by residues 589 - 599 (chain C) in PDB entry 4AY6
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 THR 589 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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557C ASN* 3.6 24.2 + - + +
587C ASP* 2.7 39.1 + - + +
588C GLY* 1.3 82.0 - - - +
590C ASN* 1.3 64.5 + - - +
591C PHE* 3.2 8.1 + - - -
592C ARG* 3.2 18.9 + - - +
593C VAL* 3.3 10.7 + - - +
806C LYS* 4.6 2.7 - - - +
811C GLU* 3.2 22.4 - - - +
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Residues in contact with ASN 590 (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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565C GLN* 5.2 0.4 - - - -
588C GLY 5.0 1.4 - - - +
589C THR* 1.3 68.0 - - - +
591C PHE* 1.3 67.3 + - + +
593C VAL* 3.5 13.2 - - + +
594C LYS* 2.9 26.0 + - - +
806C LYS* 4.4 10.7 + - - +
811C GLU* 2.5 57.6 + - + +
812C GLU* 4.3 11.3 + - - +
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Residues in contact with PHE 591 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556C GLY* 3.6 15.9 - - - +
557C ASN* 3.2 46.9 - - + -
561C SER* 4.1 12.3 - - - +
562C HIS* 3.7 18.6 - + - -
565C GLN* 3.3 28.9 - - + +
589C THR* 3.2 5.8 - - - -
590C ASN* 1.3 78.6 - - + +
592C ARG* 1.3 65.5 + - - +
593C VAL 3.0 1.4 + - - -
594C LYS* 3.2 8.7 + - - +
595C VAL* 3.2 20.2 + - - +
701C MET* 3.6 23.8 - - + -
809C THR* 3.8 19.5 - - - -
810C GLY 3.8 9.6 - - - -
811C GLU* 3.7 22.2 - - + -
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Residues in contact with ARG 592 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555C PHE* 3.2 30.5 + - - +
556C GLY* 4.3 2.2 - - - -
582C ALA* 3.6 10.4 - - - +
584C SER* 2.9 32.5 + - - -
585C PRO 3.4 11.3 + - - -
586C ASP* 3.4 43.0 + - - +
587C ASP* 3.7 12.1 - - - +
589C THR* 3.2 12.0 + - - +
591C PHE* 1.3 76.6 - - - +
593C VAL* 1.3 62.8 + - + +
595C VAL* 3.4 4.4 + - - +
596C MET* 3.1 33.3 + - - +
602C PHE* 3.3 39.5 - - - -
604C ASP* 3.7 18.4 + - - +
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Residues in contact with VAL 593 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586C ASP* 5.6 3.8 - - - +
588C GLY 4.6 7.0 - - - +
589C THR 3.5 16.2 - - - +
590C ASN* 3.5 16.8 - - + +
591C PHE 3.0 1.6 + - - -
592C ARG* 1.3 76.1 - - + +
594C LYS* 1.3 54.8 + - - +
596C MET* 3.3 7.2 + - - +
597C ALA* 2.7 42.8 + - + +
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Residues in contact with LYS 594 (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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565C GLN* 3.6 36.8 - - + +
566C SER* 3.8 22.4 + - - +
590C ASN 2.9 15.4 + - - +
591C PHE 3.7 3.4 - - - +
593C VAL* 1.3 78.2 - - - +
595C VAL* 1.3 56.6 + - + +
597C ALA* 3.1 7.9 + - - +
598C GLU* 2.7 75.2 + - - +
700C ASN* 4.4 13.7 + - - +
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Residues in contact with VAL 595 (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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555C PHE* 4.1 27.1 - - + -
561C SER* 5.1 3.8 - - - +
564C MET* 5.6 0.9 - - + -
565C GLN* 4.5 27.8 - - + +
568C PRO* 4.1 15.5 - - + -
580C CYS* 3.9 25.6 - - - -
591C PHE 3.2 19.4 + - - +
592C ARG* 3.9 5.6 - - - +
594C LYS* 1.3 74.9 - - - +
596C MET* 1.3 58.3 + - - +
598C GLU* 4.9 2.5 - - - -
599C ALA* 2.9 31.0 + - - +
602C PHE* 4.2 9.9 - - + -
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Residues in contact with MET 596 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586C ASP* 3.9 11.2 - - - +
592C ARG* 3.1 44.6 + - - +
593C VAL* 3.7 7.4 - - + +
595C VAL* 1.3 75.1 - - - +
597C ALA* 1.3 62.4 + - - +
598C GLU 3.4 0.7 + - - -
599C ALA 4.0 8.8 - - - +
602C PHE* 3.4 48.4 - - + +
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Residues in contact with ALA 597 (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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806B LYS* 5.8 1.6 - - - +
812B GLU* 3.9 22.9 - - - +
815B ARG* 4.8 1.9 + - - -
593C VAL* 2.7 27.4 + - + +
594C LYS* 3.5 8.5 - - - +
596C MET* 1.3 74.7 - - - +
598C GLU* 1.3 62.3 + - + +
599C ALA 4.4 2.1 - - - +
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Residues in contact with GLU 598 (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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812B GLU* 4.6 6.1 - - - +
815B ARG* 3.5 42.9 + - - +
565C GLN 4.2 2.6 - - - +
566C SER 4.0 4.5 - - - +
568C PRO* 4.1 9.6 - - + +
569C GLY* 3.3 28.8 + - - +
594C LYS* 2.7 59.3 + - - +
595C VAL* 4.3 2.0 - - - +
597C ALA* 1.3 80.8 - - + +
599C ALA* 1.3 68.0 + - - +
600C ASN* 3.7 2.4 + - - -
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Residues in contact with ALA 599 (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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568C PRO* 4.4 12.4 - - + +
578C VAL* 4.3 7.4 - - + +
580C CYS* 3.7 24.7 - - + -
595C VAL 2.9 18.3 + - - +
596C MET 4.0 9.6 - - - +
597C ALA 4.4 2.1 - - - +
598C GLU* 1.3 81.3 - - - +
600C ASN* 1.3 62.9 + - - +
601C HIS* 3.3 21.0 + - - +
602C PHE* 4.9 1.8 - - + -
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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