Contacts of the strand formed by residues 587 - 593 (chain C) in PDB entry 2DB3
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 587 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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464C ASP 2.9 9.1 + - - +
465C VAL* 4.0 3.6 - - - -
466C LYS* 2.8 27.4 + - - +
559C LYS 4.4 2.7 - - - -
580C THR* 3.6 19.3 - - - -
581C GLY* 3.7 10.2 - - - -
586C ASN* 1.3 76.2 - - - +
588C ARG* 1.3 62.7 + - - +
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Residues in contact with ARG 588 (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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266B LYS* 6.2 2.6 - - - +
465C VAL* 4.2 0.2 - - - -
466C LYS* 3.5 13.5 - - + +
484C ILE* 4.8 5.3 - - - +
488C GLN* 3.1 33.7 + - - +
559C LYS* 3.3 19.4 + - - +
560C HIS* 3.0 52.9 + - + +
561C VAL 3.0 21.1 + - - -
580C THR* 3.5 7.9 - - - +
587C GLY* 1.3 77.2 - - - +
589C ALA* 1.3 63.8 + - - +
590C THR* 4.2 4.0 + - - -
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Residues in contact with ALA 589 (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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465C VAL* 3.7 19.3 - - + -
466C LYS 2.9 9.3 + - - +
467C GLN* 3.6 4.8 - - + -
468C THR* 2.8 29.1 + - - +
560C HIS* 4.1 0.2 - - - -
561C VAL* 3.1 14.6 - - + +
573C TYR* 5.4 0.7 - - - +
577C ILE* 3.8 27.4 - - + -
588C ARG* 1.3 76.4 - - - +
590C THR* 1.3 64.3 + - - +
591C SER* 5.1 1.3 - - - +
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Residues in contact with THR 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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468C THR* 3.3 13.6 - - + +
470C TYR* 3.5 38.6 - - + -
484C ILE* 4.2 5.1 - - + +
560C HIS* 2.7 32.7 + - - -
561C VAL 2.8 7.3 + - - +
562C ILE* 3.1 10.8 - - - +
563C ASN* 2.7 31.7 + - - -
588C ARG* 4.2 4.2 + - - -
589C ALA* 1.3 72.6 + - - +
591C SER* 1.3 60.9 + - - +
592C PHE* 4.2 13.5 - - + -
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Residues in contact with SER 591 (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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468C THR 2.9 6.9 + - - -
469C ILE* 3.6 22.9 - - - +
470C TYR* 3.0 26.5 + - - +
563C ASN* 3.1 35.0 + - - -
566C MET* 3.8 15.5 - - - -
573C TYR* 3.4 12.3 + - - -
577C ILE* 4.9 1.2 - - - +
589C ALA 5.1 1.4 - - - -
590C THR* 1.3 76.2 + - - +
592C PHE* 1.3 66.2 + - - +
593C PHE 3.5 0.5 + - - -
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Residues in contact with PHE 592 (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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470C TYR* 3.7 7.0 - + - -
472C VAL* 4.0 17.5 - - + -
477C LYS* 3.7 44.9 + - + -
480C LYS* 3.6 23.8 - - + -
481C LEU* 3.8 9.2 - - + -
484C ILE* 3.6 27.8 - - + -
562C ILE* 4.4 11.0 - - + -
563C ASN 2.9 13.3 + - - +
564C TYR* 3.5 42.6 - + - +
566C MET* 3.4 21.3 + - - +
590C THR* 4.2 11.4 - - + -
591C SER* 1.3 76.1 - - - +
593C PHE* 1.3 61.2 + - - +
594C ASP 3.7 2.0 + - - -
598C ASP* 4.1 1.2 - - - +
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Residues in contact with PHE 593 (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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469C ILE* 3.8 15.3 - - + -
470C TYR 2.6 18.0 + - - +
471C GLU* 3.4 2.5 - - - -
472C VAL 2.7 28.4 + - - +
566C MET* 4.3 7.0 - - + -
591C SER 3.5 1.0 + - - -
592C PHE* 1.3 73.0 - - - +
594C ASP* 1.3 55.8 + - - +
595C PRO* 3.3 29.7 - - + +
598C ASP* 3.2 42.6 - - + -
599C ARG* 3.9 26.7 - - - -
601C ILE* 4.4 2.9 - - + -
602C ALA* 4.0 17.5 - - + -
605C LEU* 4.4 10.3 - - + -
619C PHE* 3.8 20.9 - + + -
620C LEU* 3.7 21.5 - - + -
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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