Contacts of the strand formed by residues 587 - 593 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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464B ASP 3.1 6.3 + - - +
465B VAL* 3.2 6.8 - - - -
466B LYS* 3.0 23.9 + - - +
559B LYS* 4.2 4.5 - - - -
580B THR* 3.2 19.3 - - - -
581B GLY* 3.8 5.8 - - - -
586B ASN* 1.3 77.1 - - - +
588B ARG* 1.3 62.2 + - - +
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Residues in contact with ARG 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465B VAL* 3.8 3.4 - - - -
466B LYS* 3.6 13.5 - - + +
484B ILE* 4.8 5.7 + - - +
487B GLU* 4.0 14.5 + - - -
488B GLN* 2.9 35.3 + - - +
559B LYS* 3.5 16.5 + - - +
560B HIS* 3.1 54.3 + - + +
561B VAL 2.9 23.2 + - - -
580B THR* 3.8 5.0 - - - +
587B GLY* 1.3 74.8 - - - +
589B ALA* 1.3 62.3 + - - +
590B THR* 4.6 2.4 + - - +
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Residues in contact with ALA 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465B VAL* 3.8 14.1 - - + -
466B LYS 3.0 9.7 + - - +
467B GLN* 3.6 7.3 - - + -
468B THR* 2.9 28.8 + - - +
561B VAL* 3.1 12.3 - - + +
563B ASN* 5.6 0.2 - - - +
573B TYR* 5.1 1.1 - - - +
577B ILE* 3.8 31.9 - - + -
588B ARG* 1.3 76.3 - - - +
590B THR* 1.3 64.7 + - - +
591B SER* 4.2 1.8 - - - +
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Residues in contact with THR 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468B THR* 3.5 10.5 - - - +
470B TYR* 3.8 35.0 - - + -
484B ILE* 4.0 17.0 - - + -
560B HIS* 2.4 36.1 + - - -
561B VAL 2.7 8.5 + - - -
562B ILE* 3.1 12.5 - - - +
563B ASN 2.7 30.0 + - - -
588B ARG* 4.6 2.1 + - - +
589B ALA* 1.3 74.2 + - - +
591B SER* 1.3 56.2 + - - +
592B PHE* 4.1 5.8 - - + -
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Residues in contact with SER 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468B THR 2.9 7.3 + - - -
469B ILE* 3.5 23.3 - - - +
470B TYR* 3.0 26.0 + - - +
563B ASN* 2.9 34.1 + - - -
566B MET* 3.9 14.4 - - - -
573B TYR* 3.2 12.8 + - - -
577B ILE* 4.9 1.0 - - - +
589B ALA 4.2 1.6 - - - -
590B THR* 1.3 76.4 + - - +
592B PHE* 1.3 67.0 + - - +
593B PHE 3.6 0.7 + - - -
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Residues in contact with PHE 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470B TYR* 4.0 9.6 - + - -
472B VAL* 4.5 16.8 - - + -
477B LYS* 3.7 44.9 + - + -
480B LYS* 3.5 22.2 - - + -
481B LEU* 3.8 8.5 - - + -
484B ILE* 3.6 28.7 - - + -
562B ILE* 4.5 8.7 - - + -
563B ASN 2.9 13.0 + - - +
564B TYR* 3.5 42.8 - + - +
566B MET* 3.5 19.8 + - - +
590B THR* 4.1 11.7 - - + -
591B SER* 1.3 76.8 - - - +
593B PHE* 1.3 62.2 + - - +
594B ASP 3.7 1.7 + - - -
598B ASP* 3.9 1.6 - - - +
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Residues in contact with PHE 593 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469B ILE* 3.7 14.4 - - + -
470B TYR 2.9 18.7 + - - +
471B GLU* 3.6 0.9 - - - -
472B VAL 2.8 29.4 + - - +
566B MET* 4.2 10.1 - - + -
591B SER 3.6 1.0 + - - -
592B PHE* 1.3 72.4 - - - +
594B ASP* 1.3 56.8 + - - +
595B PRO* 3.2 30.1 - - + +
598B ASP* 3.1 44.9 - - + -
599B ARG* 4.5 3.6 - - - -
601B ILE* 4.2 8.3 - - + -
602B ALA* 3.9 19.3 - - + -
605B LEU* 4.6 7.0 - - + -
619B PHE* 3.5 26.5 - + + -
620B LEU* 3.9 20.4 - - + -
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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