Contacts of the strand formed by residues 568 - 575 (chain B) in PDB entry 2O8C
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 PHE 568 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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559B CYS* 4.5 9.9 - - - -
560B PHE 3.8 2.7 - - - -
561B VAL* 3.6 33.2 - - + -
566B GLY 3.2 25.6 - - - -
567B LYS* 1.3 70.3 - - - +
569B PHE* 1.3 63.9 + - - +
570B ILE 3.9 0.3 + - - -
684B LEU* 4.9 2.2 - - + -
687B CYS* 4.0 13.2 - - - -
688B VAL* 5.8 0.2 - - + -
691B LEU* 3.6 28.7 - - + -
700B LEU* 3.8 31.9 - - + -
701B LEU* 3.7 19.7 - - + -
705B ASN 2.9 12.9 + - - +
706B PHE* 3.4 37.4 - + + -
707B GLU* 3.0 26.5 + - - +
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Residues in contact with PHE 569 (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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538B TYR* 4.4 18.2 - + - -
559B CYS* 3.3 4.5 - - - -
560B PHE* 2.8 76.8 + + + +
567B LYS* 3.6 46.7 - - + -
568B PHE* 1.3 74.3 - - - +
570B ILE* 1.3 60.5 + - - +
589B TYR* 4.2 22.2 - + - -
707B GLU* 3.3 37.9 - - + +
709B TYR* 4.6 11.7 - + + -
776B GLN* 6.0 1.8 - - - -
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Residues in contact with ILE 570 (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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558B VAL 3.5 12.6 - - - +
559B CYS* 4.2 9.6 - - + -
568B PHE 4.5 0.2 - - - +
569B PHE* 1.3 77.1 - - - +
571B GLY* 1.3 61.3 - - - +
658B VAL* 4.4 14.7 - - + +
659B LEU* 3.8 24.0 - - + -
662B MET* 3.9 22.6 - - + +
680B ALA* 3.9 10.5 - - + +
681B LEU* 4.5 1.3 - - + -
684B LEU* 3.8 28.5 - - + -
706B PHE* 4.1 21.8 - - + -
707B GLU 3.0 10.7 + - - +
708B GLU* 3.2 10.6 - - - +
709B TYR* 3.1 17.5 + - - +
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Residues in contact with GLY 571 (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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558B VAL* 2.9 43.4 + - - +
570B ILE* 1.3 76.2 - - - +
572B GLN* 1.3 60.1 + - - -
573B PHE* 4.9 0.7 - - - -
662B MET* 5.1 3.6 - - - -
680B ALA* 3.3 12.5 - - - +
708B GLU* 4.6 5.6 - - - -
709B TYR* 3.7 18.6 - - - +
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Residues in contact with GLN 572 (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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555B ALA* 5.3 4.1 - - + +
556B TYR 3.4 15.7 - - - +
571B GLY* 1.3 74.3 - - - +
573B PHE* 1.3 70.0 + - - +
662B MET* 5.6 0.2 - - - +
675B GLU 4.9 2.0 + - - -
676B LYS* 3.4 31.7 + - - +
677B SER* 3.1 15.1 - - - +
678B GLU* 4.5 1.6 - - - +
679B LEU* 3.1 44.7 + - + +
680B ALA* 3.3 11.1 + - + +
708B GLU* 5.4 5.4 + - - +
709B TYR 4.3 4.8 + - - +
711B PRO* 5.3 1.4 - - - +
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Residues in contact with PHE 573 (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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555B ALA* 3.4 4.2 - - - -
556B TYR* 2.9 63.1 + + + +
558B VAL* 3.9 33.2 - - + -
572B GLN* 1.3 84.0 - - - +
574B SER* 1.3 73.4 + - - +
575B ASP* 4.0 1.8 - - - -
581B ARG* 3.7 40.2 - - + +
582B PHE* 4.4 6.5 - - + -
585B LEU* 4.5 4.0 - - + -
709B TYR* 3.9 17.9 - + - -
711B PRO* 3.6 28.5 - - + -
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Residues in contact with SER 574 (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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550B SER* 6.2 0.9 - - - -
552B HIS* 2.8 45.6 + - - -
554B ARG 3.6 8.5 - - - -
555B ALA* 3.9 7.9 - - - +
573B PHE* 1.3 77.7 - - - +
575B ASP* 1.3 58.8 + - - +
581B ARG* 3.3 32.2 + - - +
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Residues in contact with ASP 575 (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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552B HIS* 4.0 7.8 - - - -
553B THR 3.6 14.7 + - - -
554B ARG* 2.9 24.4 + - + +
556B TYR* 3.2 36.3 - - + -
573B PHE* 4.3 1.1 - - + -
574B SER* 1.3 75.5 - - - +
576B ASP* 1.3 88.2 + - - +
579B CYS* 3.4 12.3 - - - -
580B SER 3.4 4.3 + - - -
581B ARG* 3.0 30.3 + - - +
582B PHE* 2.9 23.2 + - - +
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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