Contacts of the strand formed by residues 555 - 561 (chain B) in PDB entry 2O8F
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 ALA 555 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544B GLU* 3.5 2.3 - - - -
545B LYS* 3.1 32.8 + - + +
547B GLU* 5.1 2.5 - - + -
550B SER* 4.0 16.8 - - - +
554B ARG* 1.3 80.1 - - - +
556B TYR* 1.3 64.0 + - - +
572B GLN* 6.1 0.7 - - + +
573B PHE 3.4 12.6 - - - +
574B SER* 3.9 9.6 - - - +
575B ASP 4.2 0.9 - - - +
679B LEU* 3.4 18.4 - - + +
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Residues in contact with TYR 556 (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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542B LEU* 3.6 27.4 - - + -
543B LYS 3.3 4.0 - - - -
544B GLU* 3.7 22.9 - - + -
554B ARG* 3.5 23.6 - - - -
555B ALA* 1.3 73.8 - - - +
557B GLY* 1.3 58.5 - - - +
558B VAL* 4.2 1.6 - - + -
572B GLN* 3.3 8.0 - - - +
573B PHE* 2.8 63.2 + + + +
575B ASP* 3.6 10.5 - - + -
579B CYS* 3.2 21.6 - - + +
582B PHE* 3.6 31.0 - + + -
605B THR* 2.7 40.9 + - + +
679B LEU* 4.2 1.6 - - - -
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Residues in contact with GLY 557 (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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542B LEU 3.8 0.5 - - - -
543B LYS* 2.7 37.6 + - - +
556B TYR* 1.3 73.6 - - - +
558B VAL* 1.3 62.9 + - - +
571B GLY 3.6 7.2 - - - -
572B GLN* 4.0 1.1 - - - -
679B LEU* 3.7 24.4 - - - +
680B ALA* 3.8 1.8 - - - -
683B ALA* 3.4 12.1 - - - +
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Residues in contact with VAL 558 (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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540B LEU* 4.2 9.4 - - + -
541B SER 3.5 5.8 - - - +
542B LEU* 3.8 23.3 - - + -
556B TYR* 4.2 3.3 - - + -
557B GLY* 1.3 77.9 - - - +
559B CYS* 1.3 64.8 + - - +
560B PHE* 4.0 14.1 - - + -
569B PHE 4.4 0.2 - - - -
570B ILE* 3.5 6.4 - - - +
571B GLY 2.8 46.2 + - - +
573B PHE* 4.1 16.6 - - + -
582B PHE* 4.9 1.3 - - + -
585B LEU* 3.7 33.9 - - + -
680B ALA* 4.4 0.7 - - - +
683B ALA* 3.9 3.5 - - - +
709B TYR* 4.2 5.4 - - + -
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Residues in contact with CYS 559 (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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539B LEU 3.8 1.0 - - - +
540B LEU* 3.8 1.1 - - - -
541B SER* 2.9 32.0 + - - -
558B VAL* 1.3 78.0 - - - +
560B PHE* 1.3 60.9 + - - +
568B PHE* 4.1 12.6 - - - -
569B PHE 3.4 8.5 - - - -
570B ILE* 4.6 7.9 - - + -
683B ALA* 3.9 5.4 - - + +
684B LEU* 3.7 44.4 - - + +
687B CYS* 3.6 29.7 - - + -
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Residues in contact with PHE 560 (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* 4.1 16.2 - + + -
539B LEU 3.1 12.3 - - - +
540B LEU* 3.7 26.2 - - + -
558B VAL* 4.0 11.2 - - + -
559B CYS* 1.3 74.4 - - - +
561B VAL* 1.3 64.3 + - - +
568B PHE* 3.6 1.3 - - - +
569B PHE* 2.8 77.7 + + + +
585B LEU* 3.9 13.7 - - + -
589B TYR* 3.5 42.6 - + + -
709B TYR* 3.5 32.8 - + - -
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Residues in contact with VAL 561 (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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520B GLY 4.8 0.2 - - - +
537B LYS 3.9 0.2 - - - +
538B TYR* 3.3 10.0 - - - -
539B LEU* 2.9 46.0 + - + +
560B PHE* 1.3 79.2 - - - +
562B ASP* 1.3 76.1 + - - +
563B THR* 3.5 16.4 + - + +
566B GLY* 4.2 2.0 - - - -
567B LYS 3.4 25.4 - - - +
568B PHE* 3.7 40.6 - - + -
687B CYS* 4.3 8.7 - - - -
691B LEU* 5.0 1.1 - - + -
700B LEU* 5.1 0.4 - - + -
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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