Contacts of the strand formed by residues 777 - 781 (chain A) 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 PHE 777 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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628A GLY* 5.1 5.4 - - - -
630A GLY* 3.6 28.0 - - - -
631A ARG 3.9 15.7 - - - -
632A ILE* 3.9 27.4 - - + -
657A PHE* 3.7 31.4 - + + -
663A MET* 3.7 23.8 - - + -
703A SER* 4.6 4.9 - - - -
704A ILE 5.9 0.2 - - - -
705A VAL* 4.7 3.1 - - + -
741A LYS 3.7 17.9 - - - -
742A ASP* 3.8 14.8 - - - -
743A SER 3.2 18.4 + - - +
744A LEU* 3.4 17.5 - - + -
745A ILE* 2.8 26.3 + - - +
776A ALA* 1.3 71.6 - - - +
778A CYS* 1.3 59.3 + - - +
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Residues in contact with CYS 778 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657A PHE* 3.7 4.2 - - - -
663A MET 2.8 15.7 + - - +
664A PHE* 3.5 39.9 - - + -
665A HIS 3.0 22.6 + - - -
744A LEU* 5.0 0.2 - - - -
745A ILE* 3.4 31.9 - - + -
747A ILE* 4.1 12.1 - - - -
770A ILE* 4.2 9.4 - - + -
776A ALA 4.1 5.2 - - - +
777A PHE* 1.3 76.2 - - - +
779A MET* 1.3 75.6 + - - +
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Residues in contact with MET 779 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655A VAL* 4.8 1.6 - - + -
657A PHE* 3.4 28.7 - - + -
665A HIS* 3.6 15.3 - - + +
667A ILE* 4.1 5.4 - - + -
678A TYR* 3.5 34.8 - - + +
679A ILE* 3.7 33.3 - - + +
682A THR* 3.6 38.4 - - - +
744A LEU* 5.3 4.7 - - + -
745A ILE 3.0 10.7 + - - +
746A ILE* 3.6 5.7 - - + +
747A ILE 3.0 26.3 + - - +
778A CYS* 1.3 73.5 - - - +
780A PHE* 1.3 61.5 + - - +
781A ALA 4.1 0.9 - - - -
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Residues in contact with PHE 780 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664A PHE* 4.0 22.4 - + + -
665A HIS 2.8 10.4 + - - -
666A ILE* 3.5 7.7 - - + +
667A ILE* 3.1 19.9 + - - +
679A ILE* 5.2 0.2 - - - +
747A ILE* 3.3 33.2 - - + -
750A LEU* 3.5 42.8 - - + -
763A ALA* 4.3 7.0 - - + -
767A SER* 3.5 22.0 - - - -
778A CYS 4.3 0.4 - - - -
779A MET* 1.3 73.9 - - - +
781A ALA* 1.3 73.2 + - - +
782A THR* 3.5 17.1 + - + -
787A LEU* 3.4 34.5 - - + -
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Residues in contact with ALA 781 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667A ILE* 3.6 21.9 - - + +
675A LYS* 4.3 22.0 - - + -
679A ILE* 4.0 26.9 - - + +
747A ILE 3.1 5.7 + - - -
748A ASP* 4.0 11.0 - - - +
749A GLU* 2.7 31.8 + - - -
779A MET 4.1 0.6 - - - -
780A PHE* 1.3 76.8 - - - +
782A THR* 1.3 54.5 + - - +
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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