Contacts of the strand formed by residues 826 - 831 (chain A) in PDB entry 3OPY
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 LYS 826 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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756A LYS* 3.5 13.2 - - - +
765A ARG 3.4 8.5 + - - +
766A THR* 3.4 7.0 - - + -
767A PHE* 3.0 24.1 + - - +
788A GLY 2.9 28.6 + - - -
790A LEU* 3.8 44.4 - - + +
811A LEU* 4.4 4.3 - - + -
814A THR* 4.4 13.5 - - + -
815A TYR* 3.6 27.9 + - + +
824A SER* 6.3 0.2 - - - -
825A GLY* 1.4 78.4 - - - +
827A ILE* 1.4 92.2 + - - +
981A SER* 6.4 0.4 - - - -
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Residues in contact with ILE 827 (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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752A CYS* 4.2 13.2 - - + +
755A VAL* 3.7 30.7 - - + -
756A LYS* 3.8 28.9 - - + -
767A PHE* 3.4 9.2 - - + +
769A VAL* 4.6 4.5 - - + -
787A THR* 3.3 28.3 - - - +
789A ALA* 3.4 24.0 - - + -
790A LEU* 2.8 31.9 + - - +
826A LYS* 1.4 88.6 - - - +
828A PHE* 1.3 66.5 + - - +
829A ILE* 3.7 17.9 - - + -
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Residues in contact with PHE 828 (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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766A THR* 3.7 27.1 - - + -
767A PHE 2.8 9.8 + - - +
768A VAL* 3.6 11.5 - - + -
769A VAL* 3.0 27.4 + - - +
790A LEU* 4.0 14.6 - - + -
791A ALA* 3.3 23.6 - - + +
793A TYR* 3.4 41.3 - + + -
807A ASP* 4.0 15.7 - - + -
808A ILE* 5.9 0.7 - - + -
811A LEU* 3.8 34.8 - - + -
827A ILE* 1.3 79.1 - - - +
829A ILE* 1.4 65.8 + - - +
830A HIS 3.9 0.2 - - - -
843A ILE* 4.5 0.2 - - + -
847A ILE* 4.0 19.5 - - + -
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Residues in contact with ILE 829 (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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752A CYS* 4.7 5.6 - - - -
769A VAL* 3.5 10.8 - - + +
771A VAL* 3.8 23.8 - - + -
780A ALA* 3.6 29.8 - - + +
783A ALA* 3.7 27.1 - - + -
784A GLY* 3.7 2.7 - - - +
787A THR* 3.4 28.3 - - + +
789A ALA* 4.2 1.9 - - + +
791A ALA 2.8 11.3 + - - -
792A VAL* 3.2 14.6 - - + -
793A TYR* 2.6 35.9 + - - +
827A ILE* 3.7 14.1 - - + -
828A PHE* 1.4 74.6 - - - +
830A HIS* 1.3 54.8 + - - +
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Residues in contact with HIS 830 (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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768A VAL* 3.8 15.9 - - + -
769A VAL 2.9 10.9 + - - +
770A GLU* 3.1 6.1 - - - +
771A VAL 2.8 24.5 + - - -
793A TYR* 3.5 32.8 - + + +
799A ILE* 4.9 0.4 - - - +
828A PHE 3.8 0.6 + - - -
829A ILE* 1.3 73.6 - - - +
831A ASN* 1.3 81.4 + - - +
832A GLU* 3.4 5.8 + - - -
834A ALA* 4.1 10.0 - - + +
835A SER 4.8 3.4 - - - -
838A TYR 2.8 28.0 + - - -
839A THR* 3.5 5.6 - - - -
840A THR* 3.2 36.0 + - - +
843A ILE* 3.8 15.5 - - + +
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Residues in contact with ASN 831 (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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771A VAL* 3.2 19.6 - - - +
773A GLY* 3.4 20.4 + - - -
774A GLY 3.3 14.8 + - - -
776A SER 4.0 11.5 + - - +
777A GLY* 5.1 0.2 - - - -
780A ALA* 3.9 16.9 + - + +
793A TYR 3.0 21.7 + - - +
794A THR* 4.4 0.7 - - - -
795A PRO* 3.4 17.9 - - + +
829A ILE 4.0 0.6 + - - -
830A HIS* 1.3 80.8 + - - +
832A GLU* 1.3 65.0 + - - +
833A LYS 2.9 30.0 + - - +
834A ALA* 3.1 12.4 + - + +
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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