Contacts of the strand formed by residues 779 - 783 (chain A) in PDB entry 2RD0
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 LEU 779 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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712A LEU* 4.5 19.3 - - + -
715A LEU* 4.4 12.8 - - + -
716A THR* 3.6 28.3 - - + -
719A LEU* 4.3 9.0 - - + -
735A LEU* 3.6 35.4 - - + -
739A MET* 5.8 0.9 - - - -
770A ARG 3.7 1.3 - - - +
771A ILE* 3.8 22.2 - - + -
777A ARG 4.4 1.6 - - - +
778A PRO* 1.3 72.4 - - - +
780A TRP* 1.3 60.4 + - - +
781A LEU* 3.6 22.5 + - + +
799A ILE 3.6 1.2 - - - +
800A ILE* 3.3 7.8 - - - -
801A PHE* 2.9 38.7 + - + +
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Residues in contact with TRP 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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768A GLU 3.6 17.7 + - - -
769A CYS* 3.5 4.7 - - - -
770A ARG* 2.8 60.4 + - + +
772A MET* 3.4 35.5 - - + +
778A PRO 4.0 1.0 + - - -
779A LEU* 1.3 70.0 - - - +
781A LEU* 1.3 70.0 + - - +
798A GLU* 3.2 38.7 + - + +
799A ILE 4.0 2.7 - - - -
800A ILE* 4.1 19.1 - - + -
850A VAL* 3.6 34.1 - - + -
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Residues in contact with LEU 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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712A LEU* 3.7 37.5 - - + -
735A LEU* 6.0 1.3 - - + -
739A MET* 3.9 20.2 - - + -
748A LEU* 5.3 0.2 - - + -
764A LEU* 4.7 2.0 - - + -
769A CYS* 3.8 17.3 - - + -
779A LEU* 4.1 26.2 - - + +
780A TRP* 1.3 85.0 - - - +
782A ASN* 1.3 61.2 + - - +
783A TRP* 4.0 29.5 + - + +
797A ASN 3.9 0.2 - - - +
798A GLU* 3.4 10.4 - - - +
799A ILE* 2.9 39.4 + - + +
801A PHE* 4.5 6.5 - - + -
847A LEU* 6.4 0.2 - - + -
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Residues in contact with ASN 782 (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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764A LEU* 3.5 7.5 - - - +
765A ARG* 2.7 58.4 + - + +
766A LEU 4.3 0.3 + - - -
768A GLU* 3.5 46.5 + - + +
769A CYS* 3.5 7.4 - - - -
781A LEU* 1.3 76.4 - - - +
783A TRP* 1.3 58.8 + - - +
796A ASN* 2.8 17.1 + - - +
797A ASN 3.6 1.6 - - - -
798A GLU* 2.7 35.7 + - + -
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Residues in contact with TRP 783 (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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712A LEU* 5.5 1.3 - - + -
748A LEU* 2.4 48.7 - - + -
751A PHE* 3.5 28.0 - + - -
761A LEU* 3.5 40.8 - - + +
762A GLY 3.9 13.0 - - - +
763A ASN 3.6 5.4 - - - +
764A LEU* 3.4 26.2 - - + -
781A LEU* 4.0 27.8 - - + +
782A ASN* 1.3 80.1 + - - +
784A GLU* 1.3 68.4 + - - +
796A ASN* 3.6 2.1 - - - -
797A ASN* 2.7 54.3 + - - +
799A ILE* 3.3 27.3 - - + +
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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