Contacts of the strand formed by residues 797 - 803 (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 ASN 797 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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753A SER* 5.4 1.9 - - - -
759A HIS* 3.5 29.4 + - - +
760A GLN 3.6 12.1 + - - +
761A LEU* 3.6 24.6 - - + +
782A ASN* 3.6 1.9 - - - +
783A TRP* 2.7 50.5 + - + +
785A ASN* 4.6 11.1 - - + +
795A GLN* 3.2 30.0 + - - +
796A ASN* 1.3 68.8 - - - +
798A GLU* 1.3 71.9 + - - +
799A ILE* 5.6 1.2 - - - +
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Residues in contact with GLU 798 (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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-24A HIS* 5.4 9.3 - - + -
755A LEU* 5.8 0.5 - - - +
768A GLU* 4.3 5.9 - - - +
780A TRP* 3.2 33.2 + - - +
781A LEU 3.4 12.3 - - - +
782A ASN* 2.7 33.7 + - - +
796A ASN 3.8 9.0 + - - +
797A ASN* 1.3 80.2 + - - +
799A ILE* 1.3 66.2 + - - +
849A GLU* 4.9 2.6 - - - +
850A VAL* 3.8 34.3 + - + +
852A ARG* 4.6 16.5 + - - +
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Residues in contact with ILE 799 (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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753A SER* 4.6 6.7 - - - +
754A PRO* 5.7 0.9 - - + -
755A LEU* 3.4 28.5 - - + -
761A LEU* 5.3 7.9 - - + -
779A LEU 3.6 1.4 - - - +
780A TRP* 5.8 0.2 - - - +
781A LEU* 2.9 35.6 + - + +
783A TRP* 3.3 33.2 - - + +
797A ASN* 5.6 0.7 - - - +
798A GLU* 1.3 79.3 - - - +
800A ILE* 1.3 74.7 + - - +
801A PHE* 3.9 0.9 + - + -
847A LEU* 3.5 33.0 - - + -
848A ILE 3.6 13.5 - - - +
850A VAL* 4.0 4.8 - - - +
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Residues in contact with ILE 800 (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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772A MET* 5.1 6.1 - - + -
778A PRO* 3.9 25.1 - - + -
779A LEU 3.3 11.4 - - - +
780A TRP* 4.1 23.8 - - + +
799A ILE* 1.3 75.0 - - - +
801A PHE* 1.3 62.3 + - - +
802A LYS* 4.5 3.4 - - + +
846A GLY 3.7 0.7 - - - +
847A LEU* 3.1 6.6 - - - -
848A ILE* 2.7 59.8 + - + +
849A GLU 5.3 1.1 - - - +
850A VAL* 3.7 24.5 - - + -
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Residues in contact with PHE 801 (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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709A MET* 3.6 18.4 - - + -
712A LEU* 3.5 48.2 - - + -
713A ILE* 3.6 16.2 - - + -
716A THR* 3.5 37.5 - - + -
777A ARG 4.6 0.3 - - - +
778A PRO* 3.4 1.9 - - - +
779A LEU* 2.9 37.3 + - + +
781A LEU* 4.5 7.6 - - + -
799A ILE 3.9 0.8 + - - -
800A ILE* 1.3 73.6 - - - +
802A LYS* 1.3 58.8 + - - +
803A ASN* 4.0 9.6 + - + -
845A VAL* 3.6 28.3 - - + -
846A GLY 3.4 7.9 - - - -
847A LEU* 3.7 19.7 - - + -
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Residues in contact with LYS 802 (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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776A LYS* 4.0 19.7 - - + +
778A PRO* 3.7 25.6 - - + -
800A ILE* 3.9 3.5 + - + -
801A PHE* 1.3 73.9 - - - +
803A ASN* 1.3 61.5 + - - +
804A GLY 3.7 1.8 + - - -
805A ASP* 2.6 48.0 + - + +
807A LEU* 4.1 21.1 - - + +
810A ASP* 5.4 3.0 + - - -
845A VAL* 3.4 4.7 - - - -
846A GLY 2.8 35.0 + - - +
848A ILE* 4.2 21.6 - - + +
933A ASP* 5.5 6.9 + - - -
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Residues in contact with ASN 803 (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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713A ILE* 3.5 17.7 + - - +
716A THR* 2.9 37.0 + - - +
717A ASP* 2.9 29.2 + - - +
720A LYS* 2.9 30.4 + - + +
776A LYS* 3.8 5.1 - - - +
777A ARG 5.0 3.1 + - - +
778A PRO* 5.3 2.2 - - - +
801A PHE* 4.0 9.4 + - + -
802A LYS* 1.3 72.1 - - - +
804A GLY* 1.3 59.0 + - - +
844A CYS 4.1 8.3 - - - +
845A VAL* 4.2 9.4 - - + +
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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