Contacts of the strand formed by residues 815 - 821 (chain A) in PDB entry 3IAY
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 ARG 815 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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811A ILE* 3.0 27.2 + - + -
812A ASN* 3.0 22.7 + - + +
813A LYS 3.4 9.9 - - - +
814A LYS* 1.3 87.5 + - - +
816A TYR* 1.3 63.3 + - - +
833A LYS 3.4 3.1 - - - -
834A GLY* 3.2 31.8 + - - -
835A LEU* 3.9 19.3 - - + +
836A ALA* 4.5 6.7 - - - +
839A ARG* 3.9 20.4 - - - +
8T G 5.2 2.0 - - - +
9T G 3.4 52.1 + - - +
10T G 3.5 31.2 + - - +
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Residues in contact with TYR 816 (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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760A TYR* 3.8 23.3 - + - -
767A MET* 3.8 11.5 - - + +
803A LYS* 5.2 2.4 + - - -
805A TYR* 3.5 27.3 + + - -
808A TYR* 3.4 31.9 - + + +
809A LEU 3.3 15.7 - - - +
810A LEU* 4.0 7.6 - - + -
811A ILE* 4.4 1.6 - - - +
814A LYS 4.9 0.9 - - - -
815A ARG* 1.3 84.6 - - - +
817A ALA* 1.3 65.5 + - - +
831A ASP* 5.5 1.1 - - - -
832A GLN* 3.6 0.7 - - - -
833A LYS* 2.8 66.0 + - + +
835A LEU* 3.7 10.5 - - - +
11P A 4.6 1.1 - - - -
12P DOC 2.6 31.9 + - - -
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Residues in contact with ALA 817 (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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808A TYR* 3.6 8.7 - - - -
809A LEU* 2.8 36.4 + - + +
816A TYR* 1.3 79.2 - - - +
818A GLY* 1.3 60.5 + - - +
830A LEU* 4.4 4.7 - - + -
831A ASP 3.1 13.9 - - - +
832A GLN* 4.3 3.1 - - + -
835A LEU* 4.1 15.3 - - + -
854A LEU* 4.2 25.1 - - + -
858A LEU* 4.3 5.2 - - + -
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Residues in contact with GLY 818 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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805A TYR* 3.8 13.7 - - - -
807A PRO 3.3 13.7 - - - -
808A TYR* 4.4 0.4 - - - -
817A ALA* 1.3 77.0 - - - +
819A LEU* 1.3 65.4 + - - -
820A PHE 3.4 1.0 + - - -
830A LEU* 3.7 6.2 - - - +
831A ASP* 2.8 34.3 + - - +
858A LEU* 3.8 7.7 - - - +
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Residues in contact with LEU 819 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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805A TYR* 3.1 7.3 - - - -
806A PHE 3.0 38.8 + - - +
807A PRO* 3.3 19.4 + - + -
818A GLY* 1.3 69.6 - - - -
820A PHE* 1.3 58.5 + - - +
821A TRP* 3.2 14.0 - - + +
827A PHE* 4.1 29.4 - - + -
829A LYS 3.6 4.3 - - - +
830A LEU* 3.1 34.6 - - + +
858A LEU* 3.4 25.0 - - + +
859A ILE* 3.5 24.7 - - + -
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Residues in contact with PHE 820 (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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802A GLU* 5.3 2.9 - - + -
803A LYS* 3.5 37.9 - - + -
804A ALA 3.6 3.8 - - - -
805A TYR* 3.8 11.0 - + + -
818A GLY 4.1 0.2 - - - +
819A LEU* 1.3 71.1 - - - +
821A TRP* 1.3 55.0 + - - +
822A THR* 3.8 23.1 - - + -
827A PHE* 3.6 1.1 - - - +
828A ASP* 2.7 50.3 + - + +
829A LYS* 2.9 52.1 + - + +
831A ASP* 3.6 24.7 - - + -
833A LYS* 5.3 1.6 - - - -
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Residues in contact with TRP 821 (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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775A LEU* 3.3 35.4 - - + -
779A MET* 3.9 5.0 - - + +
803A LYS* 3.3 5.5 - - - +
804A ALA* 2.8 43.0 + - + +
806A PHE* 2.8 43.6 + + + +
819A LEU* 3.2 23.8 + - + +
820A PHE* 1.3 74.7 - - - +
822A THR* 1.3 62.6 + - - +
823A ASN 3.4 18.8 - - - +
824A PRO 4.0 3.4 - - - -
825A ASP 3.9 7.9 - - - -
826A LYS* 3.6 12.6 - - - -
827A PHE* 3.4 49.8 - + + +
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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