Contacts of the strand formed by residues 923 - 928 (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 923 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475A ARG* 5.2 7.9 + - - +
840A ARG* 3.0 48.4 + - - +
841A ASP* 3.7 3.0 - - - +
890A SER* 2.9 41.0 + - - -
891A LYS 3.6 5.4 - - - +
892A THR* 3.9 13.2 + - + +
918A PRO* 4.9 2.4 - - - +
921A GLY 4.0 1.5 + - - +
922A ASP* 1.3 79.9 - - - +
924A VAL* 1.3 59.7 + - - +
925A ASP* 4.0 5.6 + - - +
9P C 2.8 33.3 + - - -
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Residues in contact with VAL 924 (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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889A ILE 3.5 1.6 - - - +
890A SER* 3.2 3.3 - - - -
891A LYS 2.8 36.9 + - - +
893A LEU* 4.2 17.7 - - + -
903A HIS* 3.7 36.8 - - + +
906A LEU* 4.1 15.5 - - + -
907A ALA* 4.3 2.9 - - + +
910A MET* 5.1 2.0 - - - -
918A PRO* 3.7 38.1 - - + -
922A ASP 4.2 0.2 - - - +
923A ARG* 1.3 74.3 - - - +
925A ASP* 1.3 73.1 + - - +
926A TYR* 3.7 4.7 - - + -
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Residues in contact with ASP 925 (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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888A ILE* 3.7 19.3 - - + +
889A ILE 3.5 3.8 - - - -
890A SER* 2.5 30.1 + - - -
906A LEU* 3.7 11.4 - - - +
910A MET* 5.5 1.9 - - - +
923A ARG* 4.0 6.8 + - - +
924A VAL* 1.3 73.0 - - - +
926A TYR* 1.3 64.5 + - - +
941A ASP* 4.3 0.7 - - - -
942A PRO* 3.6 20.8 - - + +
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Residues in contact with TYR 926 (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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887A LEU 3.8 0.3 - - - +
888A ILE* 3.3 5.6 - - - +
889A ILE* 2.9 70.7 + - + +
891A LYS* 3.3 32.8 + - + +
902A PRO* 4.6 12.0 - - + +
903A HIS* 3.6 34.1 + + + -
906A LEU* 3.6 13.7 - - + -
924A VAL* 3.7 7.9 - - + -
925A ASP* 1.3 75.1 - - - +
927A VAL* 1.3 66.3 + - - +
928A ILE* 3.8 23.1 - - + -
939A ALA* 3.5 21.1 - - + -
940A GLU 3.3 13.2 - - - +
942A PRO* 4.2 3.4 - - - -
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Residues in contact with VAL 927 (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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884A ILE* 3.9 23.6 - - + -
887A LEU* 3.8 22.7 - - + +
888A ILE* 3.9 9.2 - - + +
926A TYR* 1.3 81.4 - - - +
928A ILE* 1.3 63.2 + - - +
929A ILE* 3.7 3.8 + - + +
938A ARG 3.6 0.2 - - - +
939A ALA* 3.5 1.9 - - - -
940A GLU 3.0 32.2 + - - +
942A PRO* 4.6 4.0 - - + -
945A VAL* 3.6 33.0 - - + -
952A VAL* 4.1 20.4 - - + -
957A TYR* 3.2 10.5 - - + +
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Residues in contact with ILE 928 (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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889A ILE* 4.7 2.7 - - + -
902A PRO* 4.7 3.8 - - + -
926A TYR* 3.8 25.8 - - + -
927A VAL* 1.3 72.0 - - - +
929A ILE* 1.3 61.4 + - - +
935A LEU* 3.7 27.6 - - + +
938A ARG* 3.3 37.0 - - - +
939A ALA* 4.0 10.8 - - + +
952A VAL* 3.1 11.3 - - - +
953A ASP* 2.8 25.1 + - + +
956A TYR* 3.6 41.3 - - + +
957A TYR* 3.0 11.1 + - + +
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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