Contacts of the strand formed by residues 880 - 884 (chain A) in PDB entry 3I89
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 880 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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817A VAL* 4.5 7.0 - - + -
819A CYS* 5.3 0.2 - - - -
821A LEU* 4.2 13.9 - - + +
830A ILE* 3.7 29.4 - - + -
848A ILE* 4.0 23.6 - - + -
873A MET* 4.4 15.9 - - + -
874A VAL 4.1 9.9 - - - +
875A GLU* 4.9 3.1 - - - +
879A LYS* 1.3 72.9 - - - +
881A LEU* 1.3 67.3 + - - +
882A ALA* 4.8 2.2 - - + -
890A LEU* 3.6 2.8 - - - -
891A TYR* 2.7 57.9 + - + +
892A GLU* 5.2 0.2 - - - +
899A VAL* 3.9 24.9 - - + -
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Residues in contact with LEU 881 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873A MET* 3.0 7.8 - - - +
874A VAL* 2.9 57.3 + - + +
876A PHE* 4.2 12.8 - - + +
879A LYS 4.0 1.4 + - - -
880A LEU* 1.3 70.6 - - - +
882A ALA* 1.3 63.4 + - - +
888A VAL* 4.4 5.8 - - + -
889A ARG 3.1 17.0 - - - +
890A LEU* 3.9 8.5 - - + +
914A LEU* 4.2 20.0 - - + -
915A LYS 5.3 0.2 - - - +
916A THR* 4.8 2.2 - - - +
922A LEU* 3.4 34.5 - - + -
942A PHE* 3.6 28.9 - - + -
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Residues in contact with ALA 882 (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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848A ILE* 4.9 2.0 - - + -
870A VAL* 4.6 3.1 - - + -
872A SER 3.5 7.0 - - - +
873A MET* 3.6 24.0 - - + +
880A LEU* 4.6 3.4 - - + +
881A LEU* 1.3 80.9 - - - +
883A SER* 1.3 60.1 + - - +
884A ILE* 3.2 11.4 - - + +
889A ARG 3.0 32.2 + - - +
891A TYR* 4.3 22.7 - - + -
914A LEU* 4.0 2.0 - - - +
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Residues in contact with SER 883 (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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870A VAL* 3.4 9.4 - - - +
871A TYR 3.1 20.5 + - - -
872A SER* 2.8 40.5 + - - -
882A ALA* 1.3 69.7 - - - +
884A ILE* 1.3 60.6 + - - +
885A ASN 3.8 0.4 - - - -
887A THR 3.5 5.2 - - - -
888A VAL* 4.4 2.7 - - - -
911A ALA* 3.6 37.2 + - - -
914A LEU* 3.4 17.7 - - - +
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Residues in contact with ILE 884 (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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848A ILE* 5.4 0.4 - - + -
866A VAL* 4.1 25.1 - - + -
867A LYS 4.5 2.9 - - - +
868A GLY* 3.8 35.9 - - - +
869A ALA 3.9 3.1 - - - +
870A VAL* 4.7 8.3 - - + -
882A ALA* 3.2 26.5 - - + +
883A SER* 1.3 72.6 - - - +
885A ASN* 1.3 59.4 + - + +
886A SER* 2.7 6.3 + - - -
887A THR* 2.6 43.9 + - - +
889A ARG* 3.3 46.4 - - + +
891A TYR* 4.2 7.9 - - + +
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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