Contacts of the strand formed by residues 874 - 881 (chain A) in PDB entry 1E42
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 TYR 874 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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827A VAL 4.3 0.2 - - - -
828A GLU* 2.5 33.2 + - - +
830A GLY 3.4 30.5 - - - -
831A LYS* 3.5 41.3 - - + -
869A GLN* 4.4 28.0 - - + +
872A ASN* 3.3 42.4 + - + -
873A VAL* 1.3 71.0 - - - +
875A THR* 1.3 62.2 + - - +
876A ILE* 3.6 2.8 + - + +
889A GLN* 3.0 6.4 - - - -
890A SER 2.9 34.2 + - - +
960A MG 4.1 2.8 - - - -
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Residues in contact with THR 875 (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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831A LYS* 4.1 11.6 + - - -
865A SER* 2.8 36.8 + - - +
869A GLN* 6.0 1.0 - - - +
873A VAL 4.0 1.7 + - - -
874A TYR* 1.3 70.9 - - - +
876A ILE* 1.3 62.8 + - - +
877A ALA 3.8 22.0 - - - +
878A LYS* 4.9 3.6 - - + +
887A LEU* 4.6 10.0 - - + +
888A TYR 3.4 6.5 - - - +
889A GLN* 3.3 19.3 + - - -
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Residues in contact with ILE 876 (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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831A LYS* 3.8 22.4 - - + +
832A MET 3.1 25.6 - - - +
834A ARG* 3.2 51.8 + - + +
837A PHE* 4.2 26.2 - - + -
874A TYR* 4.0 5.8 - - + +
875A THR* 1.3 78.6 - - - +
877A ALA* 1.3 60.9 + - + +
888A TYR* 2.6 18.2 + - + +
890A SER* 3.7 24.0 - - - +
950A DTD 4.8 2.5 - - - -
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Residues in contact with ALA 877 (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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834A ARG* 3.5 30.1 - - - +
875A THR* 3.6 7.9 - - - +
876A ILE* 1.3 84.9 - - + +
878A LYS* 1.3 65.0 + - - +
879A ARG* 5.1 2.9 - - - +
886A MET 3.9 0.4 - - - +
887A LEU* 3.7 1.6 - - - -
888A TYR* 2.9 30.0 + - + +
950A DTD 4.0 28.3 - - + -
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Residues in contact with LYS 878 (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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834A ARG* 4.8 1.4 - - - +
861A ALA* 4.0 17.6 - - + +
862A ASP* 4.8 7.7 - - - +
875A THR* 5.0 4.7 - - + -
877A ALA* 1.3 77.4 - - - +
879A ARG* 1.3 85.0 + - - +
880A ASN* 4.2 4.9 + - - -
885A ASP* 3.8 18.7 + - - +
886A MET 3.4 4.5 - - - +
887A LEU* 3.7 26.7 - - + -
888A TYR* 5.3 0.7 - - - -
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Residues in contact with ARG 879 (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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834A ARG* 4.1 17.5 - - - +
877A ALA* 5.4 1.8 - - - -
878A LYS* 1.3 95.2 + - - +
880A ASN* 1.3 63.7 + - - +
881A VAL* 3.7 18.8 - - + -
884A GLN 3.5 2.8 - - - +
885A ASP* 3.5 1.7 - - - -
886A MET* 2.8 49.9 + - + +
888A TYR* 4.4 9.6 - - + +
950A DTD 2.6 48.8 + - - +
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Residues in contact with ASN 880 (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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878A LYS* 4.2 5.6 + - - +
879A ARG* 1.3 76.5 - - - +
881A VAL* 1.3 67.5 + - - +
882A GLU 3.9 2.0 + - - -
883A GLY* 3.2 24.5 + - - +
884A GLN 3.3 8.0 - - - +
885A ASP* 4.7 10.0 - - - +
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Residues in contact with VAL 881 (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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879A ARG* 3.7 26.0 - - + -
880A ASN* 1.3 79.4 + - - +
882A GLU* 1.3 88.0 + - + +
883A GLY 3.3 0.2 - - - -
884A GLN* 2.9 37.3 + - + +
886A MET* 4.2 13.2 - - + -
904A ARG* 6.1 1.3 - - - +
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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