Contacts of the strand formed by residues 887 - 894 (chain A) in PDB entry 2VJ0
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 PHE 887 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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862A THR* 4.0 28.7 - - + -
865A THR* 3.7 27.6 - - + -
866A LYS* 3.8 33.4 - - + -
869A ILE* 3.6 27.4 - - + -
876A LEU* 4.3 8.1 - - + -
884A PRO 5.8 2.0 - - - -
885A ALA 3.5 17.7 - - - -
886A ASN* 1.3 75.9 - - - +
888A VAL* 1.3 66.2 + - - +
904A LEU* 5.1 1.1 - - - -
905A ARG* 3.3 4.7 - - - +
906A LEU* 2.8 52.1 + - + +
908A PRO* 4.2 13.2 - - + -
915A TYR* 5.2 1.3 - + - -
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Residues in contact with VAL 888 (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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836A PHE* 3.3 42.4 - - + -
869A ILE* 5.7 0.2 - - - -
876A LEU* 3.7 9.1 - - - +
877A LEU* 2.9 43.9 + - + +
880A VAL* 4.1 9.2 - - + -
881A ASP* 3.6 38.4 - - + +
886A ASN 5.3 0.4 - - - +
887A PHE* 1.3 80.9 - - - +
889A GLY* 1.3 61.7 + - - +
904A LEU* 3.4 7.0 - - - +
905A ARG* 4.5 4.0 - - + -
1Q PHE* 4.2 11.7 - - + -
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Residues in contact with GLY 889 (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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836A PHE* 3.7 5.7 - - - -
869A ILE* 5.0 1.3 - - - -
874A SER* 3.1 9.4 - - - -
875A ALA 3.1 14.1 - - - -
876A LEU* 4.8 0.2 - - - -
877A LEU* 4.4 4.3 - - - -
888A VAL* 1.3 74.5 - - - +
890A ALA* 1.3 62.1 + - - +
903A LEU* 3.4 3.1 - - - -
904A LEU* 2.9 44.2 + - - +
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Residues in contact with ALA 890 (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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826A PHE* 4.4 0.9 - - - -
829A THR 3.0 18.3 + - - +
831A MET* 3.5 32.1 - - + -
874A SER* 3.1 6.9 + - - -
875A ALA* 2.8 27.4 + - - +
877A LEU* 3.9 11.3 - - + +
889A GLY* 1.3 75.7 - - - +
891A GLY* 1.3 59.5 + - - +
902A CYS 3.3 6.3 - - - -
903A LEU* 3.7 11.9 - - + -
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Residues in contact with GLY 891 (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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826A PHE* 3.2 17.5 - - - -
827A GLN 3.2 13.7 - - - -
828A PRO* 4.2 0.2 - - - -
829A THR* 3.4 7.5 + - - -
873A GLY 4.8 0.2 - - - -
890A ALA* 1.3 75.9 - - - +
892A ILE* 1.3 65.3 + - - +
901A GLY* 3.6 0.7 - - - -
902A CYS 2.8 34.7 + - - -
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Residues in contact with ILE 892 (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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826A PHE* 3.5 4.4 - - - -
827A GLN 2.8 29.5 + - - +
829A THR* 3.4 24.0 - - + +
891A GLY* 1.3 76.6 - - - +
893A ILE* 1.3 72.2 + - - +
894A HIS* 3.3 29.7 - - + +
899A GLN* 3.8 26.0 - - + +
900A ILE 3.4 6.7 - - - +
901A GLY* 4.4 8.7 - - - +
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Residues in contact with ILE 893 (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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794A ASP* 5.4 1.6 - - + -
822A LEU* 3.6 48.0 - - + +
825A PHE* 3.4 3.8 - - + +
826A PHE* 3.4 34.1 - - + -
892A ILE* 1.3 72.0 - - - +
894A HIS* 1.3 61.9 + - - +
895A THR* 3.8 17.0 + - + -
898A THR 4.0 0.2 - - - +
899A GLN* 3.1 11.4 - - - +
900A ILE* 2.8 39.8 + - + +
902A CYS* 3.8 21.8 - - - -
926A VAL* 4.5 7.0 - - + -
930A LEU* 4.3 11.2 - - + -
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Residues in contact with HIS 894 (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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732A GLN* 3.8 36.2 - - + +
733A ASN* 3.3 11.6 - - + +
791A CYS* 4.3 0.5 - - - -
825A PHE* 2.8 37.4 + - - +
827A GLN* 4.3 18.4 - - + +
892A ILE* 3.3 34.1 + - + +
893A ILE* 1.3 71.9 - - - +
895A THR* 1.3 63.9 + - - +
899A GLN* 3.5 30.0 + - - +
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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