Contacts of the strand formed by residues 914 - 921 (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 MET 914 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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853A ILE* 4.8 13.7 - - + -
854A PHE 3.3 15.0 - - - +
855A LYS* 4.0 14.6 - - + -
856A ALA 4.3 1.1 - - - +
860A MET* 3.4 4.7 - - - +
909A ASN* 2.8 33.3 + - - +
912A ALA* 3.2 32.2 - - + +
913A GLN* 1.3 84.2 - - - +
915A TYR* 1.3 61.5 + - - +
5Q PHE* 3.7 16.9 - - + -
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Residues in contact with TYR 915 (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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852A ASN 3.9 0.6 - - - +
853A ILE* 3.3 7.6 - - - +
854A PHE* 2.9 66.9 + + + -
856A ALA* 3.7 26.9 - - + -
859A PRO 4.6 1.0 + - - -
860A MET* 3.5 32.6 - - + +
865A THR* 3.7 16.1 + - + -
887A PHE* 5.2 1.6 - + - -
906A LEU* 3.6 35.0 - - + -
907A GLU 3.3 5.8 - - - -
908A PRO* 3.7 29.1 - - + +
914A MET* 1.3 77.6 - - - +
916A ARG* 1.3 58.5 + - - +
917A LEU 4.2 0.2 - - - -
938A PHE* 3.5 25.1 + + + +
5Q PHE* 3.7 5.4 - - - -
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Residues in contact with ARG 916 (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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851A GLN* 3.6 32.3 + - + +
852A ASN 3.3 10.1 - - - +
853A ILE* 3.9 15.5 - - + +
905A ARG* 3.6 4.8 - - - +
906A LEU* 3.6 3.4 - - - +
907A GLU* 2.8 60.8 + - - +
915A TYR* 1.3 73.9 - - - +
917A LEU* 1.3 67.7 + - - +
918A THR* 4.6 0.4 + - - +
3Q ASP* 3.0 47.3 + - - -
4Q ASN 4.6 2.0 + - - -
5Q PHE* 3.5 49.8 - - + +
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Residues in contact with LEU 917 (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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850A VAL 4.0 0.3 - - - +
851A GLN* 3.2 6.8 - - - +
852A ASN 2.9 32.2 + - - +
854A PHE* 4.1 10.5 - - + -
904A LEU* 4.6 4.3 - - + -
905A ARG 3.4 17.5 - - - +
906A LEU* 4.0 23.3 - - + -
915A TYR 4.2 0.4 - - - -
916A ARG* 1.3 74.8 - - - +
918A THR* 1.3 63.7 + - - +
919A LEU* 3.8 20.0 - - + -
931A CYS* 3.7 27.0 - - - +
934A LEU* 3.8 39.7 - - + -
935A SER* 3.7 13.2 - - - +
938A PHE* 5.7 0.2 - - + -
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Residues in contact with THR 918 (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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840A TRP* 3.7 24.1 - - + -
849A GLU* 3.5 39.0 - - + +
850A VAL 3.6 2.5 - - - -
851A GLN* 3.0 25.9 + - + +
904A LEU* 3.2 6.1 - - - +
905A ARG* 2.9 40.6 + - - +
907A GLU* 4.4 5.5 + - - -
916A ARG* 4.4 6.1 + - - -
917A LEU* 1.3 73.4 - - - +
919A LEU* 1.3 67.5 + - - +
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Residues in contact with LEU 919 (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* 6.0 0.7 - - + -
848A GLN 3.6 0.9 - - - +
849A GLU* 3.3 6.2 - - - +
850A VAL 2.9 33.7 + - - +
872A PHE* 5.9 0.9 - - + -
902A CYS* 4.7 3.6 - - + -
903A LEU 3.4 14.6 - - - +
904A LEU* 4.1 15.3 - - + -
917A LEU* 3.8 26.2 - - + -
918A THR* 1.3 78.9 - - - +
920A ARG* 1.3 62.0 + - - +
921A THR* 4.3 8.1 - - + -
927A SER* 3.9 19.3 - - - +
930A LEU* 4.0 26.9 - - + +
931A CYS* 3.9 27.8 - - + +
934A LEU* 4.7 3.8 - - + -
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Residues in contact with ARG 920 (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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840A TRP* 2.9 76.3 + - + +
841A LYS* 4.5 3.2 - - - +
843A LEU* 3.3 40.2 + - + +
844A SER* 4.1 10.4 + - - +
848A GLN 3.3 3.6 - - - +
849A GLU* 2.9 41.9 + - + +
902A CYS* 3.5 0.7 - - - -
903A LEU* 2.9 34.5 + - + -
918A THR 4.4 0.2 + - - -
919A LEU* 1.3 77.6 - - - +
921A THR* 1.3 64.7 + - - +
2Q GLU 6.1 1.2 - - - +
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Residues in contact with THR 921 (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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843A LEU* 3.6 8.1 - - - -
848A GLN* 3.2 27.6 + - - +
900A ILE* 3.9 7.6 - - - -
901A GLY 3.5 14.8 - - - -
902A CYS* 3.6 25.8 - - + -
919A LEU* 4.3 8.7 - - + -
920A ARG* 1.3 82.5 - - - +
922A SER* 1.3 62.0 + - - +
923A LYS 2.9 19.3 + - - -
926A VAL* 3.8 6.2 - - + +
927A SER* 2.9 31.7 + - - +
930A LEU* 4.6 0.4 - - + -
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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