Contacts of the strand formed by residues 899 - 909 (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 GLN 899 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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892A ILE* 3.8 19.2 - - + +
893A ILE 3.1 12.1 - - - +
894A HIS* 3.5 32.5 + - - +
895A THR 4.7 5.0 - - - +
898A THR* 1.3 84.7 + - - +
900A ILE* 1.3 71.1 + - - +
901A GLY 4.2 0.7 + - - -
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Residues in contact with ILE 900 (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* 4.9 4.5 - - + +
892A ILE* 3.4 4.2 - - - -
893A ILE* 2.8 47.5 + - + -
895A THR* 6.0 0.7 - - + -
898A THR* 4.2 22.7 - - + +
899A GLN* 1.3 82.6 - - - +
901A GLY* 1.3 72.4 + - - +
902A CYS* 3.4 9.2 - - - -
921A THR* 3.9 18.6 - - - +
922A SER* 3.6 26.2 - - - +
923A LYS* 4.5 15.7 - - + +
926A VAL* 4.2 20.2 - - + -
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Residues in contact with GLY 901 (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* 4.5 7.0 - - - +
891A GLY 3.6 7.0 - - - -
892A ILE* 4.4 10.7 - - - +
899A GLN 4.2 0.8 + - - -
900A ILE* 1.3 74.0 - - - +
902A CYS* 1.3 59.3 + - - -
903A LEU* 5.5 1.3 - - - -
920A ARG 4.1 0.2 - - - +
921A THR* 3.5 21.8 - - - -
922A SER* 3.9 4.7 + - - -
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Residues in contact with CYS 902 (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* 3.8 20.2 - - + -
890A ALA* 3.3 3.8 - - - -
891A GLY 2.8 34.7 + - - +
893A ILE* 3.8 13.0 - - - -
900A ILE 3.4 17.9 - - - -
901A GLY* 1.3 74.7 - - - -
903A LEU* 1.3 65.8 + - - +
904A LEU* 5.9 0.2 - - - +
919A LEU* 4.7 4.0 - - + -
920A ARG 3.5 4.3 - - - -
921A THR* 3.6 20.4 - - + -
926A VAL* 4.1 4.7 - - - -
930A LEU* 3.5 27.4 - - + -
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Residues in contact with LEU 903 (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 MET* 4.3 11.4 - - + -
836A PHE* 3.8 17.9 - - + +
839A ARG* 3.7 15.7 - - + +
840A TRP* 3.4 58.6 - - + +
843A LEU* 4.1 13.2 - - + -
889A GLY 3.4 2.9 - - - -
890A ALA* 3.7 20.9 - - + -
901A GLY 5.5 0.7 - - - -
902A CYS* 1.3 82.9 - - - +
904A LEU* 1.3 63.8 + - - +
919A LEU* 3.4 6.0 - - - +
920A ARG* 2.9 35.5 + - + +
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Residues in contact with LEU 904 (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* 4.6 13.5 - - + -
836A PHE* 4.4 0.7 - - - -
840A TRP* 4.5 4.5 - - - -
869A ILE* 4.6 18.4 - - + -
872A PHE* 4.9 1.8 - - + -
874A SER* 3.7 26.2 - - - +
887A PHE 4.7 1.6 - - - +
888A VAL* 3.4 10.3 - - - +
889A GLY* 2.9 48.9 + - - +
902A CYS 6.2 0.2 - - - -
903A LEU* 1.3 77.7 - - - +
905A ARG* 1.3 69.3 + - - +
906A LEU* 4.6 3.4 - - + +
917A LEU* 4.6 3.6 - - + -
918A THR 3.2 10.3 - - - +
919A LEU* 4.1 17.7 - - + -
934A LEU* 3.9 26.7 - - + -
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Residues in contact with ARG 905 (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* 4.3 9.2 - - + -
881A ASP* 3.0 31.0 + - - +
886A ASN* 3.8 5.2 - - + +
887A PHE 3.3 9.9 - - - +
888A VAL* 4.5 2.2 - - + -
904A LEU* 1.3 77.1 - - - +
906A LEU* 1.3 61.9 + - - +
907A GLU* 3.3 40.1 + - + +
916A ARG* 3.6 4.1 - - - +
917A LEU* 3.4 6.1 - - - +
918A THR* 2.9 39.6 + - - +
1Q PHE* 3.5 52.9 - - + +
3Q ASP 3.0 23.8 + - - -
4Q ASN* 3.0 22.4 + - - -
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Residues in contact with LEU 906 (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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854A PHE* 4.3 7.0 - - + -
865A THR* 3.7 30.5 - - + -
869A ILE* 4.2 7.2 - - + -
886A ASN* 3.5 5.1 - - - +
887A PHE* 2.8 48.0 + - + +
904A LEU* 4.6 3.1 - - + +
905A ARG* 1.3 74.3 - - - +
907A GLU* 1.3 60.9 + - - +
908A PRO* 3.6 2.8 - - - +
915A TYR* 3.6 39.3 - - + -
916A ARG 3.6 11.2 - - - +
917A LEU* 4.0 24.7 - - + -
934A LEU* 6.3 0.7 - - + -
938A PHE* 3.9 23.8 - - + -
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Residues in contact with GLU 907 (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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886A ASN* 3.4 17.5 + - - +
905A ARG* 3.3 44.8 + - + +
906A LEU* 1.3 75.6 - - - +
908A PRO* 1.3 67.4 - - - +
915A TYR* 3.3 5.6 - - - -
916A ARG* 2.8 67.8 + - - +
918A THR* 4.4 3.3 + - - -
4Q ASN* 3.6 1.7 - - - +
5Q PHE* 2.8 42.5 + - + +
6Q VAL* 4.5 2.1 + - + +
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Residues in contact with PRO 908 (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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860A MET* 3.6 18.4 - - + -
885A ALA* 3.2 37.5 - - + +
886A ASN* 3.4 8.0 - - - +
887A PHE* 4.2 11.2 - - + -
906A LEU 3.6 7.0 - - - +
907A GLU* 1.3 85.1 - - - +
909A ASN* 1.3 58.6 + - - +
910A LEU* 3.6 19.1 + - + +
914A MET 3.8 4.9 - - - +
915A TYR* 3.7 16.1 - - + -
6Q VAL* 3.8 12.6 - - - +
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Residues in contact with ASN 909 (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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860A MET* 3.6 1.9 - - - +
907A GLU 3.9 0.4 + - - -
908A PRO* 1.3 73.2 - - - +
910A LEU* 1.3 57.2 + - - +
911A GLN* 3.1 15.0 + - - +
912A ALA* 2.9 33.4 + - + +
913A GLN* 2.8 25.1 + - - -
914A MET 2.8 20.9 + - - +
5Q PHE* 3.9 14.9 + - + -
6Q VAL* 3.7 31.9 - - + +
7Q PRO* 6.0 1.0 - - - +
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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