Contacts of the strand formed by residues 824 - 835 (chain A) in PDB entry 2B5L
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 ASP 824 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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820A LYS* 4.4 9.7 - - - +
821A LEU 3.1 18.7 + - - +
822A GLY 4.7 0.7 - - - +
823A LYS* 1.3 76.8 - - - +
825A PRO* 1.3 72.3 - - - +
826A ASN* 3.0 22.7 + - - +
828A TYR* 2.4 36.0 + - + -
893A TRP* 2.7 29.2 + - + +
894A THR 5.7 0.7 - - - +
897A LYS* 3.5 16.3 + - - +
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Residues in contact with PRO 825 (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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820A LYS* 3.6 17.4 + - + +
823A LYS 3.5 9.2 - - - +
824A ASP* 1.3 90.9 - - - +
826A ASN* 1.3 70.8 + - - +
827A THR* 3.9 2.1 + - - -
897A LYS* 5.7 1.6 - - - +
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Residues in contact with ASN 826 (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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820A LYS* 3.6 12.6 - - - +
824A ASP* 3.0 21.3 + - - +
825A PRO* 1.3 88.9 - - - +
827A THR* 1.3 60.3 + - - +
828A TYR* 3.4 33.4 + - + +
852A GLN* 3.4 30.3 + - - +
897A LYS* 4.1 11.9 - - - +
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Residues in contact with THR 827 (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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727A GLN* 3.4 36.4 + - + +
729A VAL* 3.9 28.9 - - + +
730A SER* 5.2 0.5 + - - -
818A SER* 4.3 1.6 - - - +
819A CYS* 3.8 23.6 - - - +
820A LYS* 3.8 15.2 - - + +
825A PRO 4.3 1.7 + - - -
826A ASN* 1.3 74.3 - - - +
828A TYR* 1.3 61.3 + - - +
852A GLN* 4.6 14.7 + - - +
853A TYR 5.0 0.9 + - - -
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Residues in contact with TYR 828 (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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727A GLN* 2.9 19.1 + - - -
817A VAL 4.0 0.2 - - - +
818A SER* 3.4 0.5 - - - -
819A CYS 3.1 32.1 + - - +
820A LYS* 5.2 1.8 - - - -
821A LEU* 5.3 9.9 - - + -
824A ASP* 2.4 45.1 + - + -
826A ASN* 3.4 31.4 + - + -
827A THR* 1.3 72.9 - - - +
829A PHE* 1.3 60.4 + - - +
830A ILE* 4.0 9.0 - - + -
850A VAL* 3.5 25.8 - - + -
851A PHE 3.0 17.3 - - - +
852A GLN* 3.9 14.4 - - + +
861A VAL* 3.7 26.2 - - + -
893A TRP* 4.0 14.1 - + - -
897A LYS* 3.8 9.7 - - - +
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Residues in contact with PHE 829 (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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725A CYS* 4.2 13.7 - - + -
727A GLN* 3.2 41.3 - - + -
732A CYS* 4.5 10.3 - - - -
733A PHE 4.0 4.3 - - - -
734A GLY* 3.3 40.2 - - - -
791A LEU* 4.8 10.3 - - + -
793A ILE* 3.9 23.1 - - + -
816A LEU* 4.4 14.1 - - + -
817A VAL 3.6 2.0 - - - -
818A SER* 4.2 10.3 - - - -
828A TYR* 1.3 70.9 - - - +
830A ILE* 1.3 60.5 + - - +
831A VAL* 5.1 0.7 - - - -
851A PHE* 2.8 47.8 + - + +
853A TYR* 4.6 14.1 - - + -
858A LEU* 4.8 2.9 - - + -
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Residues in contact with ILE 830 (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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815A SER 3.9 0.2 - - - +
816A LEU* 3.5 5.0 - - - +
817A VAL* 2.8 45.0 + - + +
819A CYS* 3.8 23.8 - - - +
821A LEU* 3.7 29.8 - - + -
828A TYR* 4.1 15.7 - - + -
829A PHE* 1.3 79.3 - - - +
831A VAL* 1.3 63.5 + - - +
848A ILE* 3.7 27.6 - - + -
849A VAL 3.6 5.6 - - - +
850A VAL* 4.0 17.5 - - + -
873A MET* 3.8 15.9 - - + +
880A LEU* 4.5 10.3 - - + -
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Residues in contact with VAL 831 (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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736A LEU* 4.0 10.3 - - + -
791A LEU* 4.0 9.6 - - + -
807A PHE* 3.9 11.2 - - + -
813A ALA* 3.7 22.9 - - + -
815A SER 3.3 8.1 - - - +
816A LEU* 3.7 19.5 - - + -
829A PHE 4.9 0.4 - - - +
830A ILE* 1.3 78.6 - - - +
832A GLY* 1.3 72.9 + - - +
833A THR* 4.0 5.1 - - + +
847A ARG 3.8 0.5 - - - +
848A ILE* 3.4 5.9 - - - +
849A VAL* 3.0 33.4 + - + +
851A PHE* 3.8 26.7 - - + -
873A MET* 4.1 4.0 - - - -
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Residues in contact with GLY 832 (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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814A LEU 3.0 22.9 + - - -
815A SER* 3.0 28.0 + - - -
831A VAL* 1.3 77.2 - - - +
833A THR* 1.3 63.3 + - - +
847A ARG 3.6 5.4 - - - -
848A ILE* 3.7 15.7 - - - -
870A VAL* 3.7 7.4 - - - -
873A MET* 3.7 2.0 - - - -
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Residues in contact with THR 833 (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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807A PHE* 4.3 9.6 - - + -
811A GLU* 2.7 35.7 + - + +
812A TYR 3.2 13.9 - - - +
813A ALA* 3.9 10.5 - - + +
814A LEU* 4.4 2.5 - - - +
831A VAL* 4.0 13.2 - - + +
832A GLY* 1.3 80.6 - - - +
834A ALA* 1.3 63.3 + - - +
846A GLY* 3.7 7.6 - - - -
847A ARG* 2.9 28.7 + - + +
849A VAL* 5.2 2.5 - - + -
868A GLY 3.8 0.3 - - - +
870A VAL* 3.2 27.6 + - - +
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Residues in contact with ALA 834 (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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811A GLU* 3.4 1.3 - - - -
812A TYR 2.8 35.2 + - - +
814A LEU* 3.7 13.7 - - + -
833A THR* 1.3 82.5 - - - +
835A MET* 1.3 63.2 + - - +
836A VAL* 3.3 10.8 + - + +
843A PRO* 4.0 13.2 - - + -
845A GLN 3.7 6.3 - - - -
846A GLY* 4.1 1.3 - - - -
869A ALA* 3.6 28.7 - - + -
24C VAL* 4.6 0.2 - - + -
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Residues in contact with MET 835 (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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771A PHE* 3.1 43.7 - - + -
808A LEU* 3.6 22.0 - - + -
809A GLN 4.3 3.1 - - - +
810A ASN* 3.8 4.7 - - + +
811A GLU* 3.3 37.7 - - + +
834A ALA* 1.3 71.2 - - - +
836A VAL* 1.3 60.7 + - - +
837A TYR* 3.3 36.7 + - + +
840A GLU* 4.4 1.7 - - - +
843A PRO* 3.9 18.3 - - - +
844A LYS 4.8 0.9 + - - -
845A GLN* 2.9 36.8 + - + +
846A GLY* 4.3 1.8 - - - -
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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