Contacts of the helix formed by residues 818 - 832 (chain A) in PDB entry 2B49
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 SER 818 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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816A ASP 4.2 1.0 + - - -
817A ASP* 1.3 73.8 + - - +
819A SER* 1.3 65.2 + - - +
820A ASP 3.4 0.7 - - - -
821A PHE* 3.2 7.0 + - - +
822A LEU* 2.9 35.1 + - - +
893A PHE* 3.9 31.1 - - - -
897A ALA* 4.4 12.7 - - - +
900A ARG* 3.5 27.8 - - - +
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Residues in contact with SER 819 (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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817A ASP* 3.0 23.0 + - - -
818A SER* 1.3 77.6 + - - +
820A ASP* 1.3 68.0 + - - +
822A LEU* 3.1 11.0 + - - +
823A GLU* 3.0 26.3 + - - +
900A ARG* 3.1 25.2 + - - +
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Residues in contact with ASP 820 (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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781A ILE* 3.9 28.1 - - - +
782A ALA* 3.8 16.4 - - + +
783A TYR* 5.1 1.9 - - - -
806A TYR* 3.6 15.4 - - - +
808A ALA* 5.5 2.0 - - + +
817A ASP 4.6 4.3 + - - +
818A SER 3.4 0.6 - - - -
819A SER* 1.3 82.1 - - - +
821A PHE* 1.3 57.6 + - - +
823A GLU* 3.4 18.9 + - - +
824A PHE* 3.0 27.2 + - - +
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Residues in contact with PHE 821 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743A LEU* 4.4 13.7 - - + -
806A TYR* 3.2 32.7 + + + +
809A TRP* 4.0 20.0 - + - -
815A PRO* 5.1 5.4 - - + -
817A ASP 5.2 0.8 + - - -
818A SER* 3.2 9.3 + - - +
820A ASP* 1.3 75.8 - - - +
822A LEU* 1.3 65.9 + - + +
824A PHE* 3.2 17.1 + + - +
825A VAL* 2.9 50.0 + - + +
848A ARG* 5.0 1.6 - - + -
851A VAL* 3.8 23.8 - - + -
852A LEU* 4.1 22.2 - - + -
855A MET* 4.4 10.5 - - + -
893A PHE* 4.0 26.2 - + + -
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Residues in contact with LEU 822 (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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818A SER* 2.9 36.7 + - - +
819A SER* 3.5 8.7 - - - +
821A PHE* 1.3 79.1 - - + +
823A GLU* 1.3 59.6 + - - +
825A VAL* 3.3 2.0 + - + +
826A ASN* 2.9 35.1 + - - +
855A MET* 4.2 21.1 - - + -
859A MET* 3.6 17.5 - - + +
897A ALA* 4.2 14.1 - - + +
900A ARG* 4.6 15.0 - - + +
901A VAL* 3.7 32.5 - - + -
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Residues in contact with GLU 823 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783A TYR* 5.1 13.7 + - + +
819A SER* 3.0 14.0 + - - +
820A ASP* 3.6 22.8 - - - +
822A LEU* 1.3 75.8 - - - +
824A PHE* 1.3 57.1 + - - +
826A ASN* 3.3 7.2 + - - +
827A TYR* 2.9 28.2 + - - +
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Residues in contact with PHE 824 (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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741A VAL* 3.8 22.2 - - + -
743A LEU* 3.7 23.1 - - + -
783A TYR* 3.5 44.6 - + + -
804A LEU* 3.8 31.2 - - + -
806A TYR* 3.5 33.7 - + + -
820A ASP 3.0 14.3 + - - +
821A PHE* 3.2 19.2 + + - +
823A GLU* 1.3 77.3 - - - +
825A VAL* 1.3 60.1 + - - +
827A TYR* 3.1 9.8 + + - +
828A VAL* 2.9 38.4 + - + +
852A LEU* 4.7 3.4 - - + -
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Residues in contact with VAL 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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821A PHE* 2.9 46.8 + - + +
822A LEU* 3.8 7.4 - - + +
824A PHE* 1.3 73.5 - - + +
826A ASN* 1.3 58.4 + - - +
828A VAL* 3.2 9.9 + - + +
829A ARG* 2.9 32.5 + - + +
852A LEU* 3.6 20.0 - - + -
855A MET* 4.3 7.4 - - + -
856A GLU* 3.9 31.2 - - + +
859A MET* 3.7 25.4 - - + -
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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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822A LEU* 2.9 18.4 + - - +
823A GLU* 3.9 7.1 - - - +
825A VAL* 1.3 77.7 - - - +
827A TYR* 1.3 55.7 + - - +
829A ARG* 3.3 31.1 + - - +
830A SER* 3.0 26.9 + - - -
859A MET* 3.2 30.6 - - - +
901A VAL* 5.8 1.2 - - - +
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Residues in contact with TYR 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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783A TYR* 3.5 39.3 - + - +
785A SER* 3.1 22.3 + - - -
802A THR* 5.0 0.7 - - - +
804A LEU* 3.4 32.8 - - + +
823A GLU 2.9 13.8 + - - +
824A PHE* 3.1 10.1 + + - +
826A ASN* 1.3 73.9 - - - +
828A VAL* 1.3 65.8 + - - +
830A SER* 2.5 31.4 + - - -
831A LEU* 3.2 33.5 + - + +
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Residues in contact with VAL 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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739A LEU* 4.1 17.2 - - + +
741A VAL* 4.1 19.7 - - + -
804A LEU* 4.0 22.9 - - + -
824A PHE* 2.9 35.4 + - + +
825A VAL* 3.2 10.7 + - + +
827A TYR* 1.3 74.5 - - - +
829A ARG* 1.3 64.8 + - - +
831A LEU* 3.0 13.7 + - - +
832A ARG* 3.2 11.8 + - - +
838A VAL* 4.6 10.3 - - + -
852A LEU* 4.6 13.0 - - + -
856A GLU* 4.6 15.7 - - - +
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Residues in contact with ARG 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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825A VAL* 2.9 17.6 + - + +
826A ASN* 3.3 24.2 + - - +
828A VAL* 1.3 75.4 - - - +
830A SER* 1.3 61.5 + - - +
831A LEU 3.2 1.0 + - - -
832A ARG* 3.3 17.3 + - - +
856A GLU* 3.5 33.3 + - + +
859A MET* 3.7 41.9 + - - +
860A CYS* 3.6 32.7 - - - +
863A GLU* 3.3 37.2 + - - -
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Residues in contact with SER 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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826A ASN 3.0 14.7 + - - -
827A TYR* 2.5 36.5 + - - -
829A ARG* 1.3 77.6 - - - +
831A LEU* 1.3 63.0 + - - +
832A ARG 3.8 2.9 + - - +
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Residues in contact with LEU 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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738A SER* 5.1 3.6 + - - -
739A LEU* 4.0 24.4 - - + +
802A THR* 3.9 27.8 - - + +
804A LEU* 4.1 8.5 - - + -
827A TYR* 3.2 42.8 + - + +
828A VAL 3.0 8.2 + - - +
830A SER* 1.3 80.1 - - - +
832A ARG* 1.3 67.3 + - - +
833A VAL* 3.5 12.3 + - - +
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Residues in contact with ARG 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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710A LEU* 6.3 0.2 - - - -
711A VAL 5.9 0.2 - - - -
712A ASN* 3.9 22.6 + - - +
713A LYS 3.0 33.5 + - - +
714A TYR* 3.1 26.3 - - - -
739A LEU* 5.0 1.1 - - - -
828A VAL* 3.2 11.4 + - - +
829A ARG* 3.3 17.0 + - - +
830A SER 4.5 3.1 - - - +
831A LEU* 1.3 79.3 - - - +
833A VAL* 1.3 72.4 + - - +
834A ASP 4.4 4.8 + - - +
836A GLU 3.6 8.9 + - - +
838A VAL* 3.5 28.9 - - + +
856A GLU* 2.9 41.6 + - - -
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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