Contacts of the helix formed by residues 878 - 893 (chain A) in PDB entry 2XBB
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 878 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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807A TRP* 3.3 17.0 - - - -
876A TYR* 4.3 1.0 - - - +
877A GLU* 1.3 81.5 - - - +
879A PHE* 1.3 65.3 + - - +
880A GLU* 4.1 11.7 + - - +
881A GLU* 3.3 24.2 + - - +
882A LEU* 3.0 22.3 + - - +
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Residues in contact with PHE 879 (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 TRP* 3.7 43.9 - - + +
810A LYS* 3.7 20.9 - - + -
811A ALA* 3.6 31.2 - - + -
814A MET* 3.8 25.8 - - + -
878A SER* 1.3 72.4 - - - +
880A GLU* 1.3 88.0 + - + +
882A LEU* 3.1 6.6 + - + +
883A TRP* 2.9 46.3 + + + +
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Residues in contact with GLU 880 (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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878A SER* 3.3 10.3 - - - +
879A PHE* 1.3 98.7 + - + +
881A GLU* 1.3 63.7 + - - +
883A TRP* 3.2 7.2 + - - +
884A ASP* 3.0 27.4 + - - +
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Residues in contact with GLU 881 (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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858A PRO* 3.6 19.7 - - - +
876A TYR* 3.8 16.1 - - + -
877A GLU* 3.1 30.8 + - - +
878A SER* 3.3 19.2 + - - +
879A PHE 3.2 0.6 - - - -
880A GLU* 1.3 77.4 - - - +
882A LEU* 1.3 64.2 + - - +
884A ASP* 3.3 4.8 + - - +
885A LYS* 3.0 57.9 + - - +
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Residues in contact with LEU 882 (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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804A VAL* 3.7 38.1 - - + +
807A TRP* 3.8 15.3 - - + +
808A PHE* 3.8 14.8 - - + +
811A ALA* 4.0 26.0 - - + -
873A LEU* 4.3 11.2 - - + -
876A TYR* 3.5 25.1 - - + +
878A SER 3.0 12.8 + - - +
879A PHE* 3.5 10.8 - - + +
881A GLU* 1.3 77.0 - - - +
883A TRP* 1.3 64.6 + - - +
885A LYS* 4.2 0.2 - - - +
886A LEU* 3.0 41.2 + - + +
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Residues in contact with TRP 883 (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 ALA* 3.5 30.1 - - + -
814A MET* 3.8 17.3 - - + -
815A MET* 3.5 37.2 - - + -
819A LYS* 4.1 22.9 - - + -
879A PHE* 2.9 30.5 + + + +
880A GLU* 3.4 11.7 - - - +
882A LEU* 1.3 81.6 - - - +
884A ASP* 1.3 74.2 + - - +
886A LEU* 4.0 2.4 - - + +
887A GLN* 2.9 50.4 + - + +
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Residues in contact with ASP 884 (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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880A GLU 3.0 17.8 + - - +
881A GLU* 4.0 4.9 - - - +
883A TRP* 1.3 92.8 - - - +
885A LYS* 1.3 60.8 + - + +
887A GLN* 3.4 3.6 + - - +
888A MET* 2.8 36.6 + - + +
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Residues in contact with LYS 885 (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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858A PRO 3.5 16.3 + - - -
859A GLU* 4.3 13.9 - - - +
860A LYS 4.4 0.9 - - - -
861A LEU* 3.7 22.5 - - + +
862A PRO* 3.6 4.9 - - + +
876A TYR* 3.3 37.5 - - + +
881A GLU* 3.0 44.7 + - - +
884A ASP* 1.3 78.0 - - + +
886A LEU* 1.3 63.1 + - - +
888A MET* 3.2 13.4 + - + +
889A ALA* 3.0 24.6 + - - +
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Residues in contact with LEU 886 (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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808A PHE* 4.2 26.9 - - + -
811A ALA* 5.0 8.1 - - + -
812A VAL* 5.7 0.4 - - + -
815A MET* 5.4 7.6 - - - -
823A LEU* 4.1 26.7 - - + -
826A PHE* 4.9 2.7 - - + -
862A PRO* 3.9 26.8 - - + +
871A LEU* 4.4 15.3 - - + -
873A LEU* 5.5 2.9 - - + -
882A LEU* 3.0 29.5 + - + +
883A TRP* 4.0 3.1 - - + +
885A LYS* 1.3 78.7 - - - +
887A GLN* 1.3 64.0 + - - +
889A ALA* 3.4 1.0 + - - +
890A ILE* 3.1 39.3 + - + +
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Residues in contact with GLN 887 (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 MET* 4.7 10.7 - - - +
819A LYS* 4.3 31.2 - - - +
822A ARG* 4.9 14.6 - - - +
883A TRP* 2.9 42.1 + - - +
884A ASP* 3.8 5.2 - - - +
886A LEU* 1.3 79.3 - - - +
888A MET* 1.3 57.8 + - - +
890A ILE* 3.4 19.7 + - - +
891A GLU* 3.0 33.8 + - + +
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Residues in contact with MET 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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861A LEU* 3.9 25.8 - - + -
884A ASP* 2.8 20.3 + - + +
885A LYS* 3.6 14.8 - - + +
887A GLN* 1.3 74.7 - - - +
889A ALA* 1.3 59.5 + - - +
891A GLU* 3.3 5.2 + - - +
892A ASN* 2.9 53.1 + - - +
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Residues in contact with ALA 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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826A PHE* 3.8 20.3 - - + -
861A LEU* 4.1 9.3 - - + +
862A PRO* 3.5 35.9 - - + +
885A LYS 3.0 17.4 + - - +
886A LEU 3.8 4.0 - - - +
888A MET* 1.3 77.0 - - - +
890A ILE* 1.3 63.7 + - - +
892A ASN* 3.4 16.3 + - - +
893A THR* 3.6 10.2 + - - +
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Residues in contact with ILE 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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815A MET* 5.6 2.9 - - - -
819A LYS 5.0 2.7 - - - +
822A ARG* 3.9 33.0 - - + +
823A LEU* 3.6 42.2 - - + +
826A PHE* 3.9 27.8 - - + -
886A LEU* 3.1 26.8 + - + +
887A GLN* 3.7 20.0 - - - +
888A MET 3.3 0.2 - - - -
889A ALA* 1.3 76.7 - - - +
891A GLU* 1.3 62.5 + - - +
893A THR* 3.7 8.8 + - - -
894A GLN* 3.2 21.2 + - - +
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Residues in contact with GLU 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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822A ARG* 2.7 32.3 + - - -
887A GLN* 3.0 24.2 + - + +
888A MET* 3.3 7.2 + - - +
890A ILE* 1.3 76.2 - - - +
892A ASN* 1.3 67.5 + - - +
894A GLN* 3.0 30.0 - - - +
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Residues in contact with ASN 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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861A LEU* 3.6 28.7 - - - +
888A MET* 2.9 33.6 + - - +
889A ALA* 3.6 7.5 - - - +
890A ILE 3.3 0.2 - - - -
891A GLU* 1.3 79.9 - - - +
893A THR* 1.3 62.9 + - + +
894A GLN 3.0 5.8 + - - -
895A GLY 4.1 4.9 + - - -
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Residues in contact with THR 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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826A PHE* 3.5 31.5 - - + +
889A ALA 3.6 8.3 + - - +
890A ILE 3.7 7.0 + - - -
891A GLU 3.4 0.4 - - - -
892A ASN* 1.3 77.6 - - + +
894A GLN* 1.3 64.7 + - - +
895A GLY 3.9 0.2 - - - -
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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