Contacts of the helix formed by residues 883 - 894 (chain A) in PDB entry 4B87
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 LYS 883 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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879A TYR* 5.6 11.2 - - - -
880A SER* 5.8 3.8 - - - -
881A ILE 6.2 0.2 - - - -
882A GLY* 1.3 74.6 - - - +
884A GLU* 1.3 65.6 + - - +
885A LYS 3.2 3.4 - - - +
886A VAL* 3.1 18.4 + - - +
887A PHE* 3.7 11.4 - - + -
934A MET* 5.8 4.0 - - + -
961A PRO* 4.3 19.0 - - + +
991A TYR* 3.7 47.2 + - + -
992A SER* 4.8 0.4 - - - +
993A GLU* 2.7 37.4 + - - +
994A HIS* 6.4 0.4 - - - -
2042A EDO 4.2 27.5 - - - +
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Residues in contact with GLU 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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795A PRO* 3.3 21.4 - - + +
881A ILE* 3.6 7.8 - - - -
882A GLY* 2.7 39.9 + - - +
883A LYS* 1.3 78.7 + - - +
885A LYS* 1.3 54.3 + - + +
886A VAL 3.1 0.3 + - - -
887A PHE* 3.3 27.1 + - + -
888A LEU* 2.8 52.8 + - + +
904A LYS* 5.1 1.0 + - - -
908A LEU* 4.1 16.0 - - + +
911A LEU* 3.7 11.6 - - - +
913A ILE* 4.1 14.4 - - + -
993A GLU* 4.8 0.5 - - - +
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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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851A GLN* 4.4 11.2 - - + +
855A ILE* 3.9 17.2 - - + +
883A LYS 3.2 0.8 - - - -
884A GLU* 1.3 77.9 - - + +
886A VAL* 1.3 58.4 + - - +
888A LEU* 4.3 6.5 - - - +
889A ALA* 3.0 31.5 + - - +
991A TYR* 3.9 23.3 - - - +
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Residues in contact with VAL 886 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855A ILE* 4.2 11.2 - - + -
858A ALA* 4.6 5.8 - - + -
876A CYS* 4.7 1.8 - - - -
883A LYS 3.1 11.6 + - - +
884A GLU 3.1 0.8 - - - -
885A LYS* 1.3 76.1 - - - +
887A PHE* 1.3 67.1 + - - +
889A ALA* 3.8 1.7 - - - +
890A ILE* 3.1 40.8 + - + +
959A PHE* 5.4 0.7 - - + -
989A ILE* 4.4 11.4 - - + -
991A TYR* 3.5 45.1 - - + -
2042A EDO 3.6 31.0 - - - +
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Residues in contact with PHE 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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876A CYS* 3.9 26.9 - - + -
877A GLY 5.6 1.6 - - - -
878A THR* 5.2 6.3 - - - -
882A GLY 4.6 4.9 - - - -
883A LYS* 3.7 11.0 - - + -
884A GLU* 3.3 40.8 + - + -
886A VAL* 1.3 80.0 - - + +
888A LEU* 1.3 79.0 + - + +
890A ILE* 3.4 4.8 + - - +
891A ALA* 3.0 28.4 + - - +
898A VAL* 3.7 28.3 - - + +
900A MET* 4.8 0.4 - - + -
904A LYS* 5.0 2.9 - - - -
908A LEU* 4.3 18.6 - - + -
916A ILE* 6.4 0.2 - - + -
929A VAL* 4.4 4.4 - - + +
931A LEU* 3.6 39.7 - - + -
2042A EDO 5.8 2.2 - - - -
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Residues in contact with LEU 888 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884A GLU* 2.8 36.5 + - + +
885A LYS* 4.3 4.9 - - - +
887A PHE* 1.3 87.9 - - + +
889A ALA* 1.3 59.8 + - - +
891A ALA* 3.8 3.5 - - + +
892A ASP* 2.9 30.1 + - - +
898A VAL* 4.2 5.4 - - + -
913A ILE* 4.4 23.1 - - + -
916A ILE* 4.5 5.6 - - + -
919A LEU* 3.9 28.9 - - + -
920A ILE* 4.1 18.8 - - + -
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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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855A ILE* 3.6 28.0 - - + -
859A ILE* 3.6 11.8 - - + +
885A LYS 3.0 21.8 + - - +
886A VAL 3.8 1.8 - - - +
888A LEU* 1.3 76.4 - - - +
890A ILE* 1.3 64.3 + - - +
892A ASP* 3.4 6.7 + - - +
893A VAL* 3.0 24.8 + - - +
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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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858A ALA* 4.1 15.3 - - + +
859A ILE* 4.1 12.3 - - + -
862A ALA* 3.9 14.6 - - + -
874A VAL* 3.9 17.0 - - + -
876A CYS* 4.0 11.7 - - - -
886A VAL* 3.1 36.4 + - + +
887A PHE* 3.8 4.9 - - - +
889A ALA* 1.3 77.5 - - - +
891A ALA* 1.3 62.8 + - - +
893A VAL* 3.0 23.7 - - - +
894A LEU* 3.0 10.9 + - + +
929A VAL* 3.8 19.1 - - + -
959A PHE* 3.8 30.7 - - + -
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Residues in contact with ALA 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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887A PHE 3.0 8.3 + - - +
888A LEU* 3.8 4.7 - - + +
890A ILE* 1.3 76.8 - - - +
892A ASP* 1.3 63.5 + - - +
894A LEU* 3.2 2.9 + - - +
895A GLY 3.0 4.3 + - - -
896A SER 2.9 42.9 + - - +
897A LYS* 4.7 0.2 - - - -
898A VAL* 3.4 34.5 - - + +
919A LEU* 5.0 2.2 - - + +
929A VAL* 3.7 18.4 - - + +
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Residues in contact with ASP 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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888A LEU 2.9 18.1 + - - +
889A ALA* 3.7 7.3 - - - +
891A ALA* 1.3 79.4 - - - +
893A VAL* 1.3 65.7 + - - +
895A GLY* 3.1 13.3 + - - -
896A SER 4.8 2.2 - - - +
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Residues in contact with VAL 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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859A ILE* 3.7 44.0 - - + +
860A ASN* 5.9 0.7 - - - +
862A ALA* 4.9 1.1 - - + -
863A PHE* 4.2 29.6 - - + +
889A ALA 3.0 16.3 + - - +
890A ILE* 3.0 23.6 - - + +
892A ASP* 1.3 81.2 + - - +
894A LEU* 1.3 68.4 + - + +
895A GLY 3.3 0.8 + - - -
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Residues in contact with LEU 894 (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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862A ALA 3.9 16.2 - - - +
863A PHE* 4.2 7.6 - - + -
866A VAL* 3.3 37.7 - - + -
874A VAL* 3.8 27.8 - - + -
890A ILE* 3.0 19.1 + - + +
891A ALA 3.2 3.8 + - - +
893A VAL* 1.3 83.1 - - + +
895A GLY* 1.3 63.0 + - - +
896A SER* 3.3 7.9 + - - -
928A LEU* 3.9 32.3 - - + +
929A VAL* 3.8 18.8 - - + -
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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