Contacts of the helix formed by residues 908 - 919 (chain B) in PDB entry 4BIC
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 908 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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777B GLU* 2.7 34.8 + - - -
907B MET* 1.3 74.2 - - - +
909B ALA* 1.3 59.3 + - - +
910B GLU* 3.3 25.7 + - - +
911B ALA* 3.1 14.0 + - - +
912B LYS* 3.0 26.1 + - - +
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Residues in contact with ALA 909 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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907B MET 3.9 0.8 + - - -
908B SER* 1.3 73.1 - - - +
910B GLU* 1.4 59.4 + - - +
912B LYS* 3.4 12.8 + - - +
913B ALA* 2.8 35.3 + - - +
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Residues in contact with GLU 910 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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777B GLU* 5.1 0.2 - - - +
908B SER* 3.3 25.5 + - - +
909B ALA* 1.4 80.7 + - - +
911B ALA* 1.4 60.8 + - - +
913B ALA* 3.6 6.5 + - - +
914B PHE* 3.3 23.0 + - - +
935B ASP* 4.7 2.1 - - - +
936B GLU* 5.5 9.6 - - + +
937B PHE* 3.6 27.9 - - + +
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Residues in contact with ALA 911 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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777B GLU* 3.4 22.9 - - - +
907B MET* 4.1 15.9 - - + -
908B SER* 3.1 24.7 + - - +
910B GLU* 1.4 74.1 - - - +
912B LYS* 1.4 58.6 + - - +
914B PHE* 3.3 4.7 + - - +
915B ILE* 3.1 36.0 + - + +
937B PHE* 3.6 20.8 - - + -
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Residues in contact with LYS 912 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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903B ILE* 3.9 30.5 - - + +
904B PRO 4.4 4.5 - - - +
905B GLU* 2.7 34.3 + - - +
907B MET* 3.3 27.4 - - + +
908B SER 3.0 18.2 + - - +
909B ALA* 3.7 10.1 - - - +
911B ALA* 1.4 72.4 - - - +
913B ALA* 1.3 58.2 + - - +
915B ILE* 3.4 2.3 + - - +
916B LEU* 3.0 43.2 + - + +
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Residues in contact with ALA 913 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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909B ALA 2.8 20.7 + - - +
910B GLU* 3.8 8.3 - - - +
912B LYS* 1.3 72.7 - - - +
914B PHE* 1.4 54.8 + - - +
916B LEU* 3.3 10.5 + - - +
917B LYS* 3.1 40.9 + - - +
935B ASP* 5.8 1.8 - - - +
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Residues in contact with PHE 914 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784B THR* 3.8 11.4 - - + -
788B LEU* 3.7 25.8 - - + -
867B LEU* 5.0 1.1 - - + -
871B ILE* 3.7 31.2 - - + -
910B GLU 3.3 12.0 + - - +
911B ALA 3.3 8.7 + - - +
913B ALA* 1.4 74.0 - - - +
915B ILE* 1.3 69.5 + - + +
917B LYS* 3.4 17.7 + - - +
918B CYS* 3.5 16.3 - - - -
932B LEU* 3.4 33.6 - - + +
935B ASP* 3.7 23.5 + - + +
937B PHE* 3.5 29.6 - + + -
938B LEU* 3.7 14.1 - - + -
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Residues in contact with ILE 915 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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868B GLY* 4.4 5.8 - - - +
871B ILE* 3.9 29.8 - - + -
872B ILE* 3.8 19.7 - - + -
903B ILE* 3.8 26.5 - - + -
907B MET* 4.3 17.7 - - + -
911B ALA* 3.1 23.2 + - + +
912B LYS 3.4 3.6 + - - +
914B PHE* 1.3 79.4 - - + +
916B LEU* 1.4 63.1 + - - +
918B CYS* 3.0 20.3 + - - +
919B PHE* 3.3 39.9 + - + -
937B PHE* 6.0 2.0 - - + -
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Residues in contact with LEU 916 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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900B HIS* 3.5 33.4 - - + +
903B ILE* 3.7 15.2 - - + +
912B LYS* 3.0 29.2 + - + +
913B ALA* 3.4 12.1 - - - +
914B PHE 3.3 0.2 - - - -
915B ILE* 1.4 75.4 - - - +
917B LYS* 1.3 53.1 + - - +
919B PHE* 2.8 26.9 + - + +
920B GLU* 3.3 9.5 + - - +
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Residues in contact with LYS 917 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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913B ALA* 3.1 21.7 + - - +
914B PHE* 3.5 9.6 - - - +
916B LEU* 1.3 75.3 - - - +
918B CYS* 1.4 59.0 + - - +
919B PHE 3.6 0.2 + - - -
920B GLU* 3.7 17.7 - - - +
926B ARG* 3.8 8.0 - - - +
927B ALA* 4.0 21.8 + - + +
931B ASP 6.0 0.2 + - - -
932B LEU* 4.0 15.3 - - + -
935B ASP* 3.0 29.7 + - - +
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Residues in contact with CYS 918 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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864B ILE* 3.5 28.3 - - - +
865B TRP* 3.5 15.2 - - - -
867B LEU* 4.3 9.2 - - - -
868B GLY* 3.9 18.4 - - - -
871B ILE* 4.6 1.1 - - - -
914B PHE* 3.5 29.6 + - - -
915B ILE* 3.0 10.3 + - - +
917B LYS* 1.4 74.2 - - - +
919B PHE* 1.4 59.1 + - + +
920B GLU 3.4 1.6 - - - -
926B ARG* 3.4 20.7 - - - -
932B LEU* 4.0 23.8 - - - -
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Residues in contact with PHE 919 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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865B TRP* 3.3 52.3 - + - -
868B GLY* 3.4 26.7 - - - -
869B CYS* 3.6 7.6 - - - -
872B ILE* 3.9 8.3 - - + -
900B HIS* 3.4 43.3 - + + +
901B PRO* 3.4 33.4 - - + -
903B ILE* 4.4 1.1 - - + -
915B ILE* 3.3 32.9 + - + +
916B LEU* 2.8 14.0 + - + +
918B CYS* 1.4 78.1 - - - +
920B GLU* 1.4 62.5 + - - -
921B PRO* 3.1 9.9 - - - +
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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