Contacts of the helix formed by residues 847 - 854 (chain A) 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 ALA 847 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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845A TYR 3.6 0.8 + - - -
846A MET* 1.3 76.2 - - - +
848A PRO* 1.4 72.2 - - + +
849A GLU* 3.3 28.0 - - - +
850A ILE* 3.0 19.9 + - + +
851A ILE* 3.5 5.2 + - - +
858A TYR* 6.2 0.4 - - - -
862A ALA* 3.9 17.4 + - + +
865A TRP* 3.5 30.1 - - + -
866A SER* 5.0 1.0 + - - -
926A ARG* 4.1 0.2 - - - +
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Residues in contact with PRO 848 (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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846A MET 3.8 0.4 - - - -
847A ALA* 1.4 80.9 - - - +
849A GLU* 1.3 66.3 + - - +
850A ILE 3.0 0.9 + - - -
851A ILE* 3.1 9.6 + - + +
852A ASP* 2.9 28.0 + - - +
865A TRP* 3.6 35.0 - - + -
894A VAL* 3.7 22.0 - - + +
895A GLY* 4.9 2.4 - - - -
898A LYS* 3.6 30.6 - - + -
921A PRO* 3.9 21.3 - - + +
926A ARG* 4.1 2.5 - - - +
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Residues in contact with GLU 849 (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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847A ALA* 3.4 15.3 - - - +
848A PRO* 1.3 78.2 - - + +
850A ILE* 1.4 58.9 + - + +
852A ASP* 3.9 13.7 - - - +
853A LYS* 3.2 40.9 + - - +
857A GLY* 3.7 22.2 - - - +
861A ALA* 4.3 0.3 - - - +
862A ALA* 3.9 10.7 + - - +
923A PRO* 3.7 32.1 - - + +
926A ARG* 2.8 42.8 + - - -
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Residues in contact with ILE 850 (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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840A THR* 5.3 4.5 - - + -
846A MET* 3.6 25.3 - - + +
847A ALA* 3.0 25.9 + - + +
849A GLU* 1.4 81.0 - - + +
851A ILE* 1.3 64.0 + - - +
852A ASP 3.1 0.9 - - - -
854A GLY* 2.9 41.0 + - - +
855A PRO 4.6 0.7 - - - -
857A GLY* 3.4 10.1 - - - +
858A TYR* 3.4 79.2 - - + +
862A ALA* 4.1 4.0 - - + -
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Residues in contact with ILE 851 (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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843A LEU 5.4 0.4 - - - +
846A MET* 3.9 24.7 - - + +
847A ALA 3.8 7.9 - - - +
848A PRO* 3.5 6.1 - - + +
850A ILE* 1.3 77.5 - - - +
852A ASP* 1.3 60.5 + - - +
854A GLY* 4.6 0.5 + - - -
891A MET* 3.3 62.1 - - + +
892A PHE* 5.6 0.2 - - - -
894A VAL* 3.7 22.4 - - + -
895A GLY* 3.6 28.5 - - - +
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Residues in contact with ASP 852 (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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848A PRO 2.9 16.3 + - - +
849A GLU* 4.0 7.3 - - - +
850A ILE 3.1 0.2 - - - -
851A ILE* 1.3 79.7 - - - +
853A LYS* 1.4 83.5 + - - +
854A GLY 3.5 0.9 + - - -
895A GLY* 5.7 0.8 - - - -
898A LYS* 5.7 8.5 - - - +
830B ALA* 5.9 5.2 - - - +
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Residues in contact with LYS 853 (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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849A GLU* 3.2 24.7 + - - +
852A ASP* 1.4 89.7 - - - +
854A GLY* 1.3 61.0 + - - +
856A ARG* 4.0 15.0 - - + +
857A GLY* 3.8 26.7 + - - +
923A PRO* 5.0 12.2 - - - +
924A ASP* 5.8 1.8 + - - -
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Residues in contact with GLY 854 (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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850A ILE* 2.9 29.5 + - - +
851A ILE 4.6 1.1 + - - -
852A ASP 3.3 3.2 + - - -
853A LYS* 1.3 74.2 - - - +
855A PRO* 1.4 63.0 - - - +
856A ARG 3.1 2.9 - - - -
857A GLY* 2.7 30.1 + - - -
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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