Contacts of the helix formed by residues 846 - 851 (chain A) in PDB entry 4RIB
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 LEU 846 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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842A TYR* 3.2 44.2 + - + +
845A LEU* 1.3 103.7 - - + +
847A TRP* 1.3 57.0 - - - +
848A ASP* 3.2 2.7 - - - -
849A ILE* 2.9 13.0 + - + -
850A ILE* 2.8 45.9 + - + +
875A PHE* 6.1 0.9 - - + -
883A LEU* 3.5 32.3 - - + -
886A ARG* 4.1 17.0 - - + +
887A LEU* 4.8 10.5 - - + -
890A ILE* 4.4 9.6 - - + -
944A CYS* 4.1 11.4 - - + -
948A ALA* 5.3 0.2 - - + -
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Residues in contact with TRP 847 (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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585A PRO* 3.8 15.8 - - + +
586A SER* 5.5 3.6 + - - +
843A GLY 3.1 23.2 + - - +
844A LEU* 4.5 0.6 - - + +
845A LEU 3.8 0.2 - - - -
846A LEU* 1.3 76.3 - - - +
848A ASP* 1.3 63.3 + - + +
850A ILE* 3.4 8.0 + - + +
851A PHE* 3.0 54.8 + + + +
905A THR* 3.6 22.7 - - + +
909A GLN* 3.3 53.0 + - + +
912A ARG* 4.0 18.6 - - + +
914A ALA* 3.7 30.5 - - + -
917A VAL* 4.2 10.3 - - + -
919A TRP* 4.0 18.4 - + - -
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Residues in contact with ASP 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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845A LEU 5.4 0.2 - - - -
846A LEU 3.8 2.4 - - - -
847A TRP* 1.3 80.6 + - + +
849A ILE* 1.3 67.9 + - - +
851A PHE* 3.7 3.3 - - - +
852A MET* 3.0 27.9 + - - +
886A ARG* 3.0 40.7 + - - -
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Residues in contact with ILE 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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846A LEU* 2.9 12.9 + - + +
848A ASP* 1.3 93.1 + - - +
850A ILE* 1.3 64.0 + - - +
852A MET* 3.0 39.4 - - + +
875A PHE* 5.6 1.1 - - + -
879A ARG* 3.4 16.0 + - - -
882A ALA* 3.3 30.1 - - + +
883A LEU* 3.7 32.1 - - + +
886A ARG* 3.6 39.0 - - + +
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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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842A TYR* 4.5 10.8 - - + +
843A GLY* 4.4 12.1 - - - -
846A LEU* 2.8 35.9 + - + +
847A TRP* 3.4 10.8 - - + +
849A ILE* 1.3 76.0 - - + +
851A PHE* 1.3 79.8 + - + +
852A MET 3.0 10.1 + - - +
859A PHE* 4.3 1.2 - - - -
866A PHE* 5.3 0.2 - - - -
867A PRO* 3.7 30.7 - - + +
870A LEU* 5.1 2.9 - - + -
875A PHE* 4.3 21.8 - - + -
879A ARG* 3.7 18.2 + - - -
916A LEU* 4.0 27.8 - - + -
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Residues in contact with PHE 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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585A PRO* 3.3 33.9 - - + -
586A SER 3.8 19.5 - - - +
587A TYR* 4.2 9.3 - + + +
847A TRP* 3.0 63.8 + + + +
848A ASP* 3.7 4.9 - - - +
850A ILE* 1.3 88.1 - - + +
852A MET* 1.3 62.7 + - - +
853A ASP* 3.8 9.7 - - - +
859A PHE* 3.7 26.0 - + - -
865A ALA* 3.5 24.7 - - - -
866A PHE* 3.9 13.7 - - - -
914A ALA* 4.1 7.4 - - + -
916A LEU* 6.0 1.8 - - + -
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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