Contacts of the helix formed by residues 873 - 878 (chain B) 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 ASP 873 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655B LEU* 6.6 0.2 - - - -
737B GLU* 4.6 9.6 - - - +
739B ARG* 3.0 42.0 + - - -
872B THR* 1.3 77.3 - - + +
874B SER* 1.3 61.3 + - - +
875B PHE 3.2 1.7 + - - -
876B PHE* 3.5 10.9 + - - +
877B THR* 3.5 21.4 + - + +
949B ALA 4.7 11.7 - - - +
950B ASP* 4.4 4.7 - - - +
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Residues in contact with SER 874 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656B PHE* 4.4 10.4 - - - -
869B ASP* 3.6 15.2 - - - +
872B THR* 2.9 21.3 + - - +
873B ASP* 1.3 77.4 - - - +
875B PHE* 1.3 60.3 + - - +
876B PHE 3.3 0.2 - - - -
877B THR* 3.1 12.6 - - - -
878B SER* 2.7 40.9 + - - -
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Residues in contact with PHE 875 (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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842B TYR* 3.6 24.5 - - - -
846B LEU* 6.1 0.7 - - + -
849B ILE* 5.0 0.4 - - + -
850B ILE* 4.3 18.8 - - + -
867B PRO* 4.3 8.1 - - + -
869B ASP* 3.2 29.6 + - - +
870B LEU* 3.8 37.2 - - + +
872B THR 2.9 15.6 + - - +
874B SER* 1.3 75.1 + - - +
876B PHE* 1.3 66.1 + - - +
878B SER 3.8 0.9 + - - -
879B ARG* 3.1 65.1 + - - +
883B LEU* 4.3 13.5 - - + -
948B ALA* 3.7 24.9 - - + +
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Residues in contact with PHE 876 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873B ASP 3.5 7.6 + - - +
874B SER 3.3 0.2 - - - -
875B PHE* 1.3 76.2 - - - +
877B THR* 1.3 65.7 + - + +
879B ARG 2.9 4.5 + - - -
880B ARG* 2.8 67.8 + - + -
883B LEU* 3.6 35.4 - - + -
884B GLU* 4.1 20.9 - - + -
887B LEU* 4.3 13.2 - - + -
945B ARG* 4.2 17.3 - - + -
948B ALA* 3.8 31.8 + - + +
949B ALA* 4.1 18.4 - - + +
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Residues in contact with THR 877 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873B ASP* 3.5 17.9 - - + +
874B SER* 3.1 19.4 + - - -
876B PHE* 1.3 80.7 - - + +
878B SER* 1.3 59.5 + - - +
879B ARG 3.0 4.9 + - - -
880B ARG* 3.6 32.3 + - - +
881B PRO* 5.1 1.4 - - - +
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Residues in contact with SER 878 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855B ILE* 3.6 36.2 - - - +
869B ASP* 4.2 1.8 + - - -
874B SER* 2.7 31.7 + - - -
875B PHE 4.0 0.2 - - - -
876B PHE 3.2 0.2 - - - -
877B THR* 1.3 73.1 + - - +
879B ARG* 1.3 73.7 + - - +
881B PRO* 5.5 0.4 - - - -
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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
------------------------------------------------------------
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