Contacts of the strand formed by residues 845 - 849 (chain B) in PDB entry 3RMD
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 CYS 845 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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803B PHE* 3.4 56.1 - - + -
806B ARG* 4.2 9.4 - - - -
807B GLY* 3.6 15.2 - - - -
810B THR* 2.9 27.7 + - - +
832B VAL* 4.5 5.6 - - + -
833B LEU 3.4 15.7 - - - +
834B PRO* 3.9 1.1 - - + -
835B LEU* 4.0 8.3 - - - +
843B ASP* 3.4 1.6 + - - +
844B LYS* 1.3 79.6 - - - +
846B ILE* 1.3 62.1 + - - +
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Residues in contact with ILE 846 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807B GLY* 3.6 5.2 - - - -
810B THR* 3.8 3.4 - - + -
811B TYR* 3.7 33.0 - - + +
814B ALA* 4.4 0.2 - - + -
832B VAL* 3.8 1.7 - - - -
833B LEU* 3.2 26.4 + - + +
835B LEU* 3.9 18.4 - - + -
841B PHE* 4.0 20.9 - - + -
845B CYS* 1.3 77.3 - - - +
847B ALA* 1.3 63.8 + - - +
848B TRP* 4.1 5.2 - - + -
854B ILE* 4.7 5.2 - - + -
858B ILE* 3.3 33.2 - - + -
862B VAL* 3.9 28.9 - - + -
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Residues in contact with ALA 847 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804B HIS 3.9 2.5 - - - +
807B GLY* 3.1 7.9 + - - -
808B ILE* 3.7 24.0 - - + +
811B TYR* 3.0 28.9 - - - +
824B VAL* 5.0 0.7 - - - -
830B VAL* 3.7 13.2 - - + -
831B TYR 3.0 15.0 - - - +
832B VAL* 3.6 17.0 - - + -
846B ILE* 1.3 75.3 - - - +
848B TRP* 1.3 64.4 + - - +
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Residues in contact with TRP 848 (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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776B TYR* 3.5 23.6 - + - -
777B ILE* 4.2 5.2 - - + -
780B ALA* 4.1 4.5 - - + -
811B TYR* 4.1 8.3 - - + -
824B VAL* 4.2 3.1 - - - -
830B VAL* 3.3 6.6 - - - -
831B TYR* 2.8 69.0 + + + -
833B LEU* 3.5 40.4 - - + -
846B ILE* 4.1 9.4 - - + -
847B ALA* 1.3 81.0 - - - +
849B PRO* 1.3 92.8 + - + +
852B THR* 3.0 27.1 + - - -
853B GLU 4.1 0.4 - - - -
854B ILE* 3.6 52.4 - - + +
862B VAL* 5.0 2.0 - - + -
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Residues in contact with PRO 849 (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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811B TYR* 3.9 12.1 - - + +
822B PRO* 4.3 16.2 - - + +
823B GLN 3.7 24.9 - - - +
824B VAL* 3.5 19.0 - - + -
829B LYS 4.1 6.5 - - - +
830B VAL* 4.6 2.9 - - + -
848B TRP* 1.3 100.7 + - + +
850B SER* 1.3 63.4 + - - +
852B THR* 2.8 34.3 + - + +
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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