Contacts of the strand formed by residues 845 - 849 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803C PHE* 3.3 56.1 - - + -
806C ARG* 3.7 13.2 - - - -
807C GLY* 3.6 12.7 - - - -
810C THR* 3.1 27.9 + - - +
832C VAL* 4.8 2.9 - - + -
833C LEU 3.3 14.8 - - - +
834C PRO* 3.9 0.9 - - + -
835C LEU* 3.8 7.6 - - - +
843C ASP 3.4 1.6 + - - -
844C LYS* 1.3 79.8 - - - +
846C ILE* 1.3 61.7 + - - +
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Residues in contact with ILE 846 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807C GLY* 3.6 5.2 - - - -
810C THR* 4.1 2.7 - - + -
811C TYR* 3.9 27.1 - - + +
832C VAL* 3.9 1.7 - - - -
833C LEU* 3.0 30.7 + - + +
835C LEU* 3.7 21.3 - - + -
841C PHE* 3.8 33.4 - - + -
845C CYS* 1.3 76.2 - - - +
847C ALA* 1.3 64.9 + - - +
848C TRP* 4.1 6.8 - - + -
854C ILE* 5.0 2.5 - - + -
858C ILE* 3.9 20.2 - - + -
862C VAL* 3.8 28.3 - - + -
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Residues in contact with ALA 847 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804C HIS 4.0 5.4 - - - +
807C GLY* 3.1 21.8 + - - +
808C ILE* 3.9 8.1 - - + +
811C TYR* 3.0 28.1 - - - +
824C VAL* 4.7 1.2 - - - +
830C VAL* 3.9 14.4 - - + -
831C TYR 3.0 17.0 - - - +
832C VAL* 3.8 16.2 - - + -
846C ILE* 1.3 75.7 - - - +
848C TRP* 1.3 63.3 + - - +
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Residues in contact with TRP 848 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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776C TYR* 3.4 28.9 - + - -
777C ILE* 4.4 6.1 - - + -
780C ALA* 4.3 5.4 - - + -
811C TYR* 4.0 17.0 - - + -
822C PRO* 6.6 0.4 - - + -
824C VAL* 4.3 2.7 - - - -
830C VAL* 3.3 7.0 - - - -
831C TYR* 2.8 66.6 + + + -
833C LEU* 3.7 39.5 - - + -
846C ILE* 4.1 9.9 - - + -
847C ALA* 1.3 79.4 - - - +
849C PRO* 1.3 90.8 - - + +
852C THR* 3.1 26.5 + - - -
853C GLU 4.1 0.2 - - - -
854C ILE* 3.6 41.4 - - + +
862C VAL* 5.0 1.3 - - + -
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Residues in contact with PRO 849 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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811C TYR* 4.2 11.9 - - + +
822C PRO* 4.2 15.5 - - + +
823C GLN 3.7 24.9 - - - +
824C VAL* 3.4 20.6 - - + -
828C GLU* 5.2 8.1 - - - +
829C LYS 4.1 6.3 - - - +
830C VAL* 4.5 2.9 - - + -
831C TYR* 3.7 0.2 - - - -
848C TRP* 1.3 96.7 + - + +
850C SER* 1.3 60.9 + - - +
852C THR* 2.6 38.5 + - + +
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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