Contacts of the strand formed by residues 778 - 783 (chain C) in PDB entry 1RHM
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 LYS 778 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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730C PHE* 3.5 11.7 - - + +
765C PHE* 3.1 36.6 - - + +
767C GLY* 4.9 5.7 - - - +
773C LEU* 3.2 42.1 + - + -
774C THR* 4.6 2.4 - - - +
775C GLY 4.5 3.2 - - - +
776C LYS 2.7 28.3 + - - +
777C PRO* 1.3 72.3 - - - +
779C LEU* 1.3 63.0 + - - +
780C PHE* 3.7 20.0 - - + -
825D ALA 4.0 6.8 + - - -
826D ASP* 3.0 24.0 + - - +
827D PHE* 3.6 25.5 - - + -
828D LEU 3.2 19.8 + - - -
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Residues in contact with LEU 779 (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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693C PHE* 6.0 1.3 - - + -
698C TYR* 5.3 1.1 - - - +
729C SER* 5.6 2.0 - - - +
730C PHE 2.8 15.2 + - - +
731C VAL* 3.5 27.0 - - + -
732C CYS* 3.0 24.4 + - - +
777C PRO* 4.1 16.8 - - + +
778C LYS* 1.3 72.9 - - - +
780C PHE* 1.3 70.5 + - - +
781C ILE* 4.2 8.1 - - + -
828D LEU* 3.5 28.5 - - + +
866D PHE* 3.8 25.6 - - + -
894D LEU* 4.6 2.2 - - + -
898D LEU* 4.0 26.2 - - + -
900D PHE* 4.4 11.9 - - + -
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Residues in contact with PHE 780 (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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715C MET* 5.3 1.8 - - - -
730C PHE* 3.8 14.8 - + - -
732C CYS* 3.5 31.4 - - + +
734C LEU* 5.2 9.9 - - + -
758C LEU* 5.5 2.9 - - + -
761C ILE* 4.5 12.6 - - + -
762C THR* 4.0 22.0 - - - -
765C PHE* 3.8 27.1 - + - -
778C LYS* 3.7 15.5 - - + -
779C LEU* 1.3 79.6 - - - +
781C ILE* 1.3 64.0 + - - +
782C ILE* 3.9 10.9 + - + +
827D PHE* 3.8 28.5 - + - -
828D LEU 2.8 13.4 + - - +
829D TYR* 3.3 17.2 - + + -
830D ALA 2.9 25.2 + - - -
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Residues in contact with ILE 781 (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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689C LEU* 5.4 0.7 - - + -
693C PHE* 3.9 26.5 - - + -
731C VAL* 4.3 9.4 - - + -
732C CYS 3.2 6.0 + - - +
733C VAL* 3.4 21.7 - - + +
734C LEU 2.9 27.2 + - - +
779C LEU* 4.2 6.0 - - + -
780C PHE* 1.3 76.8 - - - +
782C ILE* 1.3 64.0 + - - +
783C GLN 4.2 0.2 - - - -
830D ALA* 3.7 14.8 - - + +
849D PHE* 3.8 16.8 - - + -
850D ILE* 4.3 11.4 - - + -
853D LEU* 3.6 35.9 - - + -
866D PHE* 5.4 11.2 - - + -
870D LEU* 6.5 0.2 - - + -
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Residues in contact with ILE 782 (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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734C LEU* 3.7 19.1 - - + +
743C ILE* 4.7 12.3 - - + -
758C LEU* 3.5 34.1 - - + -
780C PHE* 4.1 15.9 - - + +
781C ILE* 1.3 79.8 - - - +
783C GLN* 1.3 60.9 + - - +
784C ALA* 3.6 22.9 + - + +
786C ARG* 6.6 0.2 - - + -
829D TYR* 4.8 7.2 - - + -
830D ALA 3.1 10.3 + - - +
831D TYR* 3.6 33.7 - - + +
832D SER* 3.1 29.2 + - - -
849D PHE* 4.8 2.5 - - - -
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Residues in contact with GLN 783 (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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502C NA4 3.0 25.3 + - - +
679C ARG* 4.0 9.4 - - - +
685C ASP* 4.5 0.9 - - - +
734C LEU 3.0 9.6 + - - +
735C LEU* 3.5 23.1 - - + +
736C SER 3.3 21.5 + - - +
781C ILE 4.2 0.4 - - - -
782C ILE* 1.3 71.2 - - - +
784C ALA* 1.3 62.8 + - - +
832D SER* 3.0 19.5 - - - -
839D SER* 2.9 26.1 + - - -
840D TRP 4.2 5.1 + - - -
847D SER* 3.2 36.2 + - - +
849D PHE* 3.3 11.4 - - - +
850D ILE* 3.9 10.0 - - + +
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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