Contacts of the strand formed by residues 827 - 831 (chain D) 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 PHE 827 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762C THR* 3.8 26.7 - - + -
765C PHE* 3.5 31.2 - - + -
766C ARG* 3.8 15.9 - - + -
778C LYS* 3.6 20.4 - - + -
780C PHE* 3.8 27.4 - + - -
823D VAL 3.9 7.4 - - - -
824D GLU* 3.4 29.6 - - - +
825D ALA 3.3 5.6 - - - -
826D ASP* 1.3 79.0 - - - +
828D LEU* 1.3 60.4 + - - +
829D TYR* 3.4 33.0 - + + -
890D VAL 4.2 0.2 - - - +
893D MET* 2.9 33.0 + - + +
894D LEU* 3.8 1.0 + - - -
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Residues in contact with LEU 828 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778C LYS 3.2 7.7 + - - +
779C LEU* 3.5 21.3 - - + -
780C PHE* 2.8 33.5 + - - +
826D ASP 4.2 0.6 + - - -
827D PHE* 1.3 74.3 - - - +
829D TYR* 1.3 63.9 + - - +
830D ALA* 4.5 3.8 - - + +
866D PHE* 3.1 42.6 - - + -
867D MET* 3.5 17.7 - - + -
870D LEU* 4.0 4.7 - - + -
889D ILE* 4.1 9.2 - - + -
890D VAL 3.2 23.1 - - - +
892D SER* 3.8 12.1 - - - -
894D LEU* 4.1 11.9 - - + -
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Residues in contact with TYR 829 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758C LEU* 5.4 6.3 - - + -
762C THR* 3.2 40.1 - - + +
780C PHE* 3.3 20.6 - - + +
782C ILE* 4.8 5.8 - - + -
824D GLU* 4.6 6.4 + - - -
827D PHE* 3.4 36.9 - + + -
828D LEU* 1.3 77.4 - - - +
830D ALA* 1.3 59.9 + - - +
831D TYR* 3.3 40.3 + + + -
890D VAL* 2.9 53.6 + - + +
893D MET* 3.8 18.7 - - + +
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Residues in contact with ALA 830 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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780C PHE 2.9 13.4 + - - +
781C ILE* 3.7 15.0 - - + -
782C ILE* 3.1 21.9 + - - -
828D LEU* 3.9 5.9 + - + -
829D TYR* 1.3 70.5 - - - +
831D TYR* 1.3 64.1 + - - +
849D PHE* 3.7 17.4 - - + -
853D LEU* 5.8 0.4 - - + -
866D PHE* 5.8 1.3 - - + -
870D LEU* 4.0 29.2 - - + -
888D CYS 4.2 2.7 - - - -
889D ILE* 4.8 5.2 - - + +
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Residues in contact with TYR 831 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741C GLY* 5.9 4.4 - - - -
758C LEU* 3.7 20.5 - - + +
782C ILE* 3.6 33.4 - - + -
786C ARG* 3.5 46.5 + - + +
829D TYR* 3.3 39.8 - + + -
830D ALA* 1.3 75.5 - - - +
832D SER* 1.3 61.5 + - - +
833D THR 3.2 16.4 - - - +
849D PHE* 3.7 5.0 - - - -
887D PRO* 3.6 6.6 - - - +
888D CYS 3.0 39.2 + - - +
890D VAL* 3.8 15.7 - - + -
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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