Contacts of the strand formed by residues 727 - 735 (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 ARG 727 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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656C TYR* 4.1 2.5 - - - -
662C GLU* 3.1 30.7 + - + +
663C GLY* 3.6 21.1 - - - -
664C LEU* 3.2 30.6 - - - +
699C GLU* 4.0 10.7 + - - -
701C ARG* 4.2 3.8 - - - +
721C GLU* 3.1 27.7 + - - +
722C ASP 3.7 15.4 + - - -
724C HIS* 2.8 50.4 + - + +
725C SER 3.3 0.2 - - - -
726C LYS* 1.3 80.0 - - + +
728C SER* 1.3 65.4 + - - +
729C SER 4.3 4.7 - - - +
773C LEU* 4.9 1.3 - - + +
776C LYS* 3.0 26.5 + - - +
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Residues in contact with SER 728 (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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654C LYS 4.1 3.0 - - - +
655C MET* 3.7 34.9 + - - +
656C TYR* 3.1 40.8 + - - +
662C GLU* 2.9 25.5 + - - -
727C ARG* 1.3 74.8 - - - +
729C SER* 1.3 62.2 + - - +
776C LYS* 3.7 20.5 - - - +
777C PRO* 3.7 7.8 - - - +
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Residues in contact with SER 729 (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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655C MET* 4.2 7.0 - - - +
662C MET 2.8 14.5 + - - -
663C GLY* 3.2 24.4 - - - -
664C LEU 3.7 1.6 + - - -
698C TYR* 2.5 32.1 + - - -
724C HIS* 5.6 0.7 + - - -
727C ARG* 3.4 5.5 - - - +
728C SER* 1.3 76.9 - - - +
730C PHE* 1.3 63.7 + - - +
731C VAL* 4.6 1.5 - - - +
773C LEU* 4.5 9.8 - - - +
776C LYS* 4.9 0.7 - - - -
777C PRO* 3.3 28.7 - - - -
779C LEU* 5.6 2.5 - - - -
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Residues in contact with PHE 730 (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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664C LEU* 4.0 16.4 - - + +
666C ILE* 4.1 15.7 - - + -
715C MET* 5.0 2.5 - - - -
718C VAL* 3.8 24.7 - - + -
724C HIS* 4.8 4.9 - + - +
729C SER* 1.3 78.7 - - - +
731C VAL* 1.3 68.1 + - - +
732C CYS* 3.7 31.2 - - + -
765C PHE* 3.5 37.9 - + - -
773C LEU* 3.8 25.5 - - + +
777C PRO 3.3 3.9 + - - +
778C LYS* 3.5 9.8 - - + -
779C LEU* 2.8 27.2 + - - +
780C PHE* 3.8 20.6 - + - -
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Residues in contact with VAL 731 (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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664C LEU 3.1 11.2 + - - +
665C CYS* 3.1 16.7 + - - -
666C ILE 3.0 22.2 + - - -
693C PHE* 4.1 28.9 - - + -
698C TYR* 3.3 35.2 - - + +
729C SER* 4.6 0.4 - - - +
730C PHE* 1.3 82.4 - - - +
732C CYS* 1.3 66.1 + - - +
733C VAL* 4.5 3.6 - - + -
779C LEU* 3.5 25.8 - - + +
781C ILE* 4.3 14.8 - - + -
900D PHE* 5.8 0.2 - - + -
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Residues in contact with CYS 732 (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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666C ILE* 3.3 14.8 - - + +
668C ILE* 4.8 1.3 - - - -
715C MET* 4.3 17.7 - - - -
730C PHE* 3.7 24.5 - - + -
731C VAL* 1.3 77.3 - - - +
733C VAL* 1.3 61.3 + - - +
734C LEU* 3.9 27.7 + - - +
761C ILE* 6.4 0.4 - - - -
779C LEU 3.0 7.9 + - - -
780C PHE* 3.5 25.4 - - + +
781C ILE 3.2 20.6 + - - +
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Residues in contact with VAL 733 (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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665C CYS* 4.6 2.0 - - - -
666C ILE 2.7 13.0 + - - +
667C ILE* 3.4 13.8 - - + -
668C ILE* 2.8 28.9 + - - +
689C LEU* 3.4 39.9 - - + -
693C PHE* 4.4 7.9 - - + -
731C VAL* 4.5 6.3 - - + -
732C CYS* 1.3 73.7 - - - +
734C LEU* 1.3 66.8 + - - +
735C LEU* 3.7 18.2 - - + -
781C ILE* 3.4 37.9 - - + +
850D ILE* 4.8 0.4 - - + -
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Residues in contact with LEU 734 (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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668C ILE* 3.4 40.8 - - + -
715C MET* 5.8 0.2 - - - -
732C CYS* 3.9 19.5 - - - +
733C VAL* 1.3 72.6 - - - +
735C LEU* 1.3 65.6 + - - +
736C SER* 4.1 2.2 - - - -
743C ILE* 3.8 31.9 - - + -
758C LEU* 3.8 29.2 - - + -
761C ILE* 4.0 10.3 - - + -
780C PHE* 5.2 5.4 - - + -
781C ILE 2.9 10.8 + - - +
782C ILE* 4.5 15.4 - - + +
783C GLN 3.0 27.6 + - - +
784C ALA* 6.2 0.2 - - - -
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Residues in contact with LEU 735 (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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667C ILE* 4.4 5.6 - - + -
668C ILE* 2.9 15.8 + - - +
669C ASN* 3.4 27.1 - - + +
670C ASN* 3.0 23.9 + - - +
679C ARG* 3.9 7.4 - - - +
682C THR* 3.9 6.7 - - - +
685C ASP* 3.9 22.9 - - + +
686C ALA* 4.0 13.9 - - + +
689C LEU* 4.3 7.4 - - + -
733C VAL* 3.7 18.6 - - + -
734C LEU* 1.3 84.0 - - - +
736C SER* 1.3 65.6 + - - +
783C GLN* 3.5 25.8 - - + -
850D ILE* 4.1 12.8 - - + -
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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