Contacts of the helix formed by residues 707 - 721 (chain C) in PDB entry 1RHJ
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 THR 707 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674C HIS* 4.5 9.0 - - + +
705C ASP 5.4 0.9 - - - +
706C LEU* 1.3 75.7 - - - +
708C ARG* 1.3 64.5 - - - +
709C GLU* 3.5 12.7 + - - +
710C GLU* 2.9 42.2 + - - +
711C ILE* 3.0 21.5 + - - +
745C GLY* 4.0 0.9 - - - -
746C THR* 3.6 15.0 - - - +
747C ASN* 3.2 23.3 - - - +
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Residues in contact with ARG 708 (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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707C THR* 1.3 70.2 - - - +
709C GLU* 1.3 86.6 + - - +
711C ILE* 3.4 2.9 + - - +
712C VAL* 3.2 29.4 + - + +
745C GLY* 3.8 5.5 - - - -
747C ASN* 2.7 30.0 + - - +
754C GLY* 3.8 11.6 - - - +
755C PRO* 2.8 49.5 + - - +
756C VAL* 3.5 26.4 - - + +
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Residues in contact with GLU 709 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707C THR* 3.1 9.1 + - - +
708C ARG* 1.3 101.7 - - - +
710C GLU* 1.3 57.8 + - + +
712C VAL* 3.4 6.5 + - - +
713C GLU* 2.8 34.2 + - - +
747C ASN* 3.1 23.0 + - - -
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Residues in contact with GLU 710 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705C ASP 4.1 3.5 - - - +
706C LEU* 3.5 27.3 - - + +
707C THR* 2.9 43.8 + - - +
709C GLU* 1.3 75.4 - - + +
711C ILE* 1.3 61.2 + - - +
713C GLU* 3.7 13.6 - - - +
714C LEU* 2.8 32.6 + - - +
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Residues in contact with ILE 711 (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* 4.2 22.4 - - + -
670C ASN* 3.8 10.8 - - - +
706C LEU* 3.8 23.5 - - + +
707C THR 3.0 11.2 + - - +
708C ARG* 3.7 7.9 - - - +
710C GLU* 1.3 75.3 - - - +
712C VAL* 1.3 64.3 + - - +
714C LEU* 3.6 2.1 - - - +
715C MET* 2.9 29.4 + - + +
734C LEU* 5.4 1.1 - - + -
743C ILE* 3.8 21.8 - - + -
744C PHE 4.2 0.9 - - - +
745C GLY* 3.7 29.2 - - - +
756C VAL* 4.4 6.1 - - + -
761C ILE* 3.9 30.7 - - + -
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Residues in contact with VAL 712 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708C ARG 3.2 14.6 + - - +
709C GLU* 3.7 8.3 - - - +
711C ILE* 1.3 80.5 - - - +
713C GLU* 1.3 59.3 + - - +
715C MET* 3.3 2.4 + - - +
716C ARG* 2.9 33.3 + - - +
756C VAL* 4.1 15.7 - - + -
760C LYS* 3.9 42.0 - - + +
761C ILE* 4.1 9.0 - - + -
764C PHE* 3.7 14.0 - - + -
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Residues in contact with GLU 713 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709C GLU* 2.8 21.8 + - - +
710C GLU* 3.7 15.2 - - - +
712C VAL* 1.3 77.9 - - - +
714C LEU* 1.3 61.6 + - - +
716C ARG* 3.0 30.6 + - - +
717C ASP* 2.8 36.6 + - - +
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Residues in contact with LEU 714 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666C ILE* 3.9 12.8 - - + -
668C ILE* 4.2 4.0 - - + -
701C ARG* 6.0 2.7 - - - +
703C LYS* 3.7 44.2 - - + +
706C LEU* 3.9 15.7 - - + -
710C GLU 2.8 21.6 + - - +
711C ILE 3.6 2.9 - - - +
713C GLU* 1.3 74.6 - - - +
715C MET* 1.3 77.2 + - + +
717C ASP* 3.3 7.7 + - + +
718C VAL* 2.9 46.3 + - + +
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Residues in contact with MET 715 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666C ILE* 3.7 25.6 - - + -
668C ILE* 4.1 8.5 - - + -
711C ILE* 2.9 23.5 + - + +
712C VAL 3.7 3.1 - - - +
714C LEU* 1.3 98.9 - - + +
716C ARG* 1.3 64.1 + - - +
718C VAL* 3.5 6.9 + - + -
719C SER* 3.1 24.6 + - - -
730C PHE* 5.0 0.4 - - - -
732C CYS* 4.0 22.9 - - - -
761C ILE* 3.6 29.6 - - + +
764C PHE* 3.8 17.0 - - + -
765C PHE* 3.6 22.4 - - + -
780C PHE* 5.4 0.9 - - - -
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Residues in contact with ARG 716 (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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712C VAL* 2.9 15.5 + - - +
713C GLU* 3.0 39.4 + - - +
715C MET* 1.3 77.0 - - - +
717C ASP* 1.3 80.9 + - - +
719C SER* 2.6 23.8 + - - +
720C LYS* 3.0 33.6 + - + +
764C PHE* 3.6 30.9 - - + -
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Residues in contact with ASP 717 (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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713C GLU* 2.8 28.3 + - - +
714C LEU* 3.6 8.7 - - + +
716C ARG* 1.3 100.0 + - - +
718C VAL* 1.3 63.4 + - + +
720C LYS* 3.0 20.5 + - - +
721C GLU* 3.1 15.0 + - - +
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Residues in contact with VAL 718 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664C LEU* 3.9 18.2 - - + -
666C ILE* 4.2 17.5 - - + -
701C ARG* 4.7 8.3 - - - +
714C LEU* 2.9 42.7 + - + +
715C MET* 3.9 7.6 - - + +
717C ASP* 1.3 75.1 - - + +
719C SER* 1.3 58.6 + - - +
721C GLU* 3.1 21.8 + - - +
724C HIS* 2.9 24.5 + - + -
730C PHE* 3.5 34.5 - - + -
765C PHE* 4.2 4.0 - - + -
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Residues in contact with SER 719 (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 3.1 15.1 + - - -
716C ARG* 2.6 20.6 + - - +
718C VAL* 1.3 76.3 - - - +
720C LYS* 1.3 62.5 + - - +
721C GLU 3.6 3.2 + - - +
764C PHE* 3.5 37.0 + - - +
765C PHE* 3.6 21.5 - - - -
769C ARG 5.0 2.0 - - - +
770C CYS* 3.4 26.2 - - - +
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Residues in contact with LYS 720 (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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716C ARG* 3.0 42.9 + - + +
717C ASP* 3.0 14.7 + - - +
719C SER* 1.3 78.8 - - - +
721C GLU* 1.3 66.3 + - - +
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Residues in contact with GLU 721 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664C LEU* 3.5 6.0 - - - +
701C ARG* 2.8 35.9 + - - -
717C ASP 3.1 10.7 + - - +
718C VAL* 3.1 20.2 + - - +
719C SER 3.7 3.8 - - - +
720C LYS* 1.3 84.2 - - - +
722C ASP* 1.3 60.4 + - - +
724C HIS* 3.4 18.9 + - - +
727C ARG* 2.9 31.8 + - - +
772C SER* 3.7 4.3 + - - -
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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
------------------------------------------------------------
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