Contacts of the helix formed by residues 745 - 759 (chain C) in PDB entry 3RTR
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 745 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704C GLU* 4.7 13.4 + - - -
711C ILE* 5.4 0.2 - - - +
743C LYS* 3.4 9.1 + - - +
744C PRO* 1.3 74.4 - - - +
746C VAL* 1.3 66.7 + - - +
747C PRO* 3.9 14.6 - - + +
748C VAL* 3.5 36.8 + - + +
749C ILE* 3.3 14.2 + - - +
745E ARG* 4.7 14.6 - - - +
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Residues in contact with VAL 746 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731C LEU* 3.7 33.8 - - + +
735C LEU* 5.4 8.1 - - + -
744C PRO 4.4 2.2 - - - +
745C ARG* 1.3 71.7 - - - +
747C PRO* 1.3 74.0 - - + +
749C ILE* 3.1 17.6 + - - +
750C LYS* 3.2 15.1 + - + +
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Residues in contact with PRO 747 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745C ARG* 3.4 18.8 - - + +
746C VAL* 1.3 96.7 - - + +
748C VAL* 1.3 65.1 + - + +
750C LYS* 3.4 7.8 + - + +
751C LYS* 3.2 23.0 + - - +
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Residues in contact with VAL 748 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704C GLU* 5.5 4.3 - - - +
708C LYS* 3.9 32.8 - - + -
711C ILE* 3.7 23.6 - - + -
745C ARG* 3.7 49.8 - - + +
746C VAL 3.2 0.8 - - - -
747C PRO* 1.3 76.7 - - + +
749C ILE* 1.3 58.2 + - - +
751C LYS* 3.3 9.0 + - + +
752C CYS* 3.0 32.7 + - - -
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Residues in contact with ILE 749 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711C ILE* 3.8 25.1 - - + -
715C ILE* 4.0 16.4 - - + -
731C LEU* 3.5 33.4 - - + -
734C VAL* 3.7 30.5 - - + -
735C LEU* 3.9 10.5 - - + -
744C PRO* 3.8 15.7 - - + -
745C ARG 3.3 14.1 - - - +
746C VAL 3.1 6.8 + - - +
748C VAL* 1.3 78.1 - - - +
750C LYS* 1.3 62.5 + - - +
752C CYS* 3.3 3.1 + - - +
753C ILE* 3.0 34.7 + - + +
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Residues in contact with LYS 750 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727C HIS* 4.3 22.9 - - + +
731C LEU* 5.8 0.2 - - - +
746C VAL* 3.2 15.4 + - + +
747C PRO* 3.9 9.9 - - + +
748C VAL 3.3 0.2 - - - -
749C ILE* 1.3 73.9 - - - +
751C LYS* 1.3 66.2 + - - +
753C ILE* 3.2 11.9 + - + +
754C ASP* 2.9 50.9 + - - +
764C ARG* 3.4 18.4 - - - +
772C TYR* 4.0 8.3 + - - -
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Residues in contact with LYS 751 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708C LYS* 3.6 31.6 - - - +
747C PRO 3.2 12.9 + - - +
748C VAL* 3.5 10.8 - - + +
750C LYS* 1.3 79.9 - - + +
752C CYS* 1.3 56.6 + - - +
754C ASP* 3.1 10.4 + - + +
755C ILE* 2.9 48.3 + - + +
98D ASN 5.9 0.7 - - - -
100D GLU* 2.2 48.2 + - - +
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Residues in contact with CYS 752 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708C LYS* 3.7 41.5 - - - -
711C ILE* 3.9 13.0 - - + -
712C GLN* 4.3 11.9 - - + -
715C ILE* 3.5 17.5 - - + -
748C VAL* 3.0 25.1 + - - -
749C ILE 3.5 9.2 - - - +
750C LYS 3.3 0.2 - - - -
751C LYS* 1.3 76.4 - - - +
753C ILE* 1.3 60.0 + - - +
755C ILE* 3.8 10.1 - - - +
756C LEU* 3.0 32.9 + - - +
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Residues in contact with ILE 753 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715C ILE* 4.1 14.6 - - + -
727C HIS* 4.6 13.7 - - + +
730C LEU* 3.7 28.3 - - + -
731C LEU* 5.8 2.2 - - + +
749C ILE* 3.0 23.1 + - + +
750C LYS* 3.3 16.6 - - + +
751C LYS 3.1 0.2 - - - -
752C CYS* 1.3 77.4 - - - +
754C ASP* 1.3 65.5 + - - +
756C LEU* 3.4 4.5 + - - -
757C ILE* 3.0 37.3 + - + +
762C LEU* 3.6 10.2 - - + +
772C TYR* 3.7 38.4 - - + +
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Residues in contact with ASP 754 (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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750C LYS* 2.9 46.5 + - - +
751C LYS* 3.1 10.5 + - + +
753C ILE* 1.3 77.3 - - - +
755C ILE* 1.3 60.2 + - + +
757C ILE* 3.0 10.6 + - - +
758C GLU* 2.9 36.4 + - + +
764C ARG* 3.6 13.6 + - - -
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Residues in contact with ILE 755 (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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708C LYS* 4.8 8.7 - - - +
712C GLN* 4.0 9.2 - - - +
751C LYS* 2.9 50.7 + - + +
752C CYS* 3.9 10.5 - - - +
753C ILE 3.3 0.2 - - - -
754C ASP* 1.3 76.5 - - + +
756C LEU* 1.3 58.2 - - - +
758C GLU* 3.5 8.6 + - - +
759C LYS* 2.8 52.7 + - + +
93D VAL* 3.9 22.0 - - + -
98D ASN* 3.5 31.9 - - - +
100D GLU* 6.1 1.3 - - + -
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Residues in contact with LEU 756 (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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54B ILE* 4.0 25.4 - - + -
712C GLN* 4.2 20.4 - - + +
715C ILE* 3.8 33.2 - - + -
716C VAL* 4.0 17.3 - - + -
752C CYS 3.0 23.1 + - - +
753C ILE* 3.7 4.7 - - - +
754C ASP 3.2 0.2 - - - -
755C ILE* 1.3 75.2 - - - +
757C ILE* 1.3 60.9 + - - +
759C LYS* 3.5 14.4 + - + -
760C GLU 3.1 5.7 + - - -
761C TYR* 2.9 34.4 + - + -
762C LEU* 3.5 22.7 + - + -
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Residues in contact with ILE 757 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753C ILE* 3.0 18.4 + - + +
754C ASP* 3.0 14.0 + - - +
756C LEU* 1.3 76.1 - - - +
758C GLU* 1.3 65.2 + - + +
760C GLU* 3.3 13.9 + - - +
762C LEU* 3.2 33.2 - - + +
763C GLU* 4.7 6.7 - - - -
764C ARG* 3.3 50.5 - - + +
772C TYR* 4.4 11.4 - - + -
91D ARG* 5.4 0.9 + - - -
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Residues in contact with GLU 758 (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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46B ARG* 5.1 1.1 + - - -
754C ASP* 2.9 21.3 + - + +
755C ILE* 3.8 6.1 - - - +
757C ILE* 1.3 76.5 - - + +
759C LYS* 1.3 60.3 + - - +
760C GLU 3.1 2.9 + - - -
90D THR 3.9 5.1 - - - +
91D ARG* 2.6 65.3 + - + +
92D GLN* 2.2 40.0 + - - +
93D VAL* 3.2 36.3 + - + +
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Residues in contact with LYS 759 (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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44B ILE* 4.5 8.6 - - - +
45B CYS* 2.7 35.4 + - - +
46B ARG* 3.6 35.9 - - + +
54B ILE* 4.5 9.5 - - - +
86B ARG* 4.8 2.4 + - - -
712C GLN* 3.5 14.3 - - - +
755C ILE* 2.8 42.2 + - + +
756C LEU* 3.9 12.1 - - + +
757C ILE 3.3 0.4 - - - -
758C GLU* 1.3 75.5 - - + +
760C GLU* 1.3 70.5 + - - +
761C TYR* 3.4 21.3 + - + -
91D ARG* 5.7 0.4 - - - -
93D VAL* 5.0 0.9 - - + -
98D ASN* 3.4 19.9 + - - +
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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