Contacts of the helix formed by residues 756 - 771 (chain C) in PDB entry 3RMD
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 GLY 756 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696C LYS* 3.4 22.3 + - - -
698C ILE* 5.6 1.8 - - - -
751C ARG 2.7 17.3 + - - +
752C MET* 3.9 11.9 + - - -
754C GLN 3.8 0.6 - - - -
755C GLU* 1.3 74.7 - - - +
757C GLU* 1.3 67.6 + - - +
758C GLU 3.5 2.2 - - - -
759C SER* 3.1 18.4 + - - -
760C LEU* 3.2 6.6 + - - +
889C LEU* 5.4 0.2 - - - -
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Residues in contact with GLU 757 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696C LYS* 5.6 0.8 - - - +
756C GLY* 1.3 68.7 - - - -
758C GLU* 1.3 67.8 + - - +
760C LEU* 2.9 18.9 + - - +
761C GLN* 3.0 35.7 + - - +
889C LEU* 3.5 30.5 - - + +
890C ASP* 2.6 42.1 + - - +
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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
----------------------------------------------------------
696C LYS* 5.3 10.6 + - + +
756C GLY 3.4 1.0 + - - -
757C GLU* 1.3 80.4 - - + +
759C SER* 1.3 63.5 + - - +
761C GLN* 3.1 15.8 + - + +
762C GLU* 2.9 35.5 + - + +
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Residues in contact with SER 759 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751C ARG* 3.1 41.8 + - - +
755C GLU* 2.7 46.7 + - - +
756C GLY 3.1 12.2 + - - -
758C GLU* 1.3 78.5 - - - +
760C LEU* 1.3 62.9 + - - +
762C GLU* 3.2 5.8 + - - +
763C TYR 3.1 9.9 + - - -
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Residues in contact with LEU 760 (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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748C CYS* 3.5 40.8 - - + +
751C ARG* 4.2 9.6 - - + +
752C MET* 3.6 27.1 - - + +
756C GLY 3.2 6.4 + - - +
757C GLU* 2.9 11.1 + - - +
759C SER* 1.3 79.7 - - - +
761C GLN* 1.3 58.9 + - + +
762C GLU 3.0 0.7 + - - -
763C TYR* 3.0 3.0 + - + +
764C PHE* 2.8 29.1 + - + +
880C LEU* 4.6 3.1 - - + -
884C THR* 3.5 31.2 - - + -
889C LEU* 4.6 6.3 - - + -
890C ASP 4.6 4.0 - - - +
891C TYR* 4.2 20.0 - - + -
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Residues in contact with GLN 761 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757C GLU* 3.0 30.4 + - - +
758C GLU* 3.4 12.4 - - + +
760C LEU* 1.3 75.1 - - - +
762C GLU* 1.3 63.7 + - - +
764C PHE* 3.9 2.1 - - - +
765C LYS* 3.2 32.4 + - - +
890C ASP* 2.5 34.7 + - - +
891C TYR 3.6 15.8 - - - +
892C GLU* 3.3 19.6 + - - -
893C LYS* 3.5 36.0 - - + +
894C LYS 4.9 0.6 - - - +
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Residues in contact with GLU 762 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751C ARG* 4.2 7.9 - - - +
758C GLU* 2.9 30.3 + - + +
759C SER* 3.4 10.3 - - - +
760C LEU 3.0 0.2 - - - -
761C GLN* 1.3 75.4 - - - +
763C TYR* 1.3 66.0 + - - +
765C LYS* 2.8 47.9 + - - +
766C GLU* 3.1 11.9 + - - +
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Residues in contact with TYR 763 (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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743C LYS 4.9 0.3 - - - -
744C ALA* 3.5 43.3 + - + +
747C GLU* 3.9 28.4 - - + +
748C CYS* 4.0 21.1 - - - -
751C ARG* 3.6 32.9 - - - +
759C SER 3.1 1.6 + - - -
760C LEU* 3.0 6.1 + - - +
762C GLU* 1.3 75.1 - - - +
764C PHE* 1.3 66.6 + - - +
766C GLU* 3.0 33.3 + - + -
767C PHE* 2.8 49.0 + - + +
770C GLU* 4.4 4.2 + - - -
876C PHE* 5.0 0.7 - + - -
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Residues in contact with PHE 764 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748C CYS* 5.4 1.1 - - - -
760C LEU* 2.8 19.4 + - + +
761C GLN 3.9 2.0 - - - +
762C GLU 3.2 0.2 - - - -
763C TYR* 1.3 79.2 - - - +
765C LYS* 1.3 67.9 + - + +
767C PHE* 3.5 3.1 + - - +
768C GLU* 3.1 51.8 + - + +
876C PHE* 3.5 27.4 - + - -
877C ILE* 3.5 24.7 - - + -
880C LEU* 3.5 24.0 - - + -
891C TYR* 3.5 48.9 - + + +
892C GLU* 3.6 21.3 - - + -
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Residues in contact with LYS 765 (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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761C GLN* 3.2 25.8 + - - +
762C GLU* 2.8 31.1 + - - +
764C PHE* 1.3 84.8 - - + +
766C GLU* 1.3 63.0 + - - +
768C GLU* 3.5 7.7 + - - +
769C LYS* 3.1 34.0 + - + +
893C LYS* 5.7 6.5 - - - +
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Residues in contact with GLU 766 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751C ARG* 5.2 6.0 + - - -
762C GLU 3.1 8.9 + - - +
763C TYR* 3.0 36.9 + - + +
765C LYS* 1.3 75.5 - - - +
767C PHE* 1.3 65.5 + - - +
769C LYS* 3.2 17.8 + - - +
770C GLU* 3.3 28.3 + - - +
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Residues in contact with PHE 767 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740C ALA* 4.1 10.3 - - + -
741C VAL* 4.4 6.7 - - + -
744C ALA* 3.5 25.4 - - + -
763C TYR* 2.8 35.8 + - + +
764C PHE 4.1 2.5 - - - +
766C GLU* 1.3 74.7 - - - +
768C GLU* 1.3 63.1 + - - +
770C GLU* 3.4 22.1 + - - +
771C PHE* 3.0 55.6 + + - +
774C LEU* 3.7 22.4 - - + -
872C LEU* 3.9 6.3 - - + -
876C PHE* 3.4 48.0 - + + -
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Residues in contact with GLU 768 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764C PHE* 3.1 57.2 + - + +
765C LYS* 3.7 8.7 - - - +
767C PHE* 1.3 78.8 - - - +
769C LYS* 1.3 63.5 + - + +
770C GLU 3.3 0.5 + - - -
771C PHE* 3.4 16.6 + - - +
772C ARG* 4.7 8.0 + - - -
872C LEU* 3.8 26.5 - - + +
876C PHE* 5.0 2.2 - - + -
877C ILE* 4.7 3.2 - - + +
892C GLU* 4.5 3.7 - - - +
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Residues in contact with LYS 769 (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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765C LYS* 3.1 24.2 + - + +
766C GLU* 3.2 8.2 + - - +
768C GLU* 1.3 80.0 - - + +
770C GLU* 1.3 58.0 + - + +
771C PHE 3.5 0.2 - - - -
772C ARG* 5.0 1.1 + - - +
773C GLN* 4.1 13.0 + - - +
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Residues in contact with GLU 770 (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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763C TYR* 4.4 5.2 + - - -
766C GLU* 3.3 30.3 + - - +
767C PHE* 3.5 30.7 - - + +
768C GLU 3.2 0.2 - - - -
769C LYS* 1.3 76.9 - - + +
771C PHE* 1.3 69.1 + - - +
772C ARG 3.3 2.9 - - - -
773C GLN* 3.0 26.0 + - + +
774C LEU* 3.5 22.5 + - + +
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Residues in contact with PHE 771 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741C VAL* 4.6 7.2 - - + -
767C PHE* 3.0 45.3 + + + +
768C GLU* 3.4 13.5 + - - +
770C GLU* 1.3 78.1 - - - +
772C ARG* 1.3 66.6 + - + +
773C GLN 3.2 1.2 + - - -
774C LEU* 3.2 23.1 + - + +
779C ILE* 3.7 25.0 - - + +
868C TYR* 3.7 37.5 - + + -
871C LEU* 3.7 27.8 - - + -
872C LEU* 3.7 39.7 - - + -
875C THR* 5.0 2.0 - - - -
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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
------------------------------------------------------------
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