Contacts of the helix formed by residues 756 - 771 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696B LYS* 3.3 24.0 + - - -
698B ILE* 5.8 0.9 - - - -
751B ARG 2.7 18.5 + - - +
752B MET* 3.7 10.9 + - - -
754B GLN 3.8 0.2 - - - -
755B GLU* 1.3 76.0 - - - +
757B GLU* 1.3 65.7 + - - -
758B GLU 3.5 1.8 - - - -
759B SER* 3.1 5.6 + - - -
760B LEU* 3.1 19.2 + - - +
889B LEU* 5.5 1.1 - - - -
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Residues in contact with GLU 757 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696B LYS* 4.5 3.6 + - - +
756B GLY* 1.3 69.8 - - - -
758B GLU* 1.3 65.3 + - - +
760B LEU* 2.9 19.5 + - - +
761B GLN* 2.9 34.0 + - - +
889B LEU* 3.2 30.5 - - + +
890B ASP* 2.7 35.6 + - - +
640D LYS* 3.7 21.7 + - - +
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Residues in contact with GLU 758 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696B LYS* 5.1 16.8 + - + +
756B GLY 3.5 0.6 - - - -
757B GLU* 1.3 78.1 - - - +
759B SER* 1.3 62.6 + - - +
761B GLN* 3.3 16.2 + - + +
762B GLU* 2.9 23.0 + - + +
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Residues in contact with SER 759 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751B ARG* 2.8 30.9 + - - +
755B GLU* 2.6 49.1 + - - +
756B GLY 3.1 10.4 + - - -
757B GLU 3.1 0.2 - - - -
758B GLU* 1.3 79.6 - - - +
760B LEU* 1.3 64.6 + - - +
762B GLU* 3.2 11.1 + - - +
763B TYR 3.1 18.5 + - - -
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Residues in contact with LEU 760 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748B CYS* 3.6 45.1 - - + +
751B ARG* 4.2 9.8 - - + +
752B MET* 3.7 23.6 - - + -
756B GLY 3.1 7.4 + - - +
757B GLU* 2.9 10.9 + - - +
759B SER* 1.3 78.8 - - - +
761B GLN* 1.3 54.6 + - - +
762B GLU 3.1 0.7 + - - -
763B TYR* 3.2 3.0 + - + +
764B PHE* 2.8 35.4 + - + +
880B LEU* 4.3 8.1 - - + -
884B THR* 4.0 17.0 - - + -
889B LEU* 4.5 9.9 - - + -
890B ASP 4.1 7.6 - - - +
891B TYR* 4.0 25.4 - - + -
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Residues in contact with GLN 761 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757B GLU* 2.9 27.7 + - - +
758B GLU* 3.4 19.0 - - + +
760B LEU* 1.3 76.7 - - - +
762B GLU* 1.3 65.7 + - - +
764B PHE* 3.4 3.3 + - - +
765B LYS* 3.3 19.1 + - - +
890B ASP* 3.3 23.1 + - - +
891B TYR 3.3 26.3 - - - +
892B GLU 3.7 5.9 + - - +
893B LYS* 3.1 42.3 - - + +
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Residues in contact with GLU 762 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751B ARG* 3.1 36.2 + - - -
758B GLU* 2.9 15.3 + - + +
759B SER* 3.2 10.0 + - - +
760B LEU 3.1 0.2 - - - -
761B GLN* 1.3 74.3 - - - +
763B TYR* 1.3 58.5 + - - +
765B LYS* 2.8 25.7 + - - +
766B GLU* 3.1 18.7 + - + +
45C GLN* 5.5 5.2 + - - -
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Residues in contact with TYR 763 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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743B LYS* 4.8 0.3 - - - +
744B ALA* 3.4 35.1 + - + +
747B GLU* 3.4 32.5 - - + +
748B CYS* 3.7 22.0 - - - -
751B ARG* 3.1 44.4 - - - +
759B SER 3.1 2.0 + - - -
760B LEU* 3.8 3.4 - - - +
762B GLU* 1.3 84.0 - - - +
764B PHE* 1.3 63.2 + - - +
766B GLU* 4.0 24.7 - - - +
767B PHE* 2.9 40.9 + - + +
770B GLU* 5.8 1.5 + - - -
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Residues in contact with PHE 764 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748B CYS* 5.3 1.3 - - - -
760B LEU* 2.8 21.9 + - + +
761B GLN 3.7 4.9 - - - +
763B TYR* 1.3 76.6 - - - +
765B LYS* 1.3 66.6 + - + +
767B PHE* 4.2 3.4 - - - +
768B GLU* 3.1 62.3 + - - +
876B PHE* 3.7 20.8 - + - -
877B ILE* 3.6 26.0 - - + -
880B LEU* 3.5 24.0 - - + -
891B TYR* 3.6 42.4 - + + +
892B GLU* 3.7 23.6 - - - -
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Residues in contact with LYS 765 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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761B GLN 3.3 7.9 + - - +
762B GLU* 2.8 12.9 + - - +
764B PHE* 1.3 84.2 - - + +
766B GLU* 1.3 66.3 + - - +
768B GLU* 3.4 5.8 + - - +
769B LYS* 3.0 22.1 + - - +
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Residues in contact with GLU 766 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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751B ARG* 5.2 1.2 + - - -
762B GLU* 3.1 20.2 + - + +
763B TYR* 3.3 26.5 + - - +
765B LYS* 1.3 77.2 - - - +
767B PHE* 1.3 65.8 + - - +
769B LYS* 2.8 19.7 + - + +
770B GLU* 2.7 41.2 + - - +
42C PRO* 2.9 41.4 - - + +
44C SER* 5.9 2.0 - - - -
45C GLN* 5.7 2.6 + - + -
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Residues in contact with PHE 767 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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740B ALA* 4.3 9.6 - - + -
741B VAL* 4.5 7.2 - - + -
744B ALA* 3.6 25.4 - - + -
763B TYR* 2.9 41.1 + - + +
764B PHE 4.2 2.2 - - - +
766B GLU* 1.3 73.7 - - - +
768B GLU* 1.3 57.6 + - - +
770B GLU* 3.2 17.5 + - + +
771B PHE* 2.9 56.6 + + - +
774B LEU* 3.6 23.3 - - + -
872B LEU* 4.0 3.1 - - + -
876B PHE* 3.4 46.7 - + + -
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Residues in contact with GLU 768 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764B PHE* 3.1 54.9 + - + +
765B LYS* 3.6 6.6 - - - +
767B PHE* 1.3 79.7 - - - +
769B LYS* 1.3 61.2 + - - +
770B GLU 3.4 0.5 + - - -
771B PHE* 3.5 17.3 + - - +
772B ARG* 4.1 21.7 + - - +
872B LEU* 3.8 26.3 - - + +
876B PHE* 5.7 0.2 - - + -
877B ILE* 3.8 5.9 - - - +
892B GLU* 5.1 1.4 - - - +
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Residues in contact with LYS 769 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765B LYS 3.0 13.2 + - - +
766B GLU* 2.8 17.2 + - + +
768B GLU* 1.3 77.6 - - - +
770B GLU* 1.3 57.1 + - + +
771B PHE 3.5 0.2 - - - -
772B ARG* 5.0 3.9 - - - +
773B GLN* 3.5 16.1 + - - -
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Residues in contact with GLU 770 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763B TYR* 5.8 1.4 + - - -
766B GLU* 2.7 48.3 + - - +
767B PHE* 3.2 21.0 + - + +
769B LYS* 1.3 77.8 - - + +
771B PHE* 1.3 66.7 + - - +
772B ARG 3.3 2.9 - - - -
773B GLN* 3.0 28.2 + - + +
774B LEU* 3.5 20.9 + - + +
42C PRO* 4.4 4.0 - - - +
44C SER* 4.0 21.4 + - - +
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Residues in contact with PHE 771 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741B VAL* 4.6 8.1 - - + -
767B PHE* 2.9 41.7 + + + +
768B GLU* 3.5 15.3 + - - +
770B GLU* 1.3 77.0 - - - +
772B ARG* 1.3 72.4 + - - +
774B LEU* 3.1 29.9 + - + +
779B ILE* 3.5 22.6 - - + +
868B TYR* 3.4 44.4 - + - -
871B LEU* 3.9 20.0 - - + -
872B LEU* 3.8 40.6 - - + -
875B THR* 5.0 0.2 - - - -
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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