Contacts of the helix formed by residues 758 - 772 (chain B) in PDB entry 3E0D
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 SER 758 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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457B GLU* 2.4 44.3 + - - -
752B SER* 3.9 0.2 - - - -
756B GLY 3.7 1.2 + - - -
757B TYR* 1.3 73.6 - - - +
759B LEU* 1.3 57.3 + - - +
760B GLY 3.1 8.3 + - - -
761B GLU* 2.7 48.2 + - - +
762B ALA 2.9 10.4 + - - -
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Residues in contact with LEU 759 (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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449B LEU* 5.0 14.8 - - + -
451B GLU* 4.7 30.3 - - + +
457B GLU* 4.7 0.4 + - - -
748B MET* 3.3 51.7 - - + +
749B GLN* 4.1 16.8 - - + +
752B SER* 3.4 31.3 + - - +
758B SER* 1.3 72.3 + - - +
760B GLY* 1.3 60.4 + - - +
762B ALA* 3.5 1.9 + - - +
763B ASP 3.4 5.9 + - - -
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Residues in contact with GLY 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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451B GLU* 5.0 4.5 - - - +
455B ASN* 2.0 55.4 + - - -
456B PRO* 5.1 2.5 - - - +
457B GLU* 4.5 2.5 + - - -
758B SER* 3.1 8.3 + - - -
759B LEU* 1.3 76.6 - - - +
761B GLU* 1.3 62.0 + - - +
763B ASP* 3.2 11.8 - - - +
764B LEU* 3.4 7.7 + - - +
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Residues in contact with GLU 761 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B GLU* 5.3 4.9 - - + +
757B TYR* 3.3 18.9 - - + -
758B SER* 2.7 42.0 + - - +
760B GLY* 1.3 68.5 - - - +
762B ALA* 1.3 59.7 + - - +
763B ASP 3.1 1.6 - - - -
764B LEU* 3.0 24.5 + - + +
765B LEU* 2.9 26.6 + - - +
780B HIS* 5.9 0.5 - - - -
783B ARG* 3.2 35.1 + - - -
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Residues in contact with ALA 762 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747B ILE* 5.9 0.9 - - - +
748B MET* 3.2 41.4 - - - +
751B ALA* 4.3 10.0 - - + +
752B SER* 4.4 5.4 - - - +
757B TYR* 4.5 5.5 - - + +
758B SER 2.9 10.5 + - - +
759B LEU 3.6 11.2 - - - +
761B GLU* 1.3 76.0 - - - +
763B ASP* 1.3 57.5 + - - +
765B LEU* 3.3 12.3 - - - +
766B ARG* 3.0 27.2 + - - +
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Residues in contact with ASP 763 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B GLU 4.8 2.5 - - - +
452B ARG* 3.7 21.9 - - - +
455B ASN* 3.7 14.7 + - - +
748B MET* 3.8 17.4 - - + +
759B LEU 3.4 2.8 + - - -
760B GLY 3.2 13.2 + - - +
762B ALA* 1.3 75.3 - - - +
764B LEU* 1.3 69.1 + - - +
766B ARG* 2.5 46.7 + - - +
767B ARG* 2.8 46.2 + - - +
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Residues in contact with LEU 764 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B ASN* 5.2 2.0 - - - +
458B ARG* 2.2 81.7 - - + +
760B GLY 3.8 10.3 - - - +
761B GLU* 3.0 28.4 + - + +
763B ASP* 1.3 80.3 - - - +
765B LEU* 1.3 56.6 + - - +
767B ARG* 3.2 16.1 + - + +
768B ALA* 2.9 28.5 + - - +
780B HIS* 5.0 7.6 - - + -
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Residues in contact with LEU 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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747B ILE* 6.0 3.8 - - + -
751B ALA* 3.7 30.1 - - + -
757B TYR* 3.8 21.8 - - + -
761B GLU 2.9 12.7 + - - +
762B ALA* 3.3 9.9 - - - +
764B LEU* 1.3 76.0 - - - +
766B ARG* 1.3 51.9 + - - +
768B ALA* 3.0 7.6 + - - +
769B MET* 2.8 47.3 + - + +
777B MET* 4.2 6.3 - - + -
780B HIS* 3.7 40.8 - - + +
784B PHE* 5.0 1.6 - - + -
802B PHE* 4.2 22.4 - - + -
805B LEU* 5.1 5.4 - - + -
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Residues in contact with ARG 766 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B ARG* 2.0 40.7 - - - +
744B GLN* 3.6 42.0 + - - +
747B ILE* 5.3 11.9 - - + +
748B MET* 4.0 8.1 - - + -
762B ALA 3.0 10.6 + - - +
763B ASP* 2.5 40.3 + - - +
765B LEU* 1.3 76.4 - - - +
767B ARG* 1.3 92.8 + - - +
769B MET* 3.4 9.9 + - - +
770B GLY* 3.1 18.0 + - - -
809B ALA* 5.0 18.3 - - + +
1222B DTP 5.0 4.6 + - - -
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Residues in contact with ARG 767 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B ARG* 4.5 7.9 + - - +
453B PHE 5.2 4.0 + - - -
763B ASP* 2.8 41.6 + - - +
764B LEU* 3.3 17.2 - - + +
766B ARG* 1.3 99.6 - - - +
768B ALA* 1.3 57.5 + - - +
770B GLY* 3.1 3.2 + - - -
771B LYS* 2.9 35.6 + - + +
1222B DTP 4.1 27.2 + - - -
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Residues in contact with ALA 768 (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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764B LEU 2.9 12.4 + - - +
765B LEU 3.0 8.5 + - - +
767B ARG* 1.3 75.6 - - - +
769B MET* 1.3 62.8 + - - +
771B LYS* 4.1 7.8 - - - +
772B LYS* 3.2 16.5 + - - -
773B ARG* 4.1 5.0 + - + +
776B GLU* 4.2 11.7 - - - +
777B MET* 3.7 27.4 - - + +
780B HIS* 3.9 18.2 - - + +
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Residues in contact with MET 769 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747B ILE* 5.5 4.5 - - + -
765B LEU* 2.8 41.0 + - + +
766B ARG* 3.6 10.5 - - - +
768B ALA* 1.3 76.5 - - - +
770B GLY* 1.3 57.1 + - - +
772B LYS* 3.2 29.6 - - - +
777B MET* 3.5 28.9 - - + +
802B PHE* 3.7 23.1 - - + -
805B LEU* 4.1 9.9 - - - -
806B GLU* 3.4 45.8 - - + +
809B ALA* 3.9 24.2 - - + +
810B ASN* 5.2 1.4 - - - +
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Residues in contact with GLY 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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766B ARG 3.1 14.0 + - - -
767B ARG* 3.1 5.1 + - - -
769B MET* 1.3 76.1 - - - +
771B LYS* 1.3 62.4 + - - +
772B LYS* 3.2 8.7 + - - +
809B ALA 5.6 5.1 + - - -
810B ASN* 5.8 2.7 - - - -
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Residues in contact with LYS 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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767B ARG* 2.9 21.0 + - + +
768B ALA* 4.1 7.9 - - - +
769B MET 3.5 0.2 - - - -
770B GLY* 1.3 77.3 - - - +
772B LYS* 1.3 67.9 + - - +
773B ARG* 3.4 19.8 + - + +
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Residues in contact with LYS 772 (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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779A LYS* 4.2 6.6 + - - -
768B ALA 3.2 11.6 + - - -
769B MET 3.2 17.0 - - - +
770B GLY 4.2 6.1 - - - +
771B LYS* 1.3 78.9 - - - +
773B ARG* 1.3 66.3 + - - +
774B VAL* 3.1 5.9 + - - +
777B MET* 4.8 8.3 - - + -
806B GLU 5.6 1.3 - - - -
810B ASN* 2.9 44.3 + - - +
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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
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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