Contacts of the helix formed by residues 757 - 768 (chain B) in PDB entry 5VOT
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 757 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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753B LEU 2.6 13.3 + - - -
754B ASN* 3.2 10.2 + - - -
755B GLU 3.1 4.7 - - - -
756B GLN* 1.3 71.8 - - - +
758B LEU* 1.3 57.1 + - - -
759B LEU* 3.0 3.8 - - - -
760B ASP* 2.9 42.0 + - - +
761B LYS* 3.6 3.1 + - - +
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Residues in contact with LEU 758 (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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431B GLU* 4.1 27.4 - - - +
753B LEU* 3.8 12.4 + - + +
756B GLN* 2.9 15.8 + - + +
757B GLY* 1.3 77.9 - - - +
759B LEU* 1.3 63.7 + - + +
761B LYS* 3.1 26.9 + - + +
762B LEU* 2.9 41.5 + - + +
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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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424B TYR* 3.3 25.8 + - + +
428B LEU* 4.5 18.6 - - + -
431B GLU* 5.8 2.0 - - + -
495B PHE* 5.0 23.1 - - + +
750B VAL* 4.6 5.8 - - + +
753B LEU* 4.0 40.8 - - + +
754B ASN* 4.0 21.1 - - + +
757B GLY* 4.8 1.8 - - - -
758B LEU* 1.3 79.2 - - + +
760B ASP* 1.3 60.5 + - - +
762B LEU* 3.3 17.1 + - + +
763B LYS* 2.9 25.5 + - - +
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Residues in contact with ASP 760 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754B ASN* 5.3 4.1 - - - +
757B GLY* 2.9 25.3 + - - +
759B LEU* 1.3 80.8 - - - +
761B LYS* 1.3 57.2 + - - +
763B LYS* 2.9 27.4 + - - +
764B ASN* 2.9 19.4 + - - +
727C LEU 4.8 2.9 - - - +
728C ASP* 4.4 20.2 - - - +
729C SER* 5.1 9.2 + - - -
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Residues in contact with LYS 761 (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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665A ALA* 3.9 26.8 - - - +
757B GLY 3.6 2.3 + - - +
758B LEU* 3.1 28.8 + - + +
760B ASP* 1.3 77.7 - - - +
762B LEU* 1.3 59.2 + - + +
764B ASN* 3.0 19.7 + - + +
765B LYS* 2.9 25.3 + - - +
769B ASP* 4.7 3.8 + - - +
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Residues in contact with LEU 762 (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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424B TYR* 3.4 21.4 - - + -
427B ASP* 4.3 35.0 - - + +
428B LEU 5.4 1.1 - - - +
431B GLU* 5.0 12.3 - - + +
758B LEU* 2.9 35.8 + - + +
759B LEU* 3.5 23.8 - - + +
761B LYS* 1.3 76.8 - - + +
763B LYS* 1.3 65.2 + - - +
765B LYS* 3.0 16.8 + - + +
766B TRP* 2.9 27.4 + - + +
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Residues in contact with LYS 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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424B TYR* 3.6 2.6 - - + +
496B MET* 4.7 19.5 - - + +
707B THR* 6.5 0.9 - - - -
710B GLU* 4.4 15.1 + - - -
759B LEU 2.9 13.9 + - - +
760B ASP* 2.9 17.9 + - - +
762B LEU* 1.3 75.4 - - - +
764B ASN* 1.3 56.9 + - - +
767B TRP* 2.9 69.4 + - + +
768B TYR* 4.2 25.6 + - + -
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Residues in contact with ASN 764 (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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760B ASP* 2.9 22.5 + - - +
761B LYS* 3.0 19.5 + - + +
763B LYS* 1.3 76.6 - - - +
765B LYS* 1.3 54.8 + - - +
768B TYR* 2.9 32.8 + - + +
769B ASP* 2.5 50.5 + - - +
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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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427B ASP* 3.8 17.7 + - - +
761B LYS 2.9 11.4 + - - +
762B LEU* 3.0 19.4 + - + +
764B ASN* 1.3 80.3 - - - +
766B TRP* 1.3 94.5 + - + +
767B TRP 3.4 0.3 + - - -
769B ASP* 3.6 13.4 + - + +
770B LYS* 3.9 47.6 + - - +
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Residues in contact with TRP 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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404B PRO* 3.3 26.9 - - + +
407B MET* 3.7 22.7 - - + -
422B GLU* 4.2 15.5 - - + -
423B GLY* 3.3 40.6 - - - -
424B TYR* 3.5 32.4 - + + +
427B ASP* 2.9 25.8 + - - -
711B TYR* 3.1 26.9 - - - -
762B LEU* 2.9 24.7 + - + +
765B LYS* 1.3 101.4 - - + +
767B TRP* 1.3 65.2 + - + +
770B LYS* 4.8 20.4 - - + -
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Residues in contact with TRP 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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404B PRO* 4.1 13.6 - - + +
405B TYR* 3.8 28.0 - + - -
424B TYR* 3.5 42.6 - + - -
496B MET* 3.7 24.5 - - + -
707B THR* 3.7 24.5 + - + -
710B GLU* 3.5 34.6 + - + -
711B TYR* 4.4 18.2 - + + +
714B GLN* 4.4 21.7 - - - +
763B LYS* 2.9 52.1 + - + +
765B LYS 4.6 0.2 - - - -
766B TRP* 1.3 86.6 - - + +
768B TYR* 1.3 75.4 + - + +
770B LYS* 4.9 2.3 - - - -
771B GLY* 4.6 4.2 + - - -
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Residues in contact with TYR 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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710B GLU* 4.7 13.0 + - - -
714B GLN* 6.1 5.2 - - + -
763B LYS* 3.8 27.9 + - + -
764B ASN* 2.9 45.4 + - + +
767B TRP* 1.3 84.7 - - + +
769B ASP* 1.3 68.4 + - - +
770B LYS 3.0 3.6 + - - -
771B GLY* 3.1 13.3 + - - -
774B GLY 5.0 2.8 - - - +
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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