Contacts of the helix formed by residues 757 - 767 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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658B PHE* 6.6 0.2 - - - -
753C LEU 2.7 12.1 + - - -
754C ASN* 3.3 12.4 + - - -
755C GLU 3.3 1.2 + - - -
756C GLN* 1.3 71.5 - - - +
758C LEU* 1.3 58.7 + - - -
759C LEU* 3.0 8.7 + - - -
760C ASP* 3.6 12.6 + - - +
761C LYS* 3.7 9.0 + - - +
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Residues in contact with LEU 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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431C GLU* 4.6 18.2 - - + +
753C LEU* 3.6 30.6 + - + -
756C GLN* 2.8 14.4 + - + +
757C GLY* 1.3 73.9 - - - +
759C LEU* 1.3 63.4 + - - +
761C LYS* 3.2 32.0 + - + +
762C LEU* 2.9 48.3 + - + +
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Residues in contact with LEU 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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424C TYR* 4.0 19.7 + - - +
428C LEU* 4.6 13.7 - - + -
495C PHE* 4.7 27.8 - - + +
750C VAL* 4.6 7.4 - - + +
753C LEU* 3.8 34.3 - - + +
754C ASN* 3.5 37.0 - - + +
757C GLY* 3.0 2.1 - - - -
758C LEU* 1.3 76.4 - - - +
760C ASP* 1.3 64.8 + - - +
762C LEU* 3.0 15.2 + - + +
763C LYS* 2.9 24.4 + - - +
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Residues in contact with ASP 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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727B LEU 5.2 0.7 - - - +
728B ASP* 4.5 14.2 - - - +
729B SER* 4.1 19.6 + - - -
496C MET* 5.7 0.3 - - - +
757C GLY* 3.6 6.8 + - - +
759C LEU* 1.3 83.2 - - - +
761C LYS* 1.3 57.5 + - - +
763C LYS* 3.1 27.3 + - + +
764C ASN* 2.9 36.8 + - - +
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Residues in contact with LYS 761 (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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757C GLY 3.7 5.9 + - - +
758C LEU* 3.2 34.9 + - + +
759C LEU 3.1 0.2 - - - -
760C ASP* 1.3 77.9 - - - +
762C LEU* 1.3 58.5 + - + +
764C ASN* 2.9 17.3 + - + +
765C LYS* 2.9 24.5 + - + +
769C ASP* 4.8 0.7 - - - +
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Residues in contact with LEU 762 (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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424C TYR* 3.6 22.4 - - + -
427C ASP* 4.7 25.8 - - + +
428C LEU* 5.0 11.9 - - + +
431C GLU* 5.4 4.9 - - + -
753C LEU* 6.0 1.8 - - + -
758C LEU* 2.9 47.9 + - + +
759C LEU* 3.4 13.0 - - + +
761C LYS* 1.3 78.5 - - + +
763C LYS* 1.3 59.0 + - - +
765C LYS* 2.8 41.9 + - + +
766C TRP* 2.9 19.6 + - + +
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Residues in contact with LYS 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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424C TYR* 3.8 2.1 - - + +
496C MET* 3.6 38.1 - - + +
497C SER 5.5 1.8 + - - -
710C GLU* 4.4 16.2 + - - -
759C LEU 2.9 8.0 + - - +
760C ASP* 3.1 37.0 + - + +
762C LEU* 1.3 77.4 - - - +
764C ASN* 1.3 56.1 + - - +
767C TRP* 2.9 64.9 + - + +
768C TYR* 4.6 17.5 - - + -
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Residues in contact with ASN 764 (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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760C ASP* 2.9 26.1 + - - +
761C LYS* 2.9 12.8 + - + +
763C LYS* 1.3 75.3 - - - +
765C LYS* 1.3 59.7 + - - +
768C TYR* 2.9 36.7 + - + -
769C ASP* 2.6 45.4 + - - +
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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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427C ASP* 4.0 16.3 + - - -
761C LYS* 2.9 12.0 + - + +
762C LEU* 2.8 28.6 + - + +
764C ASN* 1.3 80.4 - - - +
766C TRP* 1.3 82.5 + - + +
769C ASP* 3.2 22.9 + - + +
770C LYS* 5.0 12.8 + - - +
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Residues in contact with TRP 766 (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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404C PRO* 3.4 33.2 - - + +
407C MET* 3.6 32.3 - - + -
422C GLU* 4.3 12.3 - - + -
423C GLY* 3.2 33.9 - - - -
424C TYR* 3.4 31.4 - + + +
427C ASP* 2.9 27.7 + - - +
711C TYR* 3.6 8.8 - - - -
762C LEU* 2.9 26.5 + - + +
765C LYS* 1.3 99.9 - - + +
767C TRP* 1.3 67.9 + - + +
770C LYS* 5.8 9.2 - - + -
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Residues in contact with TRP 767 (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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404C PRO* 4.1 14.6 - - + +
405C TYR* 4.1 33.4 - + - -
424C TYR* 3.7 33.2 - + + -
496C MET* 3.8 21.1 - - + -
707C THR* 3.9 13.3 + - - -
710C GLU* 4.0 21.8 + - + -
711C TYR* 3.8 40.3 - + + +
714C GLN* 4.7 18.1 - - + +
763C LYS* 2.9 55.1 + - + +
766C TRP* 1.3 87.6 - - + +
768C TYR* 1.3 76.7 + + + +
769C ASP 3.8 0.9 - - - -
770C LYS* 4.5 6.4 + - - +
771C GLY* 4.7 4.2 + - - -
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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