Contacts of the helix formed by residues 742 - 756 (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 LEU 742 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395C VAL* 4.8 23.8 - - + -
436C CYS* 5.3 11.7 - - + +
438C PHE* 4.9 17.3 - - + -
474C ILE* 5.5 8.1 - - + -
740C SER* 3.4 5.8 + - - +
741C SER* 1.3 89.5 - - - +
743C GLY* 1.3 66.0 + - - +
744C ASN 3.0 4.0 + - - -
745C ALA* 3.0 11.8 + - + +
746C VAL* 2.8 38.5 + - + +
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Residues in contact with GLY 743 (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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492C SER* 5.0 4.1 - - - -
736C THR* 4.1 27.7 - - - +
740C SER* 4.1 11.1 + - - -
741C SER 3.5 2.4 - - - -
742C LEU* 1.3 75.4 - - - +
744C ASN* 1.3 55.3 + - - +
746C VAL* 3.7 4.4 - - - +
747C ASN* 2.9 31.0 + - - +
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Residues in contact with ASN 744 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740C SER 5.4 0.6 + - - -
741C SER 4.7 4.6 + - - +
742C LEU 3.0 1.4 + - - -
743C GLY* 1.3 74.9 - - - +
745C ALA* 1.3 65.7 + - - +
747C ASN* 3.0 10.1 + - - +
748C LEU* 2.9 38.9 + - - +
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Residues in contact with ALA 745 (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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436C CYS* 4.8 11.5 - - - -
741C SER 5.3 1.7 + - - +
742C LEU* 3.0 13.9 + - + +
744C ASN* 1.3 78.9 - - - +
746C VAL* 1.3 62.5 + - - +
748C LEU* 3.1 20.9 + - + +
749C ALA* 2.9 21.5 + - - +
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Residues in contact with VAL 746 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C ILE* 3.9 23.6 - - + -
436C CYS* 4.0 20.9 - - - -
438C PHE* 6.2 0.7 - - + -
474C ILE* 4.3 13.5 - - + -
492C SER* 5.5 1.8 - - - -
734C ILE* 4.4 24.5 - - + -
742C LEU* 2.8 40.3 + - + +
743C GLY* 3.7 6.7 - - - +
745C ALA* 1.3 76.6 - - - +
747C ASN* 1.3 65.3 + - - +
749C ALA* 2.9 15.8 + - - +
750C VAL* 2.9 21.5 + - + +
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Residues in contact with ASN 747 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B GLU* 5.7 1.2 + - - -
491C PHE 5.2 0.6 + - - -
492C SER* 3.9 12.9 - - - +
493C LYS* 3.1 67.6 + - - +
743C GLY 2.9 18.9 + - - +
744C ASN* 3.3 8.3 - - - +
746C VAL* 1.3 74.9 - - - +
748C LEU* 1.3 64.0 + - + +
750C VAL* 3.1 11.3 + - - +
751C LEU* 2.9 29.7 + - - +
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Residues in contact with LEU 748 (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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483B LEU* 3.9 21.2 - - + +
486B GLU* 4.9 13.7 - - + +
487B GLU* 5.9 4.5 - - + -
744C ASN* 2.9 31.5 + - - +
745C ALA* 3.1 25.1 + - + +
747C ASN* 1.3 77.0 - - + +
749C ALA* 1.3 56.5 + - - +
751C LEU* 3.1 16.6 + - + +
752C LYS* 2.9 27.2 + - - +
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Residues in contact with ALA 749 (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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432C ILE* 4.1 18.2 - - + -
435C HIS* 4.0 29.3 - - + -
436C CYS* 5.1 4.3 - - - -
745C ALA 2.9 10.4 + - - +
746C VAL* 2.9 11.7 + - - +
748C LEU* 1.3 72.1 - - - +
750C VAL* 1.3 67.5 + - - +
752C LYS* 2.9 21.7 + - - +
753C LEU* 2.9 17.7 + - - +
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Residues in contact with VAL 750 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C LEU* 5.9 5.4 - - + -
432C ILE* 4.4 15.7 - - + +
492C SER* 4.7 4.5 - - - +
493C LYS* 4.1 19.3 - - + +
494C PRO 5.5 0.7 - - - +
495C PHE* 4.4 21.1 - - + -
734C ILE* 4.5 20.2 - - + -
746C VAL* 2.9 20.0 + - + +
747C ASN* 3.3 16.6 - - - +
749C ALA* 1.3 76.0 - - - +
751C LEU* 1.3 63.1 + - + +
753C LEU* 3.4 6.5 + - - +
754C ASN* 2.9 29.7 + - + +
759C LEU* 4.6 7.7 - - + +
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Residues in contact with LEU 751 (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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481B ILE* 5.5 10.3 - - + +
482B THR* 5.7 3.4 - - - -
483B LEU* 3.9 20.6 - - + +
486B GLU* 3.5 39.3 - - + +
493C LYS* 4.7 15.5 - - + -
747C ASN* 2.9 32.8 + - - +
748C LEU* 3.4 17.3 - - + +
750C VAL* 1.3 77.3 - - + +
752C LYS* 1.3 57.6 + - - +
754C ASN* 3.3 16.8 + - - +
755C GLU* 2.9 32.9 + - - +
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Residues in contact with LYS 752 (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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483B LEU* 4.6 19.2 - - + +
435C HIS* 3.5 38.5 + - + +
748C LEU 2.9 11.9 + - - +
749C ALA* 2.9 15.2 + - - +
751C LEU* 1.3 74.8 - - - +
753C LEU* 1.3 51.2 + - - +
755C GLU* 2.9 8.6 + - - +
756C GLN* 2.6 65.6 + - + +
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Residues in contact with LEU 753 (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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428C LEU* 4.3 19.5 - - + -
431C GLU* 3.9 30.5 - - + +
432C ILE* 4.9 6.5 - - + -
435C HIS* 4.4 18.6 - - + +
749C ALA 2.9 15.8 + - - +
750C VAL* 4.0 2.9 - - - +
752C LYS* 1.3 76.4 - - - +
754C ASN* 1.3 53.1 + - - +
756C GLN* 3.2 25.4 - - - +
757C GLY* 2.7 30.5 + - - -
758C LEU* 3.6 34.2 + - + -
759C LEU* 3.8 21.2 - - + +
762C LEU* 6.0 2.2 - - + -
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Residues in contact with ASN 754 (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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658B PHE* 5.5 4.7 - - - -
728B ASP* 5.7 2.9 - - - +
729B SER* 3.6 23.7 + - - +
730B LYS* 5.4 4.8 - - - +
495C PHE* 6.2 2.6 - - - +
750C VAL* 2.9 20.9 + - + +
751C LEU* 3.4 20.0 - - - +
752C LYS 3.1 0.2 - - - -
753C LEU* 1.3 76.3 - - - +
755C GLU* 1.3 61.8 + - + +
757C GLY* 3.3 12.5 + - - -
759C LEU* 3.5 21.5 - - + +
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Residues in contact with GLU 755 (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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482B THR* 3.2 17.3 - - + -
483B LEU* 2.5 56.4 + - - +
484B VAL* 4.4 2.4 + - - +
658B PHE* 5.2 15.3 - - + -
661B ARG* 5.1 7.8 - - + +
662B SER* 5.9 1.7 - - - -
751C LEU 2.9 13.5 + - - +
752C LYS* 3.3 7.2 - - - +
754C ASN* 1.3 78.4 - - + +
756C GLN* 1.3 60.9 + - + +
757C GLY 3.3 0.4 + - - -
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Residues in contact with GLN 756 (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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663B LYS* 5.9 2.9 - - - +
435C HIS* 4.8 5.8 + - - -
752C LYS* 2.6 52.6 + - + +
753C LEU* 2.9 29.6 + - + +
755C GLU* 1.3 75.7 - - + +
757C GLY* 1.3 50.5 + - - +
758C LEU* 2.8 20.2 + - + +
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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