Contacts of the helix formed by residues 774 - 784 (chain A) in PDB entry 6WCW
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 774 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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739A CYS* 3.2 17.1 - - - -
746A PHE* 3.4 46.7 - - - -
751A HIS* 3.5 14.6 - - - -
773A VAL* 1.3 75.8 - - - +
775A ASN* 1.3 60.8 + - - +
776A PHE* 3.5 2.4 + - - +
777A SER* 3.0 25.6 + - - -
778A LYS* 2.9 25.5 + - - +
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Residues in contact with ASN 775 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749A CYS 4.3 4.2 + - - -
750A CYS* 3.0 26.1 + - - +
751A HIS* 4.2 1.2 - - - +
752A GLU* 3.4 39.2 + - - +
754A ALA* 4.5 12.5 - - - +
773A VAL 3.7 0.6 + - - -
774A SER* 1.3 70.8 - - - +
776A PHE* 1.3 61.9 + - - +
778A LYS* 3.3 7.5 + - - +
779A ASP* 3.0 34.3 + - - +
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Residues in contact with PHE 776 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723A GLY* 5.8 3.6 - - - -
742A LEU* 3.8 32.1 - - + -
746A PHE* 4.7 10.1 - + + -
750A CYS 4.4 1.2 + - - -
774A SER* 3.3 8.4 + - - +
775A ASN* 1.3 77.7 - - - +
777A SER* 1.3 69.1 + - - +
779A ASP* 3.6 7.4 + - - +
780A LEU* 3.0 53.8 + - + +
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Residues in contact with SER 777 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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739A CYS* 3.0 29.3 - - - -
741A TYR* 3.3 32.5 - - - -
742A LEU* 3.7 7.1 - - - +
773A VAL* 4.1 4.7 - - - -
774A SER* 3.0 13.9 + - - -
776A PHE* 1.3 81.4 - - - +
778A LYS* 1.3 67.4 + - - +
780A LEU* 4.3 3.1 - - - +
781A LEU* 2.9 30.3 + - - +
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Residues in contact with LYS 778 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754A ALA* 3.5 26.2 - - + +
755A GLN 4.0 15.5 + - - +
756A MET* 4.1 19.8 - - - +
773A VAL* 3.7 19.9 - - + +
774A SER 2.9 8.8 + - - +
775A ASN* 3.3 10.3 + - - +
777A SER* 1.3 75.2 - - - +
779A ASP* 1.3 66.9 + - - +
781A LEU* 3.5 1.2 + - - +
782A ILE* 3.0 50.9 + - + +
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Residues in contact with ASP 779 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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775A ASN* 3.0 23.1 + - - +
776A PHE* 3.6 8.0 - - + +
778A LYS* 1.3 81.5 - - - +
780A LEU* 1.3 61.4 + - - +
782A ILE* 3.4 9.1 + - - +
783A LYS* 3.1 21.5 + - - +
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Residues in contact with LEU 780 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741A TYR* 3.8 27.8 - - + +
776A PHE* 3.0 44.7 + - + +
777A SER* 4.1 2.9 - - - +
779A ASP* 1.3 73.0 - - - +
781A LEU* 1.3 75.1 + - + +
783A LYS* 3.0 35.3 + - - +
784A ILE* 3.1 31.3 + - + +
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Residues in contact with LEU 781 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741A TYR* 3.4 61.0 - - + +
756A MET* 3.9 33.2 - - + -
757A ALA 3.9 12.8 - - - +
759A PRO* 4.5 7.9 - - + -
773A VAL* 4.9 1.1 - - + -
777A SER* 2.9 24.6 + - - +
778A LYS 4.0 2.2 - - - +
780A LEU* 1.3 83.6 - - + +
782A ILE* 1.3 61.4 + - - +
783A LYS 3.4 0.3 + - - -
784A ILE* 3.4 13.3 + - + +
785A TRP* 3.4 22.1 + - + +
852A LEU* 4.2 13.9 - - + +
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Residues in contact with ILE 782 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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756A MET* 3.7 20.2 - - + -
778A LYS* 3.0 49.4 + - + +
779A ASP* 3.7 9.2 - - - +
780A LEU 3.2 0.2 - - - -
781A LEU* 1.3 76.0 - - - +
783A LYS* 1.3 65.0 + - - +
785A TRP* 3.4 19.4 + - + +
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Residues in contact with LYS 783 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779A ASP 3.1 13.1 + - - +
780A LEU* 3.0 30.7 + - - +
782A ILE* 1.3 80.9 - - - +
784A ILE* 1.3 65.4 + - + +
785A TRP* 3.2 4.9 + - - +
786A ASN 4.7 1.2 + - - -
787A ASP* 4.3 6.2 - - - +
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Residues in contact with ILE 784 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741A TYR* 5.2 3.8 - - - +
759A PRO* 5.7 0.7 - - + -
780A LEU* 3.1 30.7 + - + +
781A LEU* 3.6 17.7 - - + +
783A LYS* 1.3 84.9 - - + +
785A TRP* 1.3 65.6 + - - +
786A ASN 3.3 2.7 - - - -
787A ASP* 3.2 35.2 + - - +
789A LEU* 4.0 22.4 - - + -
790A PHE* 4.1 26.8 - - + -
852A LEU* 4.1 12.5 + - + +
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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