Contacts of the helix formed by residues 838 - 846 (chain B) in PDB entry 2VKZ
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 MET 838 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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776B GLU* 2.9 17.6 + - - +
784B ILE* 3.8 29.4 - - + -
788B SER* 3.9 24.2 - - - +
789B GLU* 4.6 6.1 - - + -
792B HIS* 3.9 31.1 - - + +
837B GLY* 1.3 73.5 - - - +
839B TYR* 1.3 64.1 + - - +
841B GLU* 3.2 30.3 + - + +
842B SER* 2.9 24.9 + - - -
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Residues in contact with TYR 839 (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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773B ALA* 6.1 1.8 - - + -
774B ILE 5.6 1.8 - - - -
776B GLU* 3.2 13.5 + - + +
795B MET* 4.2 17.9 - - - -
826B MET 5.5 0.3 + - - -
827B SER* 4.0 22.4 + - - -
829B ASN 5.4 2.7 - - - -
836B ASP* 3.5 29.7 + - + +
837B GLY 3.5 0.8 - - - -
838B MET* 1.3 75.6 - - - +
840B SER* 1.3 76.2 + - - +
842B SER* 3.1 7.3 + - - -
843B LYS* 2.9 63.1 + - + +
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Residues in contact with SER 840 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827B SER* 6.2 0.7 - - - -
829B ASN 3.8 3.8 + - - -
830B HIS* 3.9 12.0 + - - +
831B GLY* 2.8 30.0 + - - -
836B ASP* 2.7 31.7 + - - +
838B MET 3.5 0.2 - - - -
839B TYR* 1.3 83.7 - - - +
841B GLU* 1.3 65.9 + - - +
843B LYS* 3.8 3.4 - - - +
844B LEU* 3.0 33.4 + - - +
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Residues in contact with GLU 841 (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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784B ILE* 5.2 5.7 - - - +
792B HIS* 3.9 9.2 - - - +
836B ASP* 5.4 0.3 - - - +
837B GLY 3.7 5.9 - - - +
838B MET* 3.2 47.3 - - + +
840B SER* 1.3 85.2 + - - +
842B SER* 1.3 62.7 + - - +
844B LEU* 4.0 4.8 - - - +
845B SER* 3.0 27.6 + - - +
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Residues in contact with SER 842 (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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792B HIS* 2.8 31.8 - - - -
795B MET* 3.4 46.6 - - - +
796B LEU* 4.2 4.3 - - - +
838B MET 2.9 11.7 + - - -
839B TYR 3.1 5.5 + - - -
841B GLU* 1.3 76.7 - - - +
843B LYS* 1.3 63.9 + - - +
844B LEU 3.3 0.9 + - - -
845B SER* 3.4 9.9 + - - -
846B LEU* 3.5 18.4 + - - +
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Residues in contact with LYS 843 (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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771B PHE* 5.8 2.4 + - - +
772B ALA 6.0 0.2 + - - -
773B ALA* 5.9 4.5 - - - +
795B MET* 5.4 11.3 + - - +
825B PRO* 3.0 51.8 + - - +
826B MET* 4.4 10.5 - - - +
827B SER* 3.9 17.8 + - - +
830B HIS* 4.1 4.0 - - + -
839B TYR* 2.9 61.5 + - + +
840B SER* 4.0 3.8 - - - +
842B SER* 1.3 80.8 - - - +
844B LEU* 1.3 60.6 + - - +
846B LEU* 3.8 21.6 - - + +
847B GLU* 3.9 11.8 - - - +
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Residues in contact with LEU 844 (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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830B HIS* 3.6 40.4 - - + +
840B SER 3.0 18.0 + - - +
841B GLU* 4.0 4.5 - - - +
843B LYS* 1.3 73.9 - - - +
845B SER* 1.3 67.5 + - - +
846B LEU 3.2 2.0 - - - -
847B GLU* 3.2 29.7 + - + +
848B THR* 4.5 2.4 + - - +
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Residues in contact with SER 845 (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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792B HIS* 4.3 2.3 + - - -
796B LEU* 3.4 39.2 - - - +
841B GLU* 3.0 18.1 + - - +
842B SER 3.6 1.6 - - - -
844B LEU* 1.3 77.7 - - - +
846B LEU* 1.3 62.6 - - - +
847B GLU 2.8 1.8 + - - -
848B THR* 3.0 30.2 + - - +
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Residues in contact with LEU 846 (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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795B MET 4.2 16.2 - - - +
796B LEU* 3.8 21.1 - - + -
799B ILE* 4.5 16.6 - - + -
800B LEU* 5.4 2.0 - - + -
824B LEU* 3.6 31.4 - - + +
825B PRO* 3.7 31.9 - - + +
826B MET* 4.5 9.6 - - + +
842B SER 3.5 14.1 - - - +
843B LYS* 3.8 19.1 - - + +
844B LEU 3.2 0.2 - - - -
845B SER* 1.3 76.6 - - - +
847B GLU* 1.3 57.1 + - - +
848B THR 3.0 6.1 + - - -
849B LEU* 3.1 32.2 + - + +
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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