Contacts of the helix formed by residues 828 - 837 (chain I) 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 PRO 828 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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827I VAL* 1.3 101.8 - - + +
829I ASP* 1.3 63.6 + - - +
830I ASP* 2.8 23.1 - - + +
831I LYS* 2.9 26.4 + - + +
832I TRP 3.6 2.6 + - - -
1058I VAL* 3.9 1.5 - - - +
1061I GLN* 3.3 17.5 - - - +
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Residues in contact with ASP 829 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736I ARG* 3.3 38.9 + - - +
745I ASP* 4.0 9.4 - - - +
746I ALA* 4.1 4.2 - - - +
747I HIS* 4.2 16.6 + - - +
828I PRO* 1.3 71.0 - - - +
830I ASP* 1.3 62.8 + - - +
831I LYS 2.9 1.4 + - - -
832I TRP* 3.5 37.1 + - - -
833I GLU* 5.8 0.9 - - - +
1058I VAL* 3.7 17.1 - - + +
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Residues in contact with ASP 830 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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828I PRO* 3.5 20.3 - - + +
829I ASP* 1.3 79.2 + - - +
831I LYS* 1.3 86.9 + - + +
833I GLU* 6.0 1.6 - - - +
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Residues in contact with LYS 831 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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827I VAL* 3.3 26.7 - - + +
828I PRO* 2.9 17.5 + - + +
830I ASP* 1.3 105.6 - - + +
832I TRP* 1.3 62.0 + - - +
833I GLU* 3.3 4.7 - - - +
834I GLN* 3.8 30.3 + - - +
840I THR* 3.5 13.0 - - + +
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Residues in contact with TRP 832 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409I PHE* 4.9 1.6 - + + -
735I GLY* 3.3 27.5 + - - -
736I ARG* 3.7 24.2 - - + -
741I HIS* 4.2 4.4 + + - -
742I SER 4.9 2.0 + - - -
743I PHE* 4.9 4.3 - - - -
744I GLU 3.3 18.2 - - - -
745I ASP* 3.5 36.1 - - + -
746I ALA 4.2 1.1 - - - -
827I VAL* 4.5 3.4 - - - -
828I PRO 3.6 2.9 + - - +
829I ASP* 3.5 45.8 + - - -
831I LYS* 1.3 74.6 - - - +
833I GLU* 1.3 95.4 + - + +
834I GLN 2.9 6.3 + - - -
835I THR* 2.5 36.1 + - - -
836I TYR* 5.2 3.9 - + - -
840I THR* 5.0 1.1 - - - +
855I HIS* 4.2 6.7 - + - -
1057I PRO* 4.4 9.6 - - + -
1058I VAL* 4.1 14.6 - - + -
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Residues in contact with GLU 833 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408I PRO* 3.8 15.7 - - + +
409I PHE* 3.1 19.7 + - - +
410I SER* 2.8 49.4 + - - +
743I PHE 5.1 0.3 - - - +
829I ASP 5.8 0.4 - - - +
830I ASP 6.0 1.3 - - - +
831I LYS* 3.3 2.9 - - - -
832I TRP* 1.3 112.3 + - + +
834I GLN* 1.3 61.4 + - + +
835I THR 3.1 1.5 + - - -
836I TYR* 3.4 32.4 + - - +
837I LYS* 5.3 1.4 - - - +
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Residues in contact with GLN 834 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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831I LYS* 3.9 36.7 - - + +
832I TRP 2.9 1.4 + - - -
833I GLU* 1.3 75.0 - - + +
835I THR* 1.3 62.0 + - - +
836I TYR 3.0 2.7 - - - -
837I LYS* 3.1 6.1 + - - +
838I LYS* 2.8 61.8 + - - +
840I THR* 3.0 20.0 + - - +
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Residues in contact with THR 835 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741I HIS* 4.7 0.2 - - - -
832I TRP* 2.5 24.4 + - - -
833I GLU 4.9 0.2 - - - -
834I GLN* 1.3 77.2 - - - +
836I TYR* 1.3 61.6 + - - +
837I LYS 3.3 1.0 + - - -
838I LYS 3.7 7.7 - - - +
840I THR* 3.7 5.1 + - - -
843I ILE* 2.9 30.5 - - + +
844I VAL* 3.3 17.3 - - - -
845I THR* 3.0 24.2 + - - -
855I HIS* 3.1 42.2 + - + +
866I LYS* 3.8 4.0 + - - -
1057I PRO* 3.7 9.5 - - + +
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Residues in contact with TYR 836 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408I PRO* 3.3 43.7 - - + -
411I GLU* 6.0 0.2 - - - +
741I HIS* 3.8 13.5 + + - -
742I SER 3.0 26.9 + - - -
743I PHE* 3.2 32.1 - + - -
832I TRP* 5.2 4.5 - + - -
833I GLU* 3.6 26.5 - - - +
834I GLN 3.0 0.6 - - - -
835I THR* 1.3 79.0 - - - +
837I LYS* 1.3 68.5 + - + +
845I THR* 3.0 37.3 + - + -
853I PRO* 4.7 5.3 - - + +
866I LYS* 3.2 16.4 + - - -
870I GLU* 5.5 0.2 - - - +
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Residues in contact with LYS 837 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408I PRO* 6.2 0.2 - - - -
411I GLU* 3.0 29.8 + - - -
833I GLU 5.3 2.7 - - - +
834I GLN* 3.1 7.6 + - - +
835I THR 3.1 0.9 - - - -
836I TYR* 1.3 90.4 - - + +
838I LYS* 1.3 72.4 + - + +
839I PRO* 4.5 1.7 - - - +
844I VAL* 4.5 1.2 - - - +
863I MET* 6.0 0.7 - - - +
866I LYS* 4.0 16.9 + - - +
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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