Contacts of the helix formed by residues 825 - 835 (chain A) in PDB entry 2VWV
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 825 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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785A ARG* 3.8 2.9 - - - +
823A ASP 4.2 1.0 + - - -
824A MET* 1.3 76.4 - - - +
826A ASN* 1.3 64.6 + - - +
827A GLN* 3.9 6.7 + - - +
828A ASP* 2.7 39.0 + - - +
829A VAL* 3.0 20.8 + - - +
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Residues in contact with ASN 826 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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782A ILE 5.5 1.2 + - - -
784A ILE* 3.8 38.4 + - + +
785A ARG* 3.0 29.4 + - - +
825A SER* 1.3 72.7 - - - +
827A GLN* 1.3 62.9 + - - +
829A VAL* 3.1 14.2 + - - +
830A ILE* 3.1 21.3 + - + +
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Residues in contact with GLN 827 (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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825A SER* 3.4 7.2 + - - +
826A ASN* 1.3 78.8 - - - +
828A ASP* 1.3 58.4 + - - +
830A ILE* 3.4 22.1 + - - +
831A ASN* 2.8 69.0 + - - +
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Residues in contact with ASP 828 (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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823A ASP 5.3 0.3 - - - +
824A MET* 3.9 18.0 - - + +
825A SER* 2.7 38.9 + - - +
827A GLN* 1.3 80.5 - - - +
829A VAL* 1.3 56.4 + - - +
831A ASN* 3.5 13.6 + - - +
832A ALA* 2.8 29.5 + - - +
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Residues in contact with VAL 829 (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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784A ILE* 4.7 7.2 - - + +
785A ARG* 4.1 23.8 - - + +
821A TYR* 3.5 58.6 - - + -
824A MET* 4.0 7.4 - - + -
825A SER 3.0 19.8 + - - +
826A ASN* 3.1 10.0 + - - +
828A ASP* 1.3 73.5 - - - +
830A ILE* 1.3 62.8 + - + +
832A ALA* 3.2 6.4 + - - +
833A ILE* 2.9 35.8 + - + +
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Residues in contact with ILE 830 (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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784A ILE* 3.5 38.6 - - + -
792A ILE* 4.3 25.4 - - + -
826A ASN* 3.1 20.5 + - + +
827A GLN* 3.9 23.1 - - - +
829A VAL* 1.3 73.6 - - + +
831A ASN* 1.3 67.3 + - - +
833A ILE* 3.2 6.7 + - + +
834A GLU* 3.0 25.5 + - + +
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Residues in contact with ASN 831 (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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827A GLN* 2.8 57.0 + - - +
828A ASP* 3.5 14.1 + - - +
830A ILE* 1.3 77.0 - - - +
832A ALA* 1.3 60.8 + - - +
834A GLU* 3.4 6.7 + - - +
835A GLN* 3.2 28.2 + - + +
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Residues in contact with ALA 832 (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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821A TYR* 5.7 0.7 - - + -
824A MET* 4.6 10.5 - - + -
828A ASP 2.8 19.2 + - - +
829A VAL* 3.2 8.0 + - - +
831A ASN* 1.3 75.2 - - - +
833A ILE* 1.3 59.0 + - + +
835A GLN* 3.0 16.7 + - - +
837A TYR* 3.0 53.2 + - + +
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Residues in contact with ILE 833 (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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789A PRO* 3.7 35.0 - - + -
804A TRP* 4.1 14.4 - - + -
821A TYR* 3.5 31.2 - - + +
829A VAL* 2.9 28.3 + - + +
830A ILE* 3.2 7.4 + - + +
832A ALA* 1.3 76.7 - - - +
834A GLU* 1.3 58.0 + - - +
836A ASP* 3.1 17.3 + - - +
837A TYR* 3.3 20.0 - - + +
838A ARG* 3.4 24.7 + - - +
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Residues in contact with GLU 834 (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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830A ILE* 3.0 18.2 + - + +
831A ASN* 3.7 7.4 - - - +
832A ALA 3.3 0.2 - - - -
833A ILE* 1.3 77.7 - - - +
835A GLN* 1.3 68.4 + - - +
836A ASP* 3.2 11.4 + - - +
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Residues in contact with GLN 835 (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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831A ASN* 3.2 14.6 + - + +
832A ALA* 3.0 11.3 + - - +
834A GLU* 1.3 89.3 + - - +
836A ASP* 1.3 68.3 + - - +
837A TYR* 3.2 4.5 + - + +
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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