Contacts of the helix formed by residues 866 - 880 (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 ARG 866 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803A ALA* 5.8 0.4 - - - -
864A ARG 3.4 5.3 + - - +
865A PRO* 1.3 76.0 - - - +
867A PHE* 1.3 63.5 + - - +
868A PRO* 3.4 13.9 - - + -
869A GLN* 2.9 25.5 + - + +
870A VAL* 2.9 22.7 + - - +
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Residues in contact with PHE 867 (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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725A ALA* 4.3 8.5 - - - +
728A MET* 3.6 43.5 - - + -
729A ARG* 3.6 22.7 - - + +
732A ALA* 4.3 12.1 - - + -
799A SER* 3.6 25.6 - - - -
802A ASP* 3.7 14.6 - - + -
803A ALA* 3.5 27.6 - - + -
806A TYR* 3.7 27.1 - + + -
866A ARG* 1.3 70.4 - - - +
868A PRO* 1.3 72.2 - - + +
870A VAL* 3.7 16.2 - - + +
871A VAL* 3.0 28.2 + - - +
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Residues in contact with PRO 868 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729A ARG* 3.8 28.9 + - + +
732A ALA* 6.2 2.7 - - + -
866A ARG* 3.5 15.3 - - + -
867A PHE* 1.3 92.8 - - + +
869A GLN* 1.3 57.8 + - + +
871A VAL* 3.4 2.4 + - - +
872A SER* 2.9 31.8 + - - -
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Residues in contact with GLN 869 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864A ARG 4.5 1.0 - - - +
865A PRO* 3.6 17.5 - - + +
866A ARG* 2.9 42.7 + - + +
868A PRO* 1.3 75.6 - - + +
870A VAL* 1.3 66.0 - - - +
872A SER* 3.3 7.0 + - - -
873A ALA* 2.9 26.0 + - - +
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Residues in contact with VAL 870 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725A ALA* 4.0 11.9 - - + -
803A ALA* 5.7 0.7 - - + -
806A TYR* 3.6 29.8 - - + -
852A LEU* 4.3 13.7 - - + -
856A CYS* 4.5 10.8 - - - -
865A PRO* 4.0 25.1 - - + +
866A ARG 2.9 19.4 + - - +
867A PHE* 3.3 23.5 + - + +
869A GLN* 1.3 74.8 - - - +
871A VAL* 1.3 64.4 + - - +
873A ALA* 3.2 6.8 + - - +
874A LEU* 3.1 27.7 + - + +
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Residues in contact with VAL 871 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722A ARG* 3.5 37.7 - - + +
725A ALA* 3.7 36.6 - - + +
726A SER* 3.7 8.5 - - - +
729A ARG* 3.5 24.5 - - - +
867A PHE 3.0 20.7 + - - +
868A PRO 3.7 3.8 - - - +
870A VAL* 1.3 78.7 - - - +
872A SER* 1.3 57.3 + - - +
874A LEU* 3.3 7.5 + - - +
875A ASP* 2.9 31.2 + - - +
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Residues in contact with SER 872 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868A PRO 2.9 19.5 + - - -
869A GLN* 3.7 8.1 - - - -
870A VAL 3.3 0.2 - - - -
871A VAL* 1.3 76.6 - - - +
873A ALA* 1.3 58.9 + - - +
875A ASP* 3.3 9.6 + - - +
876A LYS* 3.0 31.6 + - - +
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Residues in contact with ALA 873 (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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852A LEU* 4.2 23.3 - - + -
869A GLN 2.9 17.2 + - - +
870A VAL 3.6 4.5 - - - +
872A SER* 1.3 78.4 - - - +
874A LEU* 1.3 60.3 + - - +
876A LYS* 3.3 8.8 + - - +
877A MET* 3.3 31.5 + - + +
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Residues in contact with LEU 874 (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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718A VAL* 4.0 16.7 - - + +
721A LEU* 3.9 5.2 - - + +
722A ARG* 3.7 33.0 - - + +
725A ALA* 4.2 3.6 - - + -
806A TYR* 3.3 26.2 - - + +
810A MET* 4.7 4.0 - - + -
849A LEU* 3.7 29.6 - - + -
852A LEU* 4.1 14.4 - - + -
870A VAL* 3.1 24.4 + - + +
871A VAL* 3.7 6.1 - - - +
873A ALA* 1.3 74.3 - - - +
875A ASP* 1.3 63.9 + - - +
877A MET* 3.3 9.5 + - - +
878A ILE* 3.0 28.4 + - - +
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Residues in contact with ASP 875 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722A ARG* 2.7 47.3 + - - +
871A VAL* 2.9 28.7 + - - +
872A SER* 3.6 8.5 - - - +
874A LEU* 1.3 69.9 - - - +
876A LYS* 1.3 65.0 + - - +
878A ILE* 3.6 11.3 + - - +
879A ARG* 3.1 29.7 + - + +
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Residues in contact with LYS 876 (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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872A SER 3.0 15.5 + - - +
873A ALA* 3.5 11.4 - - - +
874A LEU 3.2 0.2 - - - -
875A ASP* 1.3 73.8 - - - +
877A MET* 1.3 67.9 + - + +
879A ARG* 3.2 3.0 + - - -
880A ASN* 2.6 40.1 + - - +
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Residues in contact with MET 877 (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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718A VAL* 5.0 1.8 - - + -
848A SER* 3.5 47.8 - - - +
849A LEU* 3.4 32.3 - - + -
852A LEU* 4.2 19.5 - - + -
873A ALA* 3.5 19.5 - - + +
874A LEU* 3.3 12.7 + - + +
876A LYS* 1.3 78.8 - - + +
878A ILE* 1.3 60.3 + - - +
880A ASN* 3.1 22.9 - - - +
881A PRO* 3.3 6.6 - - - +
883A SER* 3.4 16.5 + - - +
884A LEU* 3.8 17.0 - - + +
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Residues in contact with ILE 878 (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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715A ILE* 4.6 15.7 - - + +
718A VAL* 3.9 26.9 - - + +
719A GLY* 5.0 4.7 - - - +
722A ARG* 4.4 17.9 - - + -
874A LEU 3.0 21.8 + - - +
875A ASP* 3.7 22.0 - - - +
877A MET* 1.3 77.9 - - - +
879A ARG* 1.3 65.9 + - + +
880A ASN 3.4 0.7 + - - -
881A PRO* 3.7 15.6 - - - +
884A LEU* 4.6 7.0 - - + -
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Residues in contact with ARG 879 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A ASP* 3.1 18.8 + - + +
876A LYS* 3.2 4.9 + - - +
878A ILE* 1.3 77.9 - - + +
880A ASN* 1.3 69.3 + - - +
881A PRO* 3.5 6.9 - - - +
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Residues in contact with ASN 880 (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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876A LYS* 2.6 39.4 + - - +
877A MET 3.1 2.7 + - - -
879A ARG* 1.3 89.3 - - - +
881A PRO* 1.3 56.1 - - - +
882A ALA* 3.2 5.3 - - - +
883A SER* 2.7 36.4 + - - +
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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
------------------------------------------------------------
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