Contacts of the helix formed by residues 889 - 898 (chain A) in PDB entry 2NVX
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 889 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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888A GLY* 1.3 73.6 - - - -
890A ASP* 1.3 53.9 + - - +
891A ALA* 3.0 8.1 - - - -
892A ALA* 2.8 25.2 + - - +
893A PHE* 2.7 36.0 + - - +
940A ARG* 3.9 1.1 - - - -
1295A THR* 4.3 7.2 - - - -
1297A GLU* 3.4 34.5 + - - +
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Residues in contact with ASP 890 (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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888A GLY 3.9 0.4 + - - -
889A SER* 1.3 72.0 - - - +
891A ALA* 1.3 59.5 - - - +
893A PHE* 4.0 8.2 - - - +
894A GLU* 3.8 21.1 + - - +
940A ARG* 3.4 25.0 + - - +
944A ARG* 5.4 1.2 + - - -
1294A PRO 5.1 2.4 - - - +
1295A THR 3.4 16.8 + - - +
1296A GLY* 3.7 16.7 + - - -
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Residues in contact with ALA 891 (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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889A SER* 3.0 6.3 - - - -
890A ASP* 1.3 78.0 - - - +
892A ALA* 1.3 63.7 + - - +
893A PHE 3.2 2.4 + - - -
894A GLU* 3.9 3.1 + - - +
895A LYS* 3.7 19.2 + - - +
1295A THR* 4.4 6.5 + - + +
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Residues in contact with ALA 892 (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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888A GLY* 4.9 2.7 - - - -
889A SER* 2.8 29.3 + - - +
891A ALA* 1.3 77.2 - - - +
893A PHE* 1.3 60.8 + - - +
895A LYS* 3.7 16.0 - - + +
896A ARG* 3.3 27.8 + - - +
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Residues in contact with PHE 893 (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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884A ASP 5.7 0.4 - - - -
885A THR* 4.2 20.9 - - + -
887A GLY 5.5 3.1 - - - -
888A GLY* 5.5 1.6 - - - -
889A SER 2.7 21.1 + - - +
890A ASP* 4.1 12.8 - - - +
891A ALA 3.2 0.4 - - - -
892A ALA* 1.3 70.8 - - - +
894A GLU* 1.3 72.0 + - + +
896A ARG* 2.9 12.5 + - - +
897A TYR* 3.0 47.0 + + - +
933A TYR* 4.0 22.9 - + - -
936A LEU* 4.1 31.0 - - + -
937A VAL* 3.9 22.9 - - + -
940A ARG* 4.5 25.8 - - - +
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Residues in contact with GLU 894 (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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890A ASP 3.8 13.8 + - - +
891A ALA* 4.4 3.6 - - - +
893A PHE* 1.3 77.0 - - + +
895A LYS* 1.3 67.7 + - - +
896A ARG 2.7 2.1 + - - -
897A TYR 2.8 12.8 + - - -
898A ARG* 2.9 25.7 + - + +
906A HIS* 4.2 20.7 + - - +
933A TYR* 2.8 34.3 + - + +
1029A ARG* 5.0 0.2 + - - -
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Residues in contact with LYS 895 (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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891A ALA 3.7 12.0 + - - +
892A ALA* 3.7 19.3 - - + +
894A GLU* 1.3 76.2 - - - +
896A ARG* 1.3 63.0 + - + +
906A HIS* 5.8 4.6 + - - -
1029A ARG* 3.9 22.0 + - - +
1033A GLN* 5.1 3.1 + - - -
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Residues in contact with ARG 896 (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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884A ASP* 5.6 9.4 + - - +
892A ALA* 3.3 14.6 + - - +
893A PHE* 2.9 11.1 + - - +
894A GLU 2.7 5.1 + - - -
895A LYS* 1.3 83.6 - - + +
897A TYR* 1.3 90.0 + - + +
1029A ARG* 3.2 22.7 - - - +
1030A ARG* 4.5 6.5 + - - +
1034A GLU* 3.3 41.1 + - - +
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Residues in contact with TYR 897 (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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884A ASP* 3.2 35.9 - - - +
885A THR* 4.2 3.9 + - + -
893A PHE* 3.0 47.4 + + + +
894A GLU 2.8 9.9 + - - -
896A ARG* 1.3 100.1 - - + +
898A ARG* 1.3 60.0 + - - +
899A VAL* 3.5 5.2 + - - +
929A LEU* 5.7 0.3 - - - +
932A GLU* 4.7 7.6 - - - +
933A TYR* 4.2 8.7 - - + +
936A LEU* 3.6 29.2 - - + +
1024A SER* 2.9 27.8 + - - -
1027A ALA* 3.5 24.3 - - + +
1029A ARG* 4.1 13.2 + - - +
1030A ARG* 3.9 12.2 + - + -
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Residues in contact with ARG 898 (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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894A GLU* 2.9 27.3 + - + +
897A TYR* 1.3 76.4 - - - +
899A VAL* 1.3 70.5 + - - +
900A ASP* 3.2 44.2 + - + +
906A HIS* 4.4 15.9 - - + +
926A GLN* 4.1 0.6 + - - -
929A LEU 4.7 0.8 + - - -
930A ASP* 2.8 34.2 + - - +
933A TYR* 3.4 52.2 - - + +
1029A ARG* 2.8 29.3 + - - +
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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