Contacts of the helix formed by residues 797 - 806 (chain A) in PDB entry 2ITN
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 CYS 797 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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795A PHE 4.3 0.5 - - - +
796A GLY* 1.3 74.2 - - - -
798A LEU* 1.3 57.2 + - - +
799A LEU* 3.8 11.2 - - - +
800A ASP* 3.2 46.1 + - - +
801A TYR* 3.1 25.3 + - - +
841A ARG* 3.8 24.5 - - - +
843A VAL 3.4 7.6 - - - +
844A LEU* 3.7 8.1 - - + +
845A VAL* 4.2 0.7 - - - -
2021A ANP 3.5 24.6 + - - +
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Residues in contact with LEU 798 (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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797A CYS* 1.3 69.8 - - - +
799A LEU* 1.3 59.4 + - - +
801A TYR* 4.2 4.7 - - + -
802A VAL* 2.9 32.6 + - + +
817A TRP* 3.8 44.9 - - + -
821A ILE* 4.0 14.8 - - + -
840A ALA* 3.6 7.2 + - + +
843A VAL* 2.8 41.1 + - + +
845A VAL* 3.8 21.8 - - + +
851A VAL* 4.3 4.7 - - + -
907A LEU* 3.6 29.8 - - + -
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Residues in contact with LEU 799 (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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797A CYS* 3.3 3.8 - - - -
798A LEU* 1.3 77.5 - - - +
800A ASP* 1.3 66.8 + - - +
802A VAL* 3.4 7.4 - - + +
803A ARG* 3.1 64.7 + - - +
840A ALA* 3.1 29.0 + - + +
841A ARG* 3.9 21.1 - - + +
880A TRP* 6.4 0.2 - - + -
906A GLU* 3.6 24.9 - - + +
911A GLY* 3.8 20.0 - - - +
912A SER 5.3 0.2 - - - +
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Residues in contact with ASP 800 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796A GLY* 6.3 0.4 - - - -
797A CYS* 3.2 28.2 + - - +
799A LEU* 1.3 85.4 - - - +
801A TYR* 1.3 57.7 + - - +
803A ARG* 3.8 14.4 + - - +
804A GLU* 3.0 31.4 + - - +
2021A ANP 4.6 8.8 + - - -
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Residues in contact with TYR 801 (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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795A PHE* 3.9 47.4 - + + +
797A CYS 3.1 16.1 + - - +
798A LEU* 3.7 12.6 - - + +
799A LEU 3.1 0.4 - - - -
800A ASP* 1.3 77.0 - - - +
802A VAL* 1.3 66.1 + - - +
804A GLU* 3.4 0.8 + - - -
805A HIS* 3.0 54.0 + + - +
809A ILE* 4.4 5.2 - - + -
817A TRP* 4.0 34.1 - + - -
845A VAL* 4.4 8.5 - - + -
848A PRO* 3.3 28.3 - - + +
989A LEU* 3.4 26.0 - - + +
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Residues in contact with VAL 802 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798A LEU* 2.9 24.8 + - + +
799A LEU* 3.4 14.8 - - + +
801A TYR* 1.3 77.1 - - - +
803A ARG* 1.3 64.6 + - - +
806A LYS* 3.0 28.2 + - - +
809A ILE* 3.6 12.1 - - + +
814A LEU* 5.0 0.9 - - + -
817A TRP* 3.7 30.5 - - + -
906A GLU 4.4 4.9 - - - +
907A LEU* 4.2 19.7 - - + +
910A PHE* 3.6 31.3 - - + +
911A GLY* 3.7 7.2 - - - +
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Residues in contact with ARG 803 (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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799A LEU* 3.1 52.0 + - - +
800A ASP* 3.8 15.3 + - - +
801A TYR 3.3 0.2 - - - -
802A VAL* 1.3 76.7 - - - +
804A GLU* 1.3 60.7 + - - +
806A LYS* 3.6 23.7 + - - +
906A GLU* 5.7 0.2 + - - -
910A PHE 3.7 16.4 - - - +
911A GLY* 2.9 27.0 + - - +
912A SER 4.7 1.2 + - - -
913A LYS* 3.7 31.2 - - - +
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Residues in contact with GLU 804 (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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800A ASP 3.0 18.7 + - - +
801A TYR* 4.0 2.7 - - - +
803A ARG* 1.3 78.3 - - - +
805A HIS* 1.3 86.0 + - + +
806A LYS* 3.6 0.9 - - - -
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Residues in contact with HIS 805 (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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795A PHE* 5.7 1.6 - - - -
801A TYR* 3.0 60.9 + + + +
802A VAL 3.7 1.8 - - - -
804A GLU* 1.3 102.9 + - + +
806A LYS* 1.3 66.7 + - - +
807A ASP 2.7 6.0 + - - -
808A ASN* 2.8 17.8 + - + +
809A ILE* 3.5 21.3 + - + +
989A LEU* 4.2 17.4 - - + +
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Residues in contact with LYS 806 (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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802A VAL 3.0 15.5 + - - +
803A ARG* 3.6 23.3 + - - +
804A GLU 3.6 1.2 + - - -
805A HIS* 1.3 74.1 - - - +
807A ASP* 1.3 71.2 + - - +
808A ASN 3.3 2.8 + - - -
809A ILE 3.6 9.1 + - - +
910A PHE* 3.7 52.1 - - + +
981A ILE* 5.9 0.9 - - - +
987A MET* 5.1 1.7 - - - +
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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