Contacts of the helix formed by residues 795 - 806 (chain D) in PDB entry 5TWV
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 ASN 795 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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793D PRO 4.7 2.2 - - - +
794D PHE* 1.3 74.9 - - - +
796D LYS* 1.3 60.2 + - - +
797D GLN* 3.6 1.3 - - + +
798D ARG* 3.7 30.1 - - + +
799D TYR* 3.2 21.7 + - - +
845D TYR* 3.3 14.3 + - - +
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Residues in contact with LYS 796 (chain D).
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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795D ASN* 1.3 72.8 - - - +
797D GLN* 1.3 60.9 + - - +
799D TYR* 3.7 13.4 - - + +
800D LYS* 3.0 23.2 + - - +
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Residues in contact with GLN 797 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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795D ASN* 3.6 1.0 - - - +
796D LYS* 1.3 76.5 - - - +
798D ARG* 1.3 65.3 + - + +
799D TYR 3.2 0.2 - - - -
800D LYS* 3.2 7.3 + - - +
801D MET* 2.9 29.3 + - - +
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Residues in contact with ARG 798 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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795D ASN* 3.7 25.3 - - + -
797D GLN* 1.3 81.6 - - + +
799D TYR* 1.3 55.8 + - - +
801D MET* 3.4 12.7 + - - +
802D VAL* 2.8 31.6 + - - +
844D LEU 4.4 15.0 + - - -
845D TYR* 4.0 24.1 + - + +
847D GLN* 4.8 12.5 - - - +
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Residues in contact with TYR 799 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784D VAL* 5.8 1.8 - - - +
785D GLU* 5.0 11.2 + - + -
788D ILE* 4.7 21.1 - - + -
794D PHE* 6.5 1.8 - + - -
795D ASN 3.2 20.6 + - - +
796D LYS* 3.7 12.6 - - + -
798D ARG* 1.3 77.9 - - - +
800D LYS* 1.3 62.4 + - - +
802D VAL* 3.8 6.8 - - + +
803D ILE* 2.8 41.6 + - + +
819D ASP* 3.5 26.5 + - + +
845D TYR* 4.2 9.3 - + + -
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Residues in contact with LYS 800 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796D LYS 3.0 20.2 + - - +
797D GLN* 3.2 8.0 + - - +
799D TYR* 1.3 79.1 - - - +
801D MET* 1.3 56.1 + - - +
803D ILE* 3.3 6.0 + - - +
804D GLU* 3.0 29.3 + - - +
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Residues in contact with MET 801 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797D GLN 2.9 16.3 + - - +
798D ARG* 3.8 14.6 - - - +
800D LYS* 1.3 76.1 - - - +
802D VAL* 1.3 57.7 + - - +
804D GLU* 3.6 4.8 + - - +
805D ALA* 2.9 33.0 + - - +
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Residues in contact with VAL 802 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798D ARG 2.8 21.9 + - - +
799D TYR* 3.8 9.2 - - + +
801D MET* 1.3 71.6 - - - +
803D ILE* 1.3 56.2 + - - +
805D ALA* 4.4 4.5 - - - -
806D CYS* 2.7 40.4 + - + +
841D ALA* 5.2 11.0 - - + +
844D LEU* 5.7 6.5 - - + -
845D TYR* 4.5 21.8 - - + +
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Residues in contact with ILE 803 (chain D).
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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799D TYR* 2.8 37.0 + - + +
800D LYS* 3.3 6.9 + - - +
802D VAL* 1.3 75.1 - - - +
804D GLU* 1.3 61.3 + - - +
807D SER* 3.6 0.7 + - - -
808D LEU* 3.2 40.4 + - + +
809D GLN* 3.9 8.1 + - + +
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Residues in contact with GLU 804 (chain D).
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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800D LYS 3.0 15.8 + - - +
801D MET* 4.0 5.2 - - - +
803D ILE* 1.3 79.1 - - - +
805D ALA* 1.3 58.1 + - - +
807D SER* 3.5 2.3 + - - -
809D GLN* 6.0 3.1 - - - -
867D HIS* 3.1 24.8 + - - -
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Residues in contact with ALA 805 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801D MET 2.9 23.1 + - - +
802D VAL* 3.9 5.2 - - - +
804D GLU* 1.3 74.1 - - - +
806D CYS* 1.3 57.8 + - - +
807D SER 3.4 0.2 - - - -
844D LEU* 6.2 3.6 - - + -
867D HIS* 3.1 16.3 + - - -
868D LEU* 5.9 0.3 - - - -
871D ALA* 3.3 24.9 - - + +
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Residues in contact with CYS 806 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802D VAL* 2.7 22.9 + - - +
805D ALA* 1.3 72.3 - - - +
807D SER* 1.3 69.5 + - - +
808D LEU* 3.2 9.3 + - + +
837D ARG* 4.1 20.8 - - - +
840D VAL* 5.1 5.1 - - + +
841D ALA* 3.7 33.7 - - + +
844D LEU* 6.0 2.2 - - + -
867D HIS* 4.0 0.7 - - - -
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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