Contacts of the helix formed by residues 795 - 806 (chain H) in PDB entry 6BAA
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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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793H PRO 4.8 2.0 - - - +
794H PHE* 1.3 75.1 - - - +
796H LYS* 1.3 60.7 + - - +
797H GLN* 3.5 1.3 - - + +
798H ARG* 3.8 27.1 - - + +
799H TYR* 3.0 26.9 + - - +
845H TYR* 2.9 10.5 + - + +
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Residues in contact with LYS 796 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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795H ASN* 1.3 71.9 - - - +
797H GLN* 1.3 61.3 + - - +
798H ARG 3.5 0.2 - - - -
799H TYR* 3.9 11.2 - - + +
800H LYS* 3.0 27.1 + - - +
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Residues in contact with GLN 797 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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795H ASN* 3.5 1.4 - - + +
796H LYS* 1.3 75.9 - - - +
798H ARG* 1.3 64.1 + - + +
800H LYS* 3.7 5.0 - - - +
801H MET* 2.9 31.2 + - - +
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Residues in contact with ARG 798 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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795H ASN* 3.8 20.3 + - + +
797H GLN* 1.3 80.0 - - + +
799H TYR* 1.3 56.8 + - - +
801H MET* 3.4 11.4 + - - +
802H VAL* 2.8 31.0 + - - +
844H LEU* 3.0 28.1 + - - +
845H TYR* 3.6 27.9 + - + +
847H GLN* 3.9 20.3 - - - +
878H ARG* 5.3 10.5 - - - +
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Residues in contact with TYR 799 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784H VAL 5.5 0.3 - - - -
785H GLU* 4.5 11.3 + - + -
788H ILE* 4.2 25.4 - - + -
789H THR 6.1 0.2 - - - -
794H PHE* 5.3 13.7 - + + -
795H ASN 3.0 21.8 + - - +
796H LYS* 3.9 11.0 - - + -
798H ARG* 1.3 74.1 - - - +
800H LYS* 1.3 62.6 + - - +
802H VAL* 3.8 3.3 - - + +
803H ILE* 2.8 42.9 + - + +
819H ASP* 3.2 29.9 - - + +
845H TYR* 3.5 16.3 - + + +
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Residues in contact with LYS 800 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796H LYS 3.0 22.3 + - - +
797H GLN* 3.4 6.9 + - - +
799H TYR* 1.3 78.7 - - - +
801H MET* 1.3 57.4 + - - +
803H ILE* 3.8 4.4 - - - +
804H GLU* 2.9 31.6 + - - +
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Residues in contact with MET 801 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797H GLN 2.9 19.1 + - - +
798H ARG* 3.7 13.0 - - - +
800H LYS* 1.3 76.3 - - - +
802H VAL* 1.3 58.1 + - - +
804H GLU* 4.1 4.1 - - - +
805H ALA* 2.8 33.3 + - - +
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Residues in contact with VAL 802 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788H ILE* 6.3 2.5 - - + -
798H ARG 2.8 18.5 + - - +
799H TYR* 3.8 9.2 - - + +
801H MET* 1.3 75.4 - - - +
803H ILE* 1.3 57.0 + - - +
805H ALA* 3.9 3.5 - - - +
806H CYS* 2.8 39.0 + - - +
841H ALA* 4.5 23.8 - - + +
844H LEU* 5.5 5.8 - - + -
845H TYR* 4.4 15.9 - - + +
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Residues in contact with ILE 803 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799H TYR* 2.8 39.8 + - + +
800H LYS* 3.8 6.3 - - - +
802H VAL* 1.3 71.4 - - - +
804H GLU* 1.3 61.7 + - - +
807H SER 3.2 2.1 + - - -
808H LEU* 2.8 44.5 + - + -
809H GLN* 3.8 10.2 + - + +
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Residues in contact with GLU 804 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800H LYS 2.9 18.3 + - - +
801H MET* 4.1 3.8 - - - +
803H ILE* 1.3 75.6 - - - +
805H ALA* 1.3 63.7 + - - +
807H SER* 3.2 11.8 + - - +
809H GLN* 5.7 3.6 - - - +
867H HIS* 3.3 13.2 - - - -
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Residues in contact with ALA 805 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801H MET 2.8 23.9 + - - +
802H VAL* 3.9 4.7 - - - +
804H GLU* 1.3 74.5 - - - +
806H CYS* 1.3 53.9 + - - +
844H LEU* 6.5 0.9 - - + -
867H HIS* 2.4 25.9 + - - -
871H ALA* 3.5 28.9 - - + +
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Residues in contact with CYS 806 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802H VAL 2.8 21.9 + - - +
803H ILE 4.5 0.9 - - - +
805H ALA* 1.3 72.3 - - - +
807H SER* 1.3 69.3 + - - +
808H LEU* 3.2 10.5 + - + +
837H ARG* 3.9 29.7 - - + +
840H VAL* 5.8 1.8 - - + -
841H ALA* 3.8 26.9 - - + +
867H HIS* 3.5 3.8 - - - -
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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