Contacts of the helix formed by residues 824 - 833 (chain A) in PDB entry 2X8A
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 824 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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771A ASP* 3.2 21.1 + - - -
773A ASP* 4.0 4.4 + - - -
774A VAL* 3.5 4.7 - - - -
822A LYS 4.0 0.4 + - - -
823A VAL* 1.3 72.3 - - - +
825A HIS* 1.4 64.9 + - - +
826A LYS* 2.9 23.0 + - - +
827A HIS* 2.8 39.3 + - - +
828A PHE* 3.3 11.4 + - - -
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Residues in contact with HIS 825 (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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773A ASP* 2.9 36.3 + - + +
774A VAL* 3.5 9.3 - - + +
775A ASN 5.9 0.8 + - - -
778A ALA* 6.5 0.9 - - + -
779A ILE* 5.5 10.1 - - + +
824A SER* 1.4 71.2 + - - +
826A LYS* 1.4 56.0 + - - +
828A PHE* 3.3 11.0 + - + +
829A GLU* 2.8 56.6 + - + +
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Residues in contact with LYS 826 (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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824A SER* 2.9 13.3 + - - +
825A HIS* 1.4 80.4 - - - +
827A HIS* 1.4 59.9 + - + +
829A GLU* 3.2 7.9 + - - +
830A GLU* 2.9 41.2 + - + +
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Residues in contact with HIS 827 (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 ALA* 3.4 28.2 - - + +
803A CYS* 3.8 23.5 + - + -
804A ALA* 3.7 17.6 - - + +
807A GLN* 5.0 9.0 - - + +
821A LEU* 5.8 1.1 - - + -
822A LYS 3.7 15.0 - - - -
823A VAL* 3.5 6.6 - - + -
824A SER* 2.8 40.2 + - - +
826A LYS* 1.4 76.4 - - + +
828A PHE* 1.3 53.8 + - - +
830A GLU* 3.3 6.2 + - + +
831A ALA* 2.8 34.3 + - - +
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Residues in contact with PHE 828 (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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758A LEU* 5.2 0.9 - - + -
762A THR* 5.2 0.4 - - + -
770A LEU* 3.7 20.9 - - + -
774A VAL* 3.9 7.0 - - + -
776A LEU* 4.3 9.4 - - + -
779A ILE* 3.7 48.9 - - + -
796A LEU* 4.1 27.7 - - + +
797A VAL* 4.5 21.5 - - + -
800A ALA* 4.1 11.4 - - + -
823A VAL* 3.7 21.1 - - + -
824A SER 3.3 16.9 + - - -
825A HIS* 3.3 13.5 + - + +
827A HIS* 1.3 78.4 - - - +
829A GLU* 1.3 61.7 + - - +
831A ALA* 3.3 5.1 + - - +
832A PHE* 3.1 34.7 + + + -
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Residues in contact with GLU 829 (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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782A ASP* 5.4 0.5 - - - +
784A ARG* 2.8 38.5 + - - -
825A HIS* 2.8 37.7 + - + +
826A LYS* 3.2 13.2 + - - +
828A PHE* 1.3 77.1 - - - +
830A GLU* 1.3 67.2 + - - +
832A PHE* 3.5 17.5 + - - +
833A LYS* 3.8 5.9 + - - +
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Residues in contact with GLU 830 (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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803A CYS* 4.1 10.5 - - + -
826A LYS* 2.9 26.1 + - + +
827A HIS* 3.8 5.4 - - + +
829A GLU* 1.3 79.7 - - - +
831A ALA* 1.4 62.3 + - - +
833A LYS* 3.3 20.2 + - - +
834A LYS* 3.2 35.4 + - - +
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Residues in contact with ALA 831 (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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796A LEU* 3.6 19.3 - - + +
799A GLU* 3.6 11.2 - - + +
800A ALA* 3.4 25.8 - - - +
803A CYS* 4.7 0.2 - - - -
827A HIS 2.8 21.8 + - - +
828A PHE* 3.5 9.0 - - - +
829A GLU 3.3 0.2 - - - -
830A GLU* 1.4 70.8 - - - +
832A PHE* 1.4 58.8 + - - +
834A LYS* 2.9 21.1 + - - +
835A VAL* 3.0 17.3 + - - +
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Residues in contact with PHE 832 (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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779A ILE* 4.4 12.6 - - + -
782A ASP* 3.8 23.1 - - + -
784A ARG* 3.4 58.3 - - + +
785A CYS* 3.5 30.3 - - - -
788A TYR* 3.3 20.5 + - - -
796A LEU* 3.7 22.4 - - + +
828A PHE* 3.1 33.6 + - + -
829A GLU* 3.6 7.9 - - - +
831A ALA* 1.4 76.2 - - - +
833A LYS* 1.4 58.6 + - - +
834A LYS 3.2 1.1 + - - -
835A VAL* 3.6 12.8 + - - +
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Residues in contact with LYS 833 (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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829A GLU 3.8 5.7 + - - +
830A GLU* 3.3 19.4 + - - +
831A ALA 3.2 0.2 - - - -
832A PHE* 1.4 76.9 - - - +
834A LYS* 1.4 63.0 + - - +
835A VAL 3.8 0.4 - - - -
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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
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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