Contacts of the helix formed by residues 67 - 76 (chain A) in PDB entry 5XA0
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 67 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ARG* 5.6 4.3 - - - -
66A TYR* 1.4 70.7 - - - +
68A ALA* 1.3 58.8 + - - -
70A LYS* 2.4 37.6 + - - +
71A GLN* 3.2 10.8 + - - +
99A GLU* 2.5 12.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A SER* 1.3 68.8 - - - +
69A GLN* 1.3 65.0 + - - +
70A LYS 2.8 1.5 + - - -
71A GLN* 3.6 8.0 + - - +
72A PHE 3.1 12.8 + - - -
92A LEU* 3.1 14.4 - - - +
95A ALA* 2.8 37.0 - - + +
98A LEU* 5.9 1.8 - - + -
99A GLU* 3.1 12.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TYR* 3.0 53.7 + - + -
68A ALA* 1.3 73.7 - - - +
70A LYS* 1.3 55.9 + - - +
72A PHE* 2.2 35.1 + - - +
73A TRP* 2.6 18.2 + - + +
95A ALA* 4.1 0.6 - - - +
96A ALA* 2.3 57.4 + - - +
99A GLU* 2.4 37.7 - - + +
100A LYS* 3.1 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TYR 2.7 11.9 + - - +
67A SER* 2.4 38.7 + - - +
69A GLN* 1.3 74.6 - - - +
71A GLN* 1.3 56.3 + - + +
73A TRP* 2.8 57.0 + - + -
74A LYS* 3.0 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A SER 3.2 9.6 + - - +
68A ALA* 4.0 6.7 - - - +
70A LYS* 1.3 81.6 - - + +
72A PHE* 1.3 62.2 + - - +
74A LYS* 4.2 7.7 + - - +
75A ALA* 4.4 8.8 + - - +
92A LEU* 3.0 25.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLN* 2.2 35.2 + - + +
71A GLN* 1.3 72.1 - - - +
73A TRP* 1.4 56.9 + - + -
76A ALA* 2.8 39.4 + - + +
89A LEU* 3.9 34.1 - - + -
92A LEU* 2.7 61.2 - - + +
93A HIS* 3.7 28.7 - + + -
96A ALA* 5.1 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TYR* 2.7 52.4 + + + -
69A GLN* 2.6 37.1 + - + +
70A LYS* 2.8 39.0 + - + +
72A PHE* 1.4 74.5 - + + +
74A LYS* 1.3 84.0 + - + +
76A ALA* 3.3 18.8 + - - -
154A ALA* 6.5 0.4 - - + -
156A ASN* 5.5 11.2 - - - +
157A GLU* 5.4 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LYS 3.0 13.4 + - - +
71A GLN* 4.9 4.5 - - - +
72A PHE 3.6 0.2 - - - -
73A TRP* 1.3 94.1 - - + +
75A ALA* 1.3 61.5 + - - +
76A ALA 4.3 1.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLN 4.4 9.4 + - - +
72A PHE 4.3 1.2 + - - +
74A LYS* 1.3 80.9 - - - +
76A ALA* 1.3 63.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PHE* 2.8 49.2 + - + +
73A TRP* 3.3 15.9 + - - +
74A LYS 4.3 1.6 - - - -
75A ALA* 1.3 83.7 - - - +
92A LEU* 6.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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