Contacts of the strand formed by residues 64 - 70 (chain A) in PDB entry 4IXU
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 HIS 64 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A HIS* 2.6 58.1 + + - +
25A SER* 3.2 15.6 - - - +
26A VAL* 2.7 32.4 + - - +
62A GLY 3.5 3.5 + - - -
63A CYS* 1.3 71.0 - - - +
65A LEU* 1.3 55.8 + - - +
111A TYR* 4.4 2.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A VAL* 3.3 24.7 - - + +
28A VAL* 4.6 1.3 - - + -
55A MET* 3.5 48.0 - - + +
58A LEU* 3.9 26.7 - - + -
59A SER* 3.2 24.0 - - - +
63A CYS* 3.6 14.3 + - + +
64A HIS* 1.3 73.0 - - - +
66A LYS* 1.3 59.5 - - - +
67A ASP 4.0 0.6 + - - -
111A TYR* 4.6 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A VAL 2.9 7.5 + - - -
27A ALA* 3.2 3.0 - - - +
28A VAL 2.8 25.2 + - - -
55A MET* 5.1 0.4 - - - -
65A LEU* 1.3 75.2 - - - +
67A ASP* 1.3 65.7 + - - +
68A PHE* 3.4 45.8 + - + +
109A ASP* 5.5 5.8 - - - +
111A TYR* 3.5 47.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 3.4 4.6 - - - +
50A ARG* 2.6 49.5 + - - -
55A MET* 3.7 23.3 - - + +
65A LEU 4.0 1.8 + - - -
66A LYS* 1.3 77.9 + - - +
68A PHE* 1.3 61.3 + - - +
69A GLY* 2.7 19.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ALA* 3.7 22.7 - - + -
28A VAL 2.8 19.2 + - - +
29A ILE* 3.9 21.3 - - + -
66A LYS* 3.4 47.6 - - + +
67A ASP* 1.3 73.9 - - - +
69A GLY* 1.3 64.3 + - - +
70A ASP 4.8 0.9 - - - +
71A LEU* 4.2 13.8 - - + +
102A VAL* 3.7 24.5 - - + -
105A ARG* 5.5 8.7 - - + -
106A ALA* 4.0 22.7 - - + -
109A ASP* 5.9 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 3.8 1.7 - - - +
30A GLY 2.8 23.4 + - - +
50A ARG* 3.4 6.9 + - - -
67A ASP* 2.7 21.9 + - - -
68A PHE* 1.3 83.7 - - - +
70A ASP* 1.3 64.3 + - - -
71A LEU* 3.8 0.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLY* 3.5 14.4 - - - +
32A PRO* 4.5 11.9 - - + +
43A GLU 5.3 1.2 - - - +
46A PRO* 3.8 21.8 - - - +
47A ALA* 4.4 9.8 + - - +
50A ARG* 3.5 19.9 + - - -
68A PHE 4.8 1.0 - - - +
69A GLY* 1.3 76.0 - - - -
71A LEU* 1.3 68.8 + - - +
72A SER* 4.5 3.6 + - - -
----------------------------------------------------------
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