Contacts of the helix formed by residues 64 - 75 (chain A) in PDB entry 3IE7
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 64 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 3.8 15.4 - - + +
61A GLY 3.7 4.0 - - - +
63A ASP* 1.3 75.2 - - - +
65A LEU* 1.3 64.5 + - - +
66A ASP* 3.4 2.7 - - - -
67A LYS* 3.3 19.5 + - + +
68A LEU* 3.2 19.4 + - - +
88A SER* 3.8 10.4 - - - +
89A THR* 3.0 52.0 + - - +
91A GLU* 5.7 4.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
60A ALA* 4.1 17.7 - - + -
61A GLY 3.6 16.0 + - - +
62A SER* 3.3 17.2 + - - +
63A ASP 3.6 0.2 - - - -
64A ASN* 1.3 74.8 + - - +
66A ASP* 1.3 63.2 + - - +
68A LEU* 3.2 5.4 + - + +
69A TYR* 2.9 79.6 + - + +
83A VAL* 3.8 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASN 3.4 0.8 - - - -
65A LEU* 1.3 78.5 - - - +
67A LYS* 1.3 56.3 + - - +
69A TYR* 3.4 9.6 + - - +
70A ALA* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 3.6 25.1 - - + -
13A ARG* 4.5 10.3 - - - +
34A PHE* 3.6 45.5 - - - -
64A ASN* 3.3 20.5 + - + +
65A LEU 3.2 0.4 - - - -
66A ASP* 1.3 76.4 - - - +
68A LEU* 1.3 64.9 + - - +
70A ALA* 3.2 7.5 + - - +
71A ILE* 3.1 32.2 + - + +
91A GLU* 4.6 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PRO* 5.0 6.1 - - + -
10A ALA 4.2 20.0 - - - +
11A ILE* 4.0 18.8 - - + +
36A CYS* 4.9 4.7 - - + -
41A LEU* 4.5 11.0 - - + -
60A ALA* 3.6 31.0 - - + -
64A ASN 3.2 10.1 + - - +
65A LEU* 3.6 9.4 - - + +
67A LYS* 1.3 79.1 - - - +
69A TYR* 1.3 68.2 + - + +
71A ILE* 3.1 8.9 + - + +
72A LEU* 2.9 51.4 + - + +
81A PHE* 5.2 5.4 - - + -
89A THR* 4.0 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LEU* 2.9 62.2 + - + +
66A ASP* 3.8 9.6 - - - +
68A LEU* 1.3 87.6 - - + +
70A ALA* 1.3 57.3 + - - +
72A LEU* 3.3 11.3 + - + +
73A LYS* 2.9 28.9 + - - +
79A HIS* 3.4 40.8 - + + +
81A PHE* 4.0 22.5 + - + +
83A VAL* 4.2 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASP 2.9 19.0 + - - +
67A LYS* 3.2 8.7 + - + +
69A TYR* 1.3 76.0 - - - +
71A ILE* 1.3 61.5 + - + +
73A LYS* 3.4 10.2 + - - +
74A GLU* 2.8 33.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 3.6 38.1 - - + -
34A PHE* 3.9 19.5 - - + -
35A ASP* 3.6 13.9 - - - +
36A CYS* 3.5 33.9 - - + +
67A LYS* 3.1 21.1 + - + +
68A LEU* 3.4 7.6 - - + +
70A ALA* 1.3 75.4 - - + +
72A LEU* 1.3 64.7 + - - +
74A GLU* 3.1 27.9 + - - +
75A LYS* 3.1 21.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A CYS* 4.0 17.7 - - + -
41A LEU* 4.0 17.9 - - + -
68A LEU* 2.9 32.4 + - + +
69A TYR* 3.6 11.7 - - + +
71A ILE* 1.3 77.9 - - - +
73A LYS* 1.3 60.5 + - - +
75A LYS* 3.1 3.5 + - - +
76A HIS 3.0 3.8 + - - -
77A ILE* 2.9 62.1 + - + +
79A HIS* 3.5 33.7 - - + +
81A PHE* 4.1 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TYR 2.9 16.5 + - - +
70A ALA* 3.7 9.0 - - - +
71A ILE 3.2 0.2 - - - -
72A LEU* 1.3 77.6 - - - +
74A GLU* 1.3 60.7 + - - +
76A HIS* 3.1 27.5 + - - +
77A ILE 4.9 1.8 - - - +
79A HIS* 5.6 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PHE* 4.9 8.7 - - - +
70A ALA* 2.8 25.4 - - - +
71A ILE* 3.1 26.1 + - - +
73A LYS* 1.3 77.6 - - + +
75A LYS* 1.3 68.6 + - + +
76A HIS* 4.1 12.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PHE 4.2 11.2 + - - -
35A ASP* 3.2 35.8 + - - +
36A CYS* 4.4 10.1 - - - -
45A GLY* 4.7 6.6 - - - +
48A SER* 3.9 8.1 - - - -
49A LYS* 6.1 0.2 - - - +
71A ILE* 3.1 20.5 + - + +
72A LEU 3.1 3.1 + - - +
73A LYS 3.1 0.4 - - - -
74A GLU* 1.3 85.8 - - - +
76A HIS* 1.3 75.1 + - - +
77A ILE* 3.3 30.1 + - + +
288A SER* 5.7 0.4 + - - -
289A SER* 5.5 4.6 + - - -
----------------------------------------------------------
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