Contacts of the strand formed by residues 44 - 50 (chain E) in PDB entry 1MI5
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 GLU 44 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D PHE 4.5 6.4 - - - +
107D GLY 5.6 0.2 - - - +
35E TYR* 3.1 5.3 - - - -
36E GLN* 2.7 52.6 + - + +
41E GLN* 4.6 10.4 - - - +
42E GLY 2.8 16.7 - - - +
43E PRO* 1.3 94.3 - - - +
45E PHE* 1.3 71.0 + - - +
46E LEU* 3.8 2.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 45 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D TYR* 3.5 9.0 - - - -
103D LYS* 3.4 31.0 - - + -
104D LEU 4.5 5.2 + - - +
33E PHE* 4.1 9.2 - + + -
34E TRP 4.1 3.6 - - - -
35E TYR* 3.4 29.7 - + + -
43E PRO 4.3 0.2 + - - -
44E GLU* 1.3 76.8 - - - +
46E LEU* 1.3 71.1 + - - +
47E THR 3.2 35.4 - - - -
48E TYR* 3.5 8.1 - - + -
56E ASP* 3.0 44.2 - - - -
58E SER* 3.7 10.8 - - - -
59E GLY* 3.6 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E TRP* 2.8 18.5 + - + +
35E TYR* 3.8 9.9 - - - +
36E GLN* 3.7 34.8 - - + +
44E GLU* 3.8 9.9 - - + +
45E PHE* 1.3 79.2 - - - +
47E THR* 1.3 62.9 + - + +
57E LYS 3.7 2.1 - - - +
59E GLY* 3.2 42.9 + - - +
60E LEU* 3.3 19.5 + - + +
61E PRO* 3.8 17.0 - - + -
65E PHE* 5.2 3.6 - - + -
77E LEU* 4.1 15.0 - - + -
90E TYR* 3.8 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 47 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E LEU 4.2 0.2 - - - +
33E PHE* 3.6 0.5 - - - -
34E TRP* 3.0 55.3 + - + -
45E PHE* 3.2 13.5 - - - -
46E LEU* 1.3 84.1 - - + +
48E TYR* 1.3 65.2 + - - +
49E PHE* 4.1 11.4 - - + -
54E GLN* 2.8 34.8 + - - +
56E ASP 3.2 9.4 + - - -
57E LYS* 4.2 2.0 - - - -
60E LEU* 4.3 8.7 - - + -
67E ALA* 4.1 11.7 - - + -
77E LEU* 5.6 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 48 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLN* 3.7 19.5 - - - -
76A GLU* 4.1 1.2 + - - -
100D TYR* 3.2 29.2 - + - +
31E SER* 2.7 27.8 + - - -
32E LEU 3.5 7.0 - - - -
33E PHE* 3.4 41.3 - + - -
45E PHE* 3.5 7.0 - - + -
47E THR* 1.3 75.7 + - - +
49E PHE* 1.3 89.5 + - - +
50E GLN* 3.8 21.3 - - + +
54E GLN* 3.3 10.7 - - - +
55E LEU* 3.2 31.9 + - + -
56E ASP* 2.8 12.3 + - + +
98E GLN* 3.5 15.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 49 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E VAL 3.6 0.5 - - - +
31E SER* 3.3 3.8 - - - -
32E LEU* 2.8 45.2 + - + +
34E TRP* 4.5 0.9 - + - -
47E THR* 4.1 10.3 - - + -
48E TYR* 1.3 89.8 - - - +
50E GLN* 1.3 59.4 + - - +
51E ASN 3.6 9.0 - - - +
52E GLU 3.7 17.7 - - - -
53E ALA 3.4 3.4 - - - -
54E GLN* 3.4 51.8 - - + -
67E ALA* 4.0 13.2 - - + -
68E GLU* 3.7 21.3 - - - -
69E ARG* 3.7 33.4 - - + +
75E SER* 4.1 14.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 50 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLN* 3.0 42.8 + - - +
75A ARG* 3.3 26.5 - - - +
76A GLU* 3.5 25.0 - - + +
79A ARG* 5.5 6.0 + - + +
30E VAL* 4.1 10.8 - - + -
48E TYR* 3.8 17.2 + - + +
49E PHE* 1.3 70.5 - - - +
51E ASN* 1.3 73.9 + - + +
53E ALA* 2.8 24.6 + - + +
55E LEU* 3.6 22.9 - - + +
98E GLN* 4.6 2.8 + - - -
----------------------------------------------------------
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