Contacts of the helix formed by residues 103 - 109 (chain A) in PDB entry 1MDU
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 103 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A HIS* 4.2 1.6 - - - -
95A HIS* 5.6 2.0 + - - -
97A GLU* 2.8 33.8 + - - -
101A PHE 3.7 1.2 + - - -
102A GLU* 1.3 74.9 - - - +
104A ALA* 1.3 65.3 + - - +
105A THR* 3.8 8.7 + - - -
106A PHE 3.1 12.1 + - - -
107A LEU* 2.9 20.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLU 3.8 1.4 + - - -
103A SER* 1.3 71.5 - - - +
105A THR* 1.3 52.2 + - - +
107A LEU* 3.2 12.9 + - - +
108A GLY* 2.7 33.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ASP* 6.0 2.0 - - - -
62A HIS* 4.6 6.3 - - + +
95A HIS* 5.9 4.7 - - + +
103A SER* 3.2 8.9 + - - -
104A ALA* 1.3 77.6 - - - +
106A PHE* 1.3 63.7 + - - +
108A GLY* 2.9 15.1 + - - -
109A TYR* 3.4 38.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PHE* 4.2 9.2 - + - -
46A ILE* 4.0 31.6 - - + -
62A HIS* 3.4 38.1 - + + +
64A TRP* 4.0 15.0 - + + -
97A GLU* 3.5 15.0 - - + +
102A GLU* 3.7 30.3 - - + -
103A SER* 3.1 20.2 + - - +
105A THR* 1.3 78.7 - - - +
107A LEU* 1.3 63.3 + - - +
109A TYR* 2.9 33.1 + + - +
110A PHE* 3.5 23.9 - + - -
114A LEU* 4.0 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLU* 3.8 33.4 - - + +
103A SER 2.9 16.5 + - - +
104A ALA* 3.5 11.2 - - - +
106A PHE* 1.3 76.8 - - - +
108A GLY* 1.3 61.9 + - - +
109A TYR 3.2 1.0 + - - -
110A PHE* 3.3 22.4 + - - +
113A GLY* 5.8 0.3 - - - -
114A LEU* 3.9 32.1 - - + +
116A TYR* 5.2 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ALA 2.7 14.7 + - - -
105A THR* 2.9 8.8 + - - -
107A LEU* 1.3 77.4 - - - +
109A TYR* 1.3 61.7 + - - +
110A PHE 3.2 2.9 + - - -
111A LYS* 4.7 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 3.9 32.3 - - + +
46A ILE* 4.7 1.3 - - + -
48A LYS* 3.6 53.1 + - + +
60A ASP* 3.9 9.2 + - - +
62A HIS* 3.1 39.4 + + - -
105A THR* 3.4 29.3 - - + +
106A PHE* 2.9 30.5 + + - +
108A GLY* 1.3 78.5 - - - +
110A PHE* 1.3 71.7 + + + +
111A LYS* 3.7 11.5 + - - +
472A TRS 2.8 15.6 + - - -
----------------------------------------------------------
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