Contacts of the helix formed by residues 75 - 82 (chain A) in PDB entry 1MNM
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 PRO 75 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLN* 4.0 12.8 - - - +
73A SER 4.8 0.4 - - - +
74A THR* 1.3 87.1 - - + +
76A LYS* 1.3 63.6 + - + +
78A GLU* 3.5 26.8 + - - +
79A PRO* 3.8 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLN* 2.9 45.0 + - + +
75A PRO* 1.3 74.9 - - + +
77A PHE* 1.3 58.1 + - - +
79A PRO* 3.4 13.9 - - - +
93B CYS* 3.4 38.8 - - - +
94B LEU* 4.2 24.6 + - + +
95B ASN* 4.4 0.4 - - - +
96B ALA* 4.1 24.5 + - + +
97B PRO 4.0 11.9 - - - -
98B ASP 3.7 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLN* 3.7 29.1 + - + -
58A VAL 3.6 27.6 - - - +
59A LEU* 3.7 17.6 - - + +
73A SER* 4.1 9.3 - - - -
74A THR* 3.2 7.6 + - - +
76A LYS* 1.3 74.6 - - - +
78A GLU* 1.3 65.9 + - - +
79A PRO* 3.3 4.3 - - - -
80A ILE* 3.1 36.1 + - + +
81A VAL* 4.1 2.3 + - - +
61B LEU* 4.1 23.3 - - + -
63B VAL* 3.7 23.3 - - + -
90B ILE* 4.0 20.0 - - + -
93B CYS* 4.2 10.1 - - + -
94B LEU* 3.8 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A SER* 3.5 25.9 + - - +
74A THR 3.2 5.6 + - - +
75A PRO* 3.6 22.8 - - - +
76A LYS 3.3 0.4 - - - -
77A PHE* 1.3 76.7 - - - +
79A PRO* 1.3 67.5 - - + +
80A ILE 2.9 1.7 + - - -
81A VAL* 3.0 12.9 + - + +
82A THR* 2.9 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A PRO 3.8 5.6 - - - +
76A LYS 3.4 17.3 - - - +
77A PHE 3.3 1.6 - - - -
78A GLU* 1.3 91.6 - - + +
80A ILE* 1.3 58.6 + - - +
81A VAL 3.3 0.4 - - - -
82A THR* 3.3 11.0 - - - +
83A GLN* 3.1 53.2 + - - +
86A GLY 4.8 2.6 + - - -
89B LEU* 6.1 1.3 - - + +
93B CYS* 3.7 16.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU* 4.0 24.0 - - + -
61A LEU* 5.8 0.4 - - + -
77A PHE* 3.3 28.5 - - + +
78A GLU 2.9 1.0 + - - -
79A PRO* 1.3 80.4 - - - +
81A VAL* 1.3 62.6 + - + +
82A THR 3.5 0.2 - - - -
86A GLY* 3.4 32.5 - - - -
87A ARG 3.4 2.6 + - - -
90A ILE* 4.0 13.1 - - + +
61B LEU* 5.2 0.2 - - + -
80B ILE* 6.4 3.4 - - + -
89B LEU* 4.2 21.5 - - + -
90B ILE* 4.4 17.3 - - + -
93B CYS* 3.5 29.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU* 4.2 8.7 - - + -
61A LEU* 3.5 31.6 - - + -
71A THR* 3.7 28.3 - - + +
73A SER* 4.1 20.9 - - - +
77A PHE 4.6 0.9 - - - +
78A GLU* 3.0 11.9 + - + +
80A ILE* 1.3 81.6 - - + +
82A THR* 1.3 64.1 + - + +
87A ARG* 3.0 31.8 + - - +
90A ILE* 4.2 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLU* 2.9 39.9 + - + +
79A PRO* 3.3 9.4 - - - +
81A VAL* 1.3 87.6 - - + +
83A GLN* 1.3 68.5 + - - +
87A ARG* 3.8 15.7 + - - +
----------------------------------------------------------
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