Contacts of the helix formed by residues 137 - 150 (chain F) in PDB entry 4MJI
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 ASP 137 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F TYR* 2.3 38.4 + - - -
121F LYS* 2.9 20.5 + - - +
123F TYR* 4.9 0.2 - - - -
135F ALA 3.0 3.4 + - - -
136F ALA* 1.3 83.6 - - + +
138F THR* 1.3 59.9 + - - +
139F ALA 2.7 5.4 + - - -
140F ALA* 2.6 27.5 + - + +
141F GLN* 3.0 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 138 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137F ASP* 1.3 72.3 + - - +
139F ALA* 1.3 69.9 + - - +
141F GLN* 2.9 24.2 + - + +
142F ILE* 3.3 14.3 + - + +
145F ARG* 5.0 1.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 139 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F TYR* 3.7 25.5 - - + +
85F TYR* 3.4 43.2 - - + +
123F TYR* 3.2 10.3 + - - +
137F ASP* 2.7 5.2 + - - +
138F THR* 1.3 76.6 - - - +
140F ALA* 1.3 63.2 + - - +
142F ILE* 2.9 28.5 + - - +
143F THR 3.5 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 140 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123F TYR* 3.2 53.5 + - + +
124F ILE* 3.9 2.6 - - + +
135F ALA* 3.6 11.0 - - + +
136F ALA 3.9 2.7 - - - +
137F ASP* 2.6 26.4 + - - +
139F ALA* 1.3 74.2 - - - +
141F GLN* 1.3 56.2 + - - +
143F THR* 3.3 3.5 - - - -
144F GLN* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 141 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E ARG* 5.2 13.5 - - - +
135F ALA* 3.6 22.2 + - + -
137F ASP* 3.0 23.9 + - - +
138F THR* 2.9 19.0 + - - +
140F ALA* 1.3 76.5 - - - +
142F ILE* 1.3 58.9 + - - +
144F GLN* 3.4 15.1 - - + +
145F ARG* 3.1 43.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 142 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F TYR* 3.4 40.4 - - + +
138F THR* 3.3 13.8 + - + +
139F ALA* 2.9 22.4 + - - +
141F GLN* 1.3 72.7 - - - +
143F THR* 1.3 56.3 + - - +
144F GLN 3.0 0.7 - - - -
145F ARG* 2.5 49.0 + - - +
146F LYS* 2.8 33.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 143 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F TYR* 3.5 1.2 - - - -
123F TYR* 2.6 31.2 + - + -
124F ILE* 3.7 13.2 - - + -
139F ALA 3.5 0.6 + - - -
140F ALA 3.3 9.0 - - - -
142F ILE* 1.3 79.3 - - - +
144F GLN* 1.3 64.7 + - - +
146F LYS* 2.9 4.3 + - - +
147F TRP* 2.9 59.3 + - + -
8H ILE* 3.1 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 144 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E GLN* 5.0 4.0 + - - +
124F ILE* 3.7 17.0 - - + -
133F TRP* 3.1 51.5 + - - +
135F ALA* 4.1 12.3 + - + +
140F ALA 2.9 16.5 + - - +
141F GLN* 3.4 19.6 - - + +
142F ILE 3.0 0.2 - - - -
143F THR* 1.3 79.2 - - - +
145F ARG* 1.3 64.0 + - + +
147F TRP* 3.2 4.6 + - - +
148F GLU* 3.1 48.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 145 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138F THR* 5.0 1.6 + - - +
141F GLN* 3.1 25.7 + - - +
142F ILE* 2.5 46.2 + - - +
144F GLN* 1.3 76.2 - - + +
146F LYS* 1.3 61.8 + - + -
147F TRP 3.3 0.3 + - - -
148F GLU* 3.7 15.9 + - - +
149F ALA* 3.5 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 146 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F TYR* 4.0 14.9 + - - +
142F ILE* 2.8 38.0 + - + +
143F THR* 2.9 7.6 + - - +
145F ARG* 1.3 80.9 - - + +
147F TRP* 1.3 60.8 + - - +
148F GLU 3.6 0.2 - - - -
149F ALA* 3.9 6.9 - - - +
150F ALA* 3.4 22.7 + - - +
8H ILE* 3.8 29.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 147 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F TYR* 3.7 31.9 - + - -
123F TYR* 6.2 0.2 - + - -
124F ILE* 3.6 30.1 - - + -
133F TRP* 3.7 38.6 - + + +
143F THR* 2.9 36.3 + - + +
144F GLN* 3.8 4.3 - - - +
145F ARG 3.1 0.2 - - - -
146F LYS* 1.3 87.2 - - + +
148F GLU* 1.3 64.9 + - - +
149F ALA 3.1 0.9 - - - -
150F ALA* 3.9 4.3 - - + +
151F ARG* 3.2 1.7 + - - -
152F GLU* 2.8 49.7 + - + +
153F ALA 4.4 1.4 + - - -
6H PRO* 3.4 26.1 - - + +
7H SER 2.7 27.9 + - - -
8H ILE* 3.9 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 148 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133F TRP* 4.6 11.7 - - + +
144F GLN* 3.1 45.6 + - - +
145F ARG* 4.0 16.2 - - - +
147F TRP* 1.3 79.5 - - - +
149F ALA* 1.3 59.1 + - - +
151F ARG* 3.4 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 149 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145F ARG 3.5 14.3 + - - +
146F LYS* 3.9 8.3 - - - +
147F TRP 3.1 0.4 - - - -
148F GLU* 1.3 76.4 - - - +
150F ALA* 1.3 58.6 + - - +
151F ARG* 3.0 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 150 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146F LYS 3.4 15.5 + - - +
147F TRP* 3.6 5.6 + - + +
148F GLU 3.5 0.4 - - - -
149F ALA* 1.3 76.7 - - - +
151F ARG* 1.3 68.1 + - - +
152F GLU* 3.4 14.6 + - + +
155F GLN* 5.4 5.0 + - - -
----------------------------------------------------------
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