Contacts of the helix formed by residues 137 - 144 (chain E) in PDB entry 3J41
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 137 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E PHE* 3.4 3.7 - - - -
98E GLY 3.6 10.8 - - - +
99E TYR* 3.6 21.4 + - + -
130E ILE* 5.3 3.5 - - - +
131E ASP* 3.1 29.7 + - - -
136E VAL* 1.3 73.8 - - - +
138E TYR* 1.3 57.5 + - - +
139E GLU* 3.0 20.4 - - - +
140E GLU* 2.8 52.9 + - - +
141E PHE* 3.1 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 138 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E ALA* 3.6 10.8 + - - +
82E GLU* 2.6 54.6 + - + +
85E ILE* 3.5 32.8 - - + -
86E ARG* 3.9 24.2 - - + -
89E PHE* 3.9 12.6 - + + -
98E GLY 4.2 3.4 + - - +
137E ASN* 1.3 72.9 - - - +
139E GLU* 1.3 79.6 + - + +
141E PHE* 3.1 18.9 + - - +
142E VAL* 3.2 27.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 139 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E ILE* 4.7 7.4 - - + -
137E ASN* 3.0 24.4 - - - +
138E TYR* 1.3 96.2 + - + +
140E GLU* 1.3 56.5 + - - +
142E VAL* 3.4 8.3 + - - +
143E GLN* 2.9 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 140 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E ILE* 4.4 1.9 - - - +
128E ALA* 4.6 3.4 - - - +
129E ASP* 3.3 29.8 - - - +
130E ILE* 4.0 23.0 - - + +
131E ASP* 4.1 1.8 - - - -
135E GLN 3.4 3.1 - - - +
136E VAL* 3.3 20.0 - - + +
137E ASN* 2.8 45.4 + - - +
139E GLU* 1.3 74.0 - - - +
141E PHE* 1.3 56.8 + - - +
143E GLN* 4.0 1.5 - - - +
144E MET* 2.8 40.0 + - + +
204E CA 2.6 30.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 141 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A LEU* 6.4 2.0 - - + -
241A ARG* 3.2 33.9 - - - -
72E MET 5.3 5.4 - - - -
75E LYS* 5.8 5.2 - - + -
85E ILE* 3.9 27.6 - - + -
89E PHE* 3.6 19.3 - + + -
100E ILE* 5.2 3.6 - - + -
136E VAL* 4.0 17.0 - - + -
137E ASN 3.1 18.9 + - - +
138E TYR 3.1 8.2 + - - +
140E GLU* 1.3 75.5 - - - +
142E VAL* 1.3 68.2 + - + +
144E MET* 3.5 8.4 + - + +
145E MET* 3.3 56.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E PHE* 4.5 22.0 - - + -
72E MET* 3.8 26.4 - - + +
73E ALA* 4.1 24.9 - - + +
85E ILE* 5.9 0.9 - - + -
138E TYR* 3.2 30.5 + - + +
139E GLU* 3.4 8.7 + - - +
141E PHE* 1.3 80.4 - - + +
143E GLN* 1.3 58.8 + - - +
145E MET* 3.0 15.3 + - - +
146E THR* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 143 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E GLU* 4.3 22.0 - - - +
12E PHE* 4.6 10.9 - - - -
128E ALA* 4.8 8.0 - - + +
130E ILE* 4.6 14.1 - - + -
139E GLU 2.9 19.5 + - - +
140E GLU* 4.0 4.9 - - - +
142E VAL* 1.3 72.0 - - - +
144E MET* 1.3 55.8 + - - +
145E MET 3.1 3.6 - - - -
146E THR* 2.9 52.4 + - - +
147E ALA* 3.1 8.4 + - - +
148E LYS* 5.6 4.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 144 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B LYS* 2.8 32.2 + - - +
124E MET 3.8 17.5 - - - +
125E ILE* 3.4 28.7 - - + +
127E GLU* 3.8 19.5 - - + +
128E ALA* 3.8 22.1 - - + +
129E ASP 5.0 0.2 - - - -
136E VAL* 3.7 41.1 - - + -
140E GLU* 2.8 32.3 + - + +
141E PHE* 3.8 9.4 - - + +
142E VAL 3.4 0.2 - - - -
143E GLN* 1.3 69.4 - - - +
145E MET* 1.3 62.0 + - + +
147E ALA* 5.2 2.0 - - - -
----------------------------------------------------------
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