Contacts of the helix formed by residues 137 - 151 (chain E) in PDB entry 1S72
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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E VAL* 3.9 28.9 - - + +
30E THR 5.6 0.7 - - - +
31E ARG* 6.1 0.8 - - - -
121E ASP 6.1 2.5 - - - +
135E GLY 3.5 0.2 - - - -
136E PRO* 1.3 80.6 - - + +
138E ILE* 1.3 63.8 + - - +
139E GLU* 2.8 26.5 + - - +
140E ALA* 3.0 22.8 + - + +
141E VAL* 3.0 24.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 138 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27810 U 3.9 26.5 - - - +
27820 G 4.5 2.5 - - - +
68E HIS* 6.1 0.9 - - - +
71E ASN* 3.6 40.4 - - + +
72E MET* 6.5 0.4 - - + -
80E TRP* 3.5 49.0 - - + +
82E TYR* 4.1 20.2 - - + +
136E PRO 3.6 5.5 + - - -
137E ASP* 1.3 72.7 + - - +
139E GLU* 1.3 65.9 + - + +
141E VAL* 4.6 3.1 - - - -
142E GLY* 2.8 27.7 + - - -
172E PRO* 5.2 1.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
27800 C 4.0 4.1 + - - +
27810 U 2.7 45.7 + - - +
27940 G 3.0 26.1 + - - +
27950 C 4.6 9.7 + - - +
31E ARG* 4.7 27.7 + - - +
68E HIS* 4.3 3.7 - - - +
137E ASP* 2.8 18.4 + - - +
138E ILE* 1.3 82.2 - - + +
140E ALA* 1.3 62.7 + - - +
142E GLY* 3.9 0.5 - - - -
143E GLN* 3.1 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 140 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119E HIS* 3.5 36.5 - - + +
120E GLY* 4.5 5.4 - - - +
121E ASP 5.3 0.4 - - - +
122E THR* 3.6 6.3 - - - +
137E ASP* 3.0 26.4 + - + +
139E GLU* 1.3 76.9 - - - +
141E VAL* 1.3 63.6 + - - +
143E GLN* 3.3 2.1 + - - +
144E THR* 2.8 28.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 141 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E TRP* 4.1 6.3 - - + +
82E TYR* 3.7 18.2 - - + -
122E THR* 3.5 19.3 - - - +
133E VAL* 3.5 36.9 - - + +
134E SER* 3.7 2.7 - - - -
135E GLY* 3.4 34.5 - - - +
137E ASP 3.0 16.7 + - - +
138E ILE* 4.1 4.5 - - - +
140E ALA* 1.3 74.4 - - - +
142E GLY* 1.3 64.1 + - - +
144E THR* 3.2 2.8 + - - -
145E ALA* 2.9 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 142 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27800 C 3.5 18.3 + - - +
27810 U 4.8 0.2 - - - -
82E TYR* 3.8 26.8 - - - -
138E ILE 2.8 18.3 + - - -
141E VAL* 1.3 77.7 - - - +
143E GLN* 1.3 55.0 + - - +
145E ALA* 3.4 3.1 + - - +
146E ALA* 3.0 28.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
27790 G 2.8 35.2 + - - +
27800 C 3.0 29.5 + - - +
27950 C 5.1 4.5 - - - +
27960 U 3.4 29.6 + - - +
119E HIS* 4.1 11.9 - - + +
139E GLU 3.1 18.5 + - - +
140E ALA 3.8 3.4 - - - +
142E GLY* 1.3 71.9 - - - +
144E THR* 1.3 57.8 + - - +
146E ALA* 3.1 5.8 + - - +
147E ASP* 2.6 72.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 144 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102E VAL* 5.3 0.9 - - + -
116E THR* 6.3 1.1 - - + -
117E THR 5.5 0.4 - - - +
118E ILE* 3.8 29.6 - - + -
119E HIS* 3.1 26.2 + - - +
122E THR* 3.9 3.4 - - + +
124E VAL* 3.9 20.0 - - + -
133E VAL* 3.9 9.6 - - + -
140E ALA 2.8 22.9 + - - -
141E VAL 3.6 4.3 - - - -
143E GLN* 1.3 76.4 - - - +
145E ALA* 1.3 63.2 + - - +
147E ASP* 3.9 8.5 - - - +
148E ILE* 3.1 29.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 145 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82E TYR* 4.0 23.8 - - + -
84E MET* 3.7 11.8 - - - +
133E VAL* 4.1 11.8 - - + +
141E VAL 2.9 12.7 + - - +
142E GLY 3.6 8.5 - - - +
144E THR* 1.3 76.9 - - - +
146E ALA* 1.3 64.1 + - - +
148E ILE* 3.0 14.4 + - - +
149E GLU 3.1 9.7 + - - -
168E ILE* 3.3 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 146 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27790 G 3.8 11.2 - - - +
27800 C 3.7 30.7 - - - +
142E GLY 3.0 17.3 + - - +
143E GLN* 3.4 9.4 - - - +
145E ALA* 1.3 77.7 - - - +
147E ASP* 1.3 52.7 + - - +
149E GLU* 2.9 8.6 + - - +
150E GLN* 2.7 39.6 + - + +
168E ILE* 4.3 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 147 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27960 U 3.5 11.8 + - - +
27970 C 6.1 0.3 - - - +
116E THR* 3.6 23.5 + - + +
117E THR 4.8 0.4 - - - +
119E HIS* 2.8 35.3 + - - -
143E GLN* 2.6 38.7 + - - +
144E THR* 3.9 5.4 - - - +
146E ALA* 1.3 72.5 - - - +
148E ILE* 1.3 57.9 + - - +
150E GLN* 3.6 10.4 - - - +
151E LEU* 2.7 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 148 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E MET* 3.2 37.2 - - + -
102E VAL* 3.7 40.4 - - + -
104E ILE* 4.8 6.4 - - + +
116E THR* 4.4 4.5 - - + -
124E VAL* 4.2 15.5 - - + -
131E LEU* 4.5 5.4 - - + -
133E VAL* 4.4 2.7 - - + -
144E THR* 3.1 19.8 + - + +
145E ALA 3.0 9.6 + - - +
147E ASP* 1.3 76.8 - - - +
149E GLU* 1.3 64.4 + - - +
151E LEU* 3.1 21.8 - - - +
152E THR* 3.8 7.8 + - - +
166E VAL* 3.8 22.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 149 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E MET* 5.4 0.7 - - - -
145E ALA 3.1 6.1 + - - +
146E ALA* 2.9 11.2 + - - +
148E ILE* 1.3 79.9 - - - +
150E GLN* 1.3 68.8 + - - +
152E THR* 2.9 23.4 + - - +
153E ARG* 3.9 2.3 + - - -
166E VAL 3.1 23.6 - - - +
167E TYR* 3.2 22.5 - - + +
168E ILE* 2.7 44.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 150 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27780 A 2.8 45.2 + - + +
27790 G 3.7 28.8 + - - +
146E ALA 2.7 27.3 + - - +
147E ASP* 3.6 11.4 - - - +
149E GLU* 1.3 80.7 - - - +
151E LEU* 1.3 54.6 + - - +
153E ARG* 2.7 43.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 151 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102E VAL* 4.2 6.1 - - + +
104E ILE* 4.3 18.2 - - + -
114E ARG* 2.8 47.3 + - + +
115E ARG* 3.0 51.6 - - - +
116E THR* 3.6 19.5 - - + -
147E ASP 2.7 13.2 + - - +
148E ILE* 3.1 15.7 - - - +
149E GLU 3.1 0.2 - - - -
150E GLN* 1.3 76.7 - - - +
152E THR* 1.3 55.6 + - - +
153E ARG 3.4 0.7 - - - -
----------------------------------------------------------
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