Contacts of the helix formed by residues 116 - 134 (chain E) in PDB entry 7RDB
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 PHE 116 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115E THR* 1.3 74.2 - - - +
117E ARG* 1.3 68.9 + - + +
119E GLN* 3.5 7.7 + - - +
120E THR* 3.5 19.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 117 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115E THR 2.9 1.2 + - - -
116E PHE* 1.3 78.8 - - + +
118E GLN* 1.3 68.3 + - - +
120E THR* 3.1 21.8 + - - +
121E ILE* 3.2 35.7 + - + +
221E ASN* 4.5 14.1 + - - +
224E ILE* 4.0 32.6 - - + +
225E ILE* 6.3 0.2 - - - +
228E MET* 5.4 5.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 118 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115E THR* 3.1 23.6 + - + -
117E ARG* 1.3 79.2 - - - +
119E GLN* 1.3 65.9 + - - +
120E THR 3.0 0.3 + - - -
121E ILE* 3.1 20.7 + - - +
122E ASP* 2.6 67.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 119 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115E THR* 3.1 29.5 - - - +
116E PHE 3.5 8.0 + - - +
117E ARG 3.3 1.0 - - - -
118E GLN* 1.3 78.4 - - - +
120E THR* 1.3 64.6 + - + +
122E ASP* 4.0 4.5 - - - +
123E PHE* 3.2 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 120 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116E PHE 3.5 17.0 - - - +
117E ARG* 3.1 10.0 + - - +
118E GLN 3.1 0.4 - - - -
119E GLN* 1.3 77.0 - - + +
121E ILE* 1.3 69.1 + - - +
123E PHE* 3.1 7.0 + - - +
124E LEU* 2.6 50.1 + - - +
224E ILE* 6.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 121 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E ARG* 3.2 51.1 + - + +
118E GLN* 3.1 22.1 + - - +
120E THR* 1.3 84.5 + - - +
122E ASP* 1.3 55.8 + - - +
124E LEU* 3.1 7.9 + - + +
125E ASN* 2.7 53.8 + - - +
220E THR* 4.7 9.6 - - + -
221E ASN* 4.7 12.3 - - - +
224E ILE* 4.4 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 122 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E GLN* 2.6 61.5 + - - +
119E GLN* 4.0 4.7 - - - +
121E ILE* 1.3 72.4 - - - +
123E PHE* 1.3 57.5 + - - +
125E ASN* 3.6 5.1 + - - +
126E ASP* 3.0 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 123 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119E GLN 3.2 11.4 + - - +
120E THR* 3.1 10.8 + - - +
122E ASP* 1.3 76.0 - - - +
124E LEU* 1.3 63.9 + - + +
126E ASP* 3.1 8.4 + - - +
127E ASN* 2.9 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 124 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120E THR* 2.6 35.9 + - - +
121E ILE* 3.6 4.7 - - + +
123E PHE* 1.3 75.7 - - + +
125E ASN* 1.3 63.3 + - - +
127E ASN* 2.8 28.0 + - - +
128E ILE* 3.1 17.5 + - + +
220E THR* 4.2 21.3 - - + -
224E ILE* 5.5 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 125 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E ILE* 2.7 38.1 + - - +
122E ASP* 4.0 6.1 + - - +
124E LEU* 1.3 71.1 - - - +
126E ASP* 1.3 63.0 + - - +
128E ILE* 3.3 7.7 - - - +
129E ARG* 2.8 28.8 + - - +
157E GLY* 3.2 10.0 + - - -
158E GLU* 3.7 31.5 - - + +
162E ASP* 5.3 3.6 - - - +
220E THR* 2.3 33.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 126 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122E ASP* 3.0 26.8 + - - +
123E PHE* 3.5 7.2 - - - +
124E LEU 3.1 0.2 - - - -
125E ASN* 1.3 79.1 - - - +
127E ASN* 1.3 65.2 + - - +
129E ARG* 4.0 9.7 - - - +
130E ARG* 3.3 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 127 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123E PHE* 2.9 20.4 + - - +
124E LEU* 2.8 25.9 + - - +
126E ASP* 1.3 73.9 - - - +
128E ILE* 1.3 61.2 + - + +
130E ARG* 3.0 9.7 + - - +
131E GLY* 3.0 22.7 + - - -
141E PHE* 5.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 128 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E LEU* 3.1 12.5 + - + +
125E ASN* 3.3 15.0 - - - +
127E ASN* 1.3 76.2 - - + +
129E ARG* 1.3 61.4 + - - +
131E GLY* 3.7 1.5 - - - +
132E ILE* 2.9 35.4 + - + +
141E PHE* 4.1 22.1 - - + -
145E MET* 4.7 13.0 - - - -
156E GLY 4.7 3.4 - - - +
157E GLY* 3.6 22.0 - - - +
162E ASP* 5.4 0.4 - - - +
219E CYS* 5.5 2.9 - - + -
220E THR* 3.5 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 129 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E ASN 2.8 18.2 + - - +
126E ASP* 4.0 13.7 - - - +
127E ASN 3.2 0.2 - - - -
128E ILE* 1.3 75.9 - - - +
130E ARG* 1.3 64.5 + - - +
132E ILE* 3.3 17.7 + - - +
133E GLU* 3.1 24.9 + - - +
162E ASP* 5.7 7.1 + - - +
165E LYS* 4.7 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 130 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E ASP 3.3 11.1 + - - +
127E ASN* 3.0 13.0 + - - +
129E ARG* 1.3 77.7 - - - +
131E GLY* 1.3 61.6 + - - +
133E GLU* 3.5 30.2 + - - +
134E ASN* 3.5 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 131 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127E ASN 3.0 12.0 + - - -
128E ILE 3.3 0.2 + - - -
129E ARG 3.2 0.4 - - - -
130E ARG* 1.3 75.4 - - - +
132E ILE* 1.3 55.4 + - - +
134E ASN* 2.7 27.1 + - - -
135E TYR 2.8 10.7 + - - -
141E PHE* 3.0 38.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 132 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128E ILE* 2.9 25.8 + - + +
129E ARG* 3.3 9.1 + - - +
131E GLY* 1.3 74.8 - - - +
133E GLU* 1.3 62.0 + - - +
135E TYR* 3.2 11.0 + - - +
141E PHE* 4.1 7.9 - - + -
145E MET* 4.8 6.5 - - + -
156E GLY* 4.4 14.8 - - - -
157E GLY 4.7 1.3 - - - +
162E ASP* 3.8 45.3 - - + +
163E TRP* 3.5 39.5 - - + -
165E LYS* 4.5 2.2 - - + -
166E ASN* 3.0 33.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 133 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129E ARG* 3.1 21.1 - - - +
130E ARG* 3.5 17.2 + - - +
131E GLY 3.1 0.4 - - - -
132E ILE* 1.3 76.4 - - - +
134E ASN* 1.3 65.0 + - - +
135E TYR 3.3 0.7 + - - -
136E TYR 5.0 0.2 + - - -
137E ASP* 3.8 9.2 - - - +
165E LYS* 3.6 31.1 - - + +
166E ASN* 3.8 12.0 + - - +
167E GLN* 5.6 3.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 134 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E ARG* 3.6 15.8 + - - +
131E GLY* 2.7 17.1 + - - +
133E GLU* 1.3 78.4 - - - +
135E TYR* 1.3 66.2 + - - +
136E TYR 3.2 2.2 - - - -
137E ASP* 2.8 37.0 + - + +
138E ASP* 3.2 19.5 + - + +
141E PHE* 4.7 4.3 - - + -
----------------------------------------------------------
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