Contacts of the helix formed by residues 116 - 125 (chain E) in PDB entry 4OA5
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 GLU 116 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C SER 4.9 2.4 - - - +
182C ASN* 3.3 42.5 - - - +
318C IOD 4.4 15.3 - - + -
89E LYS* 4.4 9.6 - - + +
115E GLY* 1.3 72.2 - - - -
117E ALA* 1.3 74.4 + - - +
118E LEU* 3.0 39.2 + - - +
119E ALA* 3.2 13.4 + - + +
120E GLN* 3.1 19.3 + - - +
138E ASN* 4.3 10.7 + - - -
141E SER* 5.6 0.2 + - - -
145E TYR* 4.2 11.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 117 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E VAL* 3.7 20.9 - - + -
87E ILE* 3.8 17.0 - - + -
115E GLY 3.6 2.2 + - - -
116E GLU* 1.3 77.2 + - - +
118E LEU* 1.3 58.1 + - - +
120E GLN* 3.2 0.3 + - - +
121E LEU* 2.7 39.1 + - + +
137E ALA* 6.1 0.2 - - + -
145E TYR* 3.5 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C SER 4.6 11.2 - - - +
141C SER* 4.5 3.6 - - - +
143C LEU* 3.9 14.4 - - + +
144C ALA* 4.0 11.9 - - + +
312C IOD 2.8 39.5 - - + -
313C IOD 3.8 27.6 - - + +
116E GLU* 3.0 19.3 + - - +
117E ALA* 1.3 76.9 - - - +
119E ALA* 1.3 63.3 + - - +
121E LEU* 3.8 6.7 - - + +
122E ASN* 3.1 22.0 + - - +
144E ALA* 4.0 22.9 - - + -
145E TYR* 4.3 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 119 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C LEU* 3.9 16.5 - - + +
182C ASN* 5.7 2.5 - - - +
185C ALA* 4.4 27.4 - - + +
186C SER* 5.1 2.2 - - - +
189C ALA* 5.9 0.9 - - + -
116E GLU* 3.2 17.5 + - + +
118E LEU* 1.3 79.0 - - - +
120E GLN* 1.3 69.4 + - - +
122E ASN* 3.3 15.8 + - - +
123E THR* 3.3 10.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 120 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E ILE* 3.7 34.1 - - + -
113E LEU* 3.5 27.2 - - + +
114E HIS 3.6 19.6 + - - -
115E GLY* 3.8 19.3 - - - +
116E GLU 3.1 15.6 + - - +
119E ALA* 1.3 81.7 + - - +
121E LEU* 1.3 65.0 + - - +
123E THR* 3.1 24.5 + - - +
124E LEU* 3.1 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 121 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E VAL* 3.6 30.5 - - + -
63E VAL* 4.4 11.4 - - + -
87E ILE* 3.7 12.3 - - + -
117E ALA 2.7 26.5 + - - +
118E LEU* 3.8 9.2 - - + +
120E GLN* 1.3 73.1 - - - +
122E ASN* 1.3 61.2 + - - +
124E LEU* 3.1 14.2 + - + +
125E LYS* 3.2 6.8 + - - +
133E ILE* 4.8 1.8 - - + -
145E TYR* 3.8 31.2 - - + -
148E TRP* 3.1 60.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 122 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C LEU* 4.0 18.6 - - + +
189C ALA* 3.5 26.8 + - + +
193C GLU* 5.4 5.7 - - - +
314C IOD 3.2 30.0 - - + +
118E LEU 3.1 13.6 + - - +
119E ALA* 3.3 11.8 - - - +
120E GLN 3.2 0.2 - - - -
121E LEU* 1.3 78.1 - - - +
123E THR* 1.3 61.3 + - - +
125E LYS* 3.3 38.8 - - - +
126E GLU* 4.5 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 123 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E LEU* 5.1 8.5 - - + -
119E ALA 3.3 9.3 + - - -
120E GLN* 3.1 25.1 + - - +
122E ASN* 1.3 80.2 + - - +
124E LEU* 1.3 63.1 + - + +
125E LYS 3.5 0.3 + - - -
126E GLU* 3.8 18.4 + - - +
127E MET* 5.0 3.0 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
61E VAL* 3.9 26.5 - - + -
85E TYR* 3.9 30.5 - - + -
87E ILE* 4.2 11.4 - - + -
113E LEU* 3.8 24.7 - - + -
120E GLN 3.1 11.3 + - - +
121E LEU* 3.1 11.2 + - + +
123E THR* 1.3 77.2 - - + +
125E LYS* 1.3 64.7 + - - +
126E GLU 3.1 2.9 - - - -
127E MET* 2.9 42.0 + - + +
130E PHE* 3.4 22.3 - - + -
148E TRP* 4.2 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 125 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C LYS* 5.9 1.3 - - - -
193C GLU* 3.5 25.7 + - - -
199C LYS* 6.0 1.0 - - - +
314C IOD 3.9 9.2 - - + -
126D GLU* 4.8 8.1 + - - +
127D MET* 4.1 9.7 - - - +
121E LEU 3.2 9.8 + - - +
122E ASN* 3.3 42.4 - - - +
124E LEU* 1.3 77.2 - - - +
126E GLU* 1.3 82.4 + - - +
128E ALA* 3.1 23.7 + - - +
148E TRP* 4.2 3.1 - - - +
152E TYR* 3.5 42.9 + - + +
----------------------------------------------------------
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