Contacts of the helix formed by residues 149 - 160 (chain D) in PDB entry 2AXZ
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 149 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10C GLN* 4.6 5.4 - - + -
11C ILE* 3.5 39.5 - - + -
14C GLU* 3.8 24.9 - - + -
15C LEU* 4.2 16.2 - - + -
56C VAL* 3.8 25.1 - - + -
60C GLU* 3.1 11.9 - - - +
64C ARG* 3.4 28.7 - - - +
107D LEU* 4.8 2.2 - - + -
145D ARG* 3.6 15.9 - - - -
147D THR* 4.1 14.4 - - + -
148D PHE* 1.3 75.6 - - - +
150D GLY* 1.3 69.3 + - - +
151D ILE* 3.2 5.6 - - + -
152D ASP* 2.7 36.0 + - - +
153D TYR* 3.3 6.8 - - - -
186D TYR* 3.9 4.3 - - - -
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Residues in contact with GLY 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C GLU* 3.0 24.0 + - - -
149D PHE* 1.3 70.0 - - - +
151D ILE* 1.3 62.3 + - - +
153D TYR* 3.1 4.3 + - - -
154D GLU* 3.0 20.0 + - - +
185D ASP 5.5 0.2 - - - -
186D TYR* 3.4 23.8 - - - -
189D THR* 3.4 18.3 + - - -
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Residues in contact with ILE 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C GLY 3.9 9.6 - - - +
56C VAL* 4.6 8.3 - - + -
57C ASN* 5.5 2.1 - - - +
60C GLU* 4.3 2.2 + - - -
107D LEU* 3.5 59.5 - - + +
108D GLN* 3.7 34.5 - - - +
111D SER* 3.8 16.6 - - - -
149D PHE* 4.3 13.5 - - + -
150D GLY* 1.3 72.6 - - - +
152D ASP* 1.3 59.3 + - - +
154D GLU* 3.3 18.1 + - - +
155D ILE* 2.9 26.4 + - + +
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Residues in contact with ASP 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D LEU* 3.5 13.5 - - - +
142D TYR* 2.9 29.0 + - + +
145D ARG* 2.7 41.5 + - - -
148D PHE* 3.4 2.9 - - + -
149D PHE* 2.7 34.9 + - - +
151D ILE* 1.3 74.9 - - - +
153D TYR* 1.3 59.4 + - - +
155D ILE* 3.1 4.7 + - - +
156D VAL* 2.9 28.8 + - - +
175D MSE 3.5 18.5 - - + +
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Residues in contact with TYR 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D PHE* 3.7 24.6 + - + +
149D PHE 3.3 14.4 - - - -
150D GLY 3.1 6.1 + - - +
152D ASP* 1.3 76.0 - - - +
154D GLU* 1.3 52.0 + - - +
156D VAL* 2.9 10.2 - - - +
157D SER* 2.6 38.8 + - - -
175D MSE 2.6 51.9 + - + +
176D TYR* 3.6 22.7 - + - -
178D ILE* 3.2 18.7 - - + +
186D TYR* 3.7 22.9 + + - -
189D THR* 3.8 20.4 - - - +
190D ILE* 3.6 20.9 - - + -
193D VAL* 3.1 3.5 - - + +
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Residues in contact with GLU 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D LYS* 2.8 28.4 + - - -
111D SER* 3.0 22.8 + - - +
150D GLY 3.0 11.7 + - - +
151D ILE* 3.3 19.4 - - + +
152D ASP 3.1 0.2 - - - -
153D TYR* 1.3 74.9 - - - +
155D ILE* 1.3 64.2 + - - +
157D SER* 3.2 7.0 + - - -
158D ASN* 2.9 28.6 + - - -
189D THR* 3.9 15.1 - - + +
5H VAL* 3.5 19.3 - - - +
6H PHE* 3.2 13.8 - - - -
7H VAL* 3.2 24.4 + - - +
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Residues in contact with ILE 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D LEU* 3.3 38.1 - - + +
110D PHE* 3.4 42.0 - - + -
111D SER* 3.7 22.4 - - - -
114D LEU* 3.4 12.1 - - + +
142D TYR* 3.8 23.3 - - + +
151D ILE 2.9 17.9 + - - +
152D ASP 3.1 6.9 + - - +
154D GLU* 1.3 75.7 - - - +
156D VAL* 1.3 54.5 + - - +
158D ASN* 3.1 2.4 + - - +
159D LEU* 2.7 41.0 + - + +
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Residues in contact with VAL 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D TYR* 4.9 1.8 + - + +
152D ASP 2.9 15.2 + - - +
153D TYR* 2.9 29.8 - - - +
155D ILE* 1.3 75.1 - - - +
157D SER* 1.3 60.6 + - - +
159D LEU* 3.5 10.1 - - - +
160D LEU* 3.1 23.9 + - + +
168D VAL* 3.9 11.4 - - + -
171D ILE* 5.1 7.0 - - + -
172D ILE* 3.6 34.1 - - + +
175D MSE 3.8 20.0 - - + -
193D VAL* 3.3 17.3 - - + -
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Residues in contact with SER 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D TYR 2.6 24.7 + - - -
154D GLU 3.3 5.2 - - - -
155D ILE 3.1 0.2 - - - -
156D VAL* 1.3 79.1 - - - +
158D ASN* 1.3 60.6 + - - +
160D LEU* 3.6 13.0 + - - +
161D ASN* 4.1 2.6 + - - +
189D THR 3.6 1.2 + - - -
192D THR* 3.6 11.7 - - - -
193D VAL* 2.9 31.4 + - - +
196D ASN* 3.4 17.3 - - - +
2H VAL* 4.5 1.6 - - - +
3H THR 4.3 1.9 - - - +
5H VAL* 3.4 22.6 - - - +
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Residues in contact with ASN 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D SER* 3.3 20.7 + - - +
114D LEU* 4.2 22.2 - - + +
115D GLY* 5.7 0.2 - - - -
118D SER* 4.5 0.7 + - - -
154D GLU* 2.9 24.8 + - - +
155D ILE 3.8 2.9 - - - +
157D SER* 1.3 74.8 - - - +
159D LEU* 1.3 64.8 + - - +
160D LEU 3.3 0.2 - - - -
161D ASN* 3.3 14.3 + - - +
162D VAL* 3.7 13.2 - - - +
4H LEU* 3.0 31.3 - - + +
5H VAL 2.9 42.4 + - - +
6H PHE* 4.0 8.4 - - - -
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Residues in contact with LEU 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D LEU* 4.1 23.8 - - + +
134D ILE* 4.6 6.1 - - + -
138D LEU* 3.6 33.7 - - + -
142D TYR* 6.1 1.8 - - + -
155D ILE* 2.7 21.0 + - + +
156D VAL* 3.5 12.6 - - + +
157D SER 3.2 0.2 - - - -
158D ASN* 1.3 74.5 - - - +
160D LEU* 1.3 59.5 + - - +
161D ASN 3.1 4.7 - - - -
162D VAL* 3.1 8.2 + - + -
163D LEU* 3.0 44.3 + - + +
168D VAL* 3.5 29.2 - - + -
171D ILE* 5.4 8.3 - - + -
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Residues in contact with LEU 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D VAL 3.1 18.6 + - - +
157D SER* 3.8 11.7 - - - +
158D ASN 3.3 0.6 - - - -
159D LEU* 1.3 76.0 - - - +
161D ASN* 1.3 57.7 + - - +
162D VAL 3.4 0.8 + - - -
163D LEU 3.7 11.9 - - - +
165D TYR* 4.2 19.3 - - + -
168D VAL* 3.4 31.4 - - + -
172D ILE* 3.9 14.8 - - + -
193D VAL* 4.0 11.4 - - + +
196D ASN* 3.9 9.9 - - + -
197D ALA* 3.8 31.9 - - + +
200D ILE* 3.5 28.9 - - + +
289D PHE* 3.7 6.1 - - - -
2H VAL* 4.3 5.8 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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