Contacts of the helix formed by residues 141 - 154 (chain E) in PDB entry 1AXC
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 SER 141 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139E MET 3.5 2.6 + - - -
140E PRO* 1.3 68.8 - - - +
142E GLY* 1.3 65.6 + - - +
144E PHE* 3.9 1.6 - - - +
145E ALA* 3.1 23.7 + - - +
219E THR* 3.6 21.7 + - - +
222E SER 2.6 29.2 + - - -
223E SER* 3.0 13.2 + - - -
224E THR 3.9 11.7 - - - -
225E VAL* 3.7 11.4 - - - -
239E TYR* 4.0 16.4 + - - -
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Residues in contact with GLY 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E PRO* 3.2 2.7 - - - +
141E SER* 1.3 82.5 + - - +
143E GLU* 1.3 56.6 + - - +
145E ALA* 3.4 6.8 + - - +
146E ARG* 3.0 28.6 + - - +
219E THR* 4.2 7.2 - - - +
223E SER 4.6 0.8 + - - -
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Residues in contact with GLU 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C LYS* 2.8 47.1 + - - +
139E MET* 4.9 1.1 - - - -
140E PRO* 3.0 31.2 + - + +
142E GLY* 1.3 74.7 - - - +
144E PHE* 1.3 65.4 + - - +
146E ARG* 3.3 6.5 + - - +
147E ILE* 2.9 25.8 + - + +
182E LEU* 4.2 25.6 - - + -
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Residues in contact with PHE 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E MET* 4.1 21.9 - - + -
140E PRO 3.0 6.7 + - - +
141E SER 3.9 3.4 - - - +
142E GLY 3.4 0.2 - - - -
143E GLU* 1.3 76.4 - - - +
145E ALA* 1.3 62.9 + - - +
147E ILE* 3.3 5.4 + - + +
148E CYS* 3.0 46.4 + - - -
160E ILE* 5.4 3.1 - - + -
169E PHE* 4.2 14.8 - + - -
212E LEU* 4.2 19.5 - - + -
215E PHE* 5.4 1.8 - - + -
216E THR* 4.2 9.6 - - + -
225E VAL* 3.7 28.7 - - + -
227E LEU* 3.5 30.1 - - + -
235E LEU* 5.3 0.9 - - + -
237E VAL* 3.6 22.9 - - + -
239E TYR* 3.8 18.4 - - - -
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Residues in contact with ALA 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E SER 3.1 18.4 + - - +
142E GLY* 3.5 8.1 - - - +
144E PHE* 1.3 77.5 - - - +
146E ARG* 1.3 63.2 + - - +
148E CYS* 3.3 1.7 + - - +
149E ARG* 3.0 25.4 + - - +
213E ASN* 4.5 1.2 - - - +
216E THR* 3.9 20.9 + - - +
219E THR* 4.0 16.6 - - + +
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Residues in contact with ARG 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LYS* 5.2 0.4 - - - +
80C LYS 3.1 17.8 + - - -
81C CYS 3.5 5.8 + - - -
82C ALA 2.9 35.5 + - - -
83C GLY* 4.6 8.8 - - - -
110C LYS* 3.6 18.8 - - - +
142E GLY 3.0 14.3 + - - +
143E GLU* 3.5 12.8 - - - +
145E ALA* 1.3 76.7 - - - +
147E ILE* 1.3 65.7 + - - +
149E ARG* 3.1 33.8 - - - +
150E ASP* 2.8 45.6 + - - +
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Residues in contact with ILE 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C LYS* 4.2 7.6 - - - +
143E GLU* 2.9 31.7 + - + +
144E PHE* 3.7 6.7 - - + +
146E ARG* 1.3 76.8 - - - +
148E CYS* 1.3 66.2 + - - +
150E ASP* 3.9 1.0 - - - +
151E LEU* 3.1 39.3 + - + +
158E VAL* 5.8 0.4 - - + -
169E PHE* 3.5 55.2 - - + -
180E ILE* 4.0 25.8 - - + -
182E LEU* 3.9 20.2 - - + -
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Residues in contact with CYS 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E PHE* 3.0 45.9 + - - +
145E ALA 3.8 2.7 - - - +
146E ARG 3.3 0.2 - - - -
147E ILE* 1.3 79.9 - - - +
149E ARG* 1.3 61.9 + - - +
151E LEU 3.7 0.2 + - - -
152E SER* 2.8 27.7 + - - -
158E VAL* 6.1 0.2 - - - -
169E PHE* 6.2 0.7 - - - -
209E LEU* 4.1 13.8 - - + +
212E LEU* 3.9 31.2 - - + -
213E ASN* 3.3 20.0 + - - +
216E THR* 4.3 9.0 - - + -
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Residues in contact with ARG 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C LYS* 3.8 7.7 + - - +
145E ALA 3.0 17.1 + - - +
146E ARG* 3.1 41.9 - - - +
148E CYS* 1.3 75.3 - - - +
150E ASP* 1.3 88.9 + - - +
152E SER* 3.1 20.5 - - - -
153E HIS* 3.5 24.2 + - + -
213E ASN* 3.2 12.7 + - - +
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Residues in contact with ASP 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C LYS 3.7 6.1 - - - +
81C CYS* 3.6 34.6 - - + +
110C LYS* 4.7 2.6 + - - -
114C TYR* 4.4 4.9 + - - +
146E ARG* 2.8 46.0 + - - +
147E ILE* 3.9 5.1 + - - +
149E ARG* 1.3 98.4 + - - +
151E LEU* 1.3 54.3 + - - +
152E SER 2.9 3.6 - - - -
153E HIS* 2.7 44.5 + - - +
154E ILE* 3.7 4.2 + - - +
180E ILE* 5.0 4.0 - - + +
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Residues in contact with LEU 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C TYR* 4.3 8.5 - - - +
147E ILE* 3.1 23.9 + - + +
148E CYS 4.3 1.1 - - - +
150E ASP* 1.3 76.1 - - - +
152E SER* 1.3 56.1 + - - +
153E HIS 3.1 0.4 - - - -
154E ILE* 3.2 8.1 + - + +
155E GLY 2.8 29.5 + - - +
158E VAL* 3.9 15.0 - - + -
169E PHE* 3.6 36.3 - - + +
170E SER 4.2 2.0 - - - +
171E ALA* 3.7 24.1 - - + +
178E GLY* 4.3 18.4 - - - -
180E ILE* 4.1 18.6 - - + -
209E LEU* 3.4 15.1 - - + +
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Residues in contact with SER 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E CYS 2.8 8.5 + - - -
149E ARG* 3.1 15.4 + - - -
150E ASP 2.8 0.6 + - - -
151E LEU* 1.3 75.7 - - - +
153E HIS* 1.3 63.9 + - - +
155E GLY 3.2 17.8 + - - +
209E LEU* 3.8 10.5 - - - +
213E ASN* 2.6 32.1 + - - -
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Residues in contact with HIS 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C LYS* 4.1 43.5 + - + +
80C LYS* 4.3 28.6 + - + +
81C CYS* 4.5 2.7 - - - -
149E ARG* 3.5 30.3 + - + -
150E ASP* 2.7 29.9 + - - +
152E SER* 1.3 80.7 - - - +
154E ILE* 1.3 63.3 + - + +
155E GLY 3.6 0.2 - - - -
175E LEU* 3.9 15.8 - - - +
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Residues in contact with ILE 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C LYS 4.9 0.9 - - - +
78C ILE* 4.0 13.9 - - + -
81C CYS* 4.7 3.6 - - - -
114C TYR* 3.7 35.4 - - + -
150E ASP 4.1 10.5 - - - +
151E LEU* 3.2 10.7 + - + +
153E HIS* 1.3 85.1 - - + +
155E GLY* 1.3 57.8 + - - +
171E ALA* 3.7 15.7 - - + +
172E SER 4.2 0.2 - - - -
173E GLY* 3.2 22.9 + - - -
175E LEU* 3.8 25.7 - - + +
176E GLY 3.9 6.0 - - - +
177E ASN* 3.9 9.0 - - - -
178E GLY 3.5 25.6 - - - +
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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