Contacts of the helix formed by residues 141 - 154 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139C MET 3.4 3.0 + - - -
140C PRO* 1.3 73.0 - - - +
142C GLY* 1.3 57.8 + - - +
144C PHE* 3.4 2.9 + - - +
145C ALA* 2.9 28.8 + - - +
219C THR* 3.4 20.5 + - - +
222C SER 2.6 27.3 + - - -
223C SER* 3.1 10.6 + - - -
224C THR* 3.6 13.6 - - - +
225C VAL* 3.8 11.7 - - - -
239C TYR* 4.1 17.7 + - - -
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Residues in contact with GLY 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C PRO* 3.2 2.0 - - - +
141C SER* 1.3 81.2 + - - +
143C GLU* 1.3 57.7 + - - +
145C ALA* 3.2 6.0 + - - +
146C ARG* 2.9 28.6 + - - +
219C THR* 3.8 10.7 - - - +
223C SER 4.9 0.6 + - - -
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Residues in contact with GLU 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LYS* 2.8 46.9 + - - +
139C MET* 4.7 2.5 - - + -
140C PRO* 3.1 30.6 + - + +
142C GLY* 1.3 73.8 - - - +
144C PHE* 1.3 66.4 + - - +
146C ARG* 3.2 6.1 + - - +
147C ILE* 3.1 21.5 + - + +
182C LEU* 4.2 27.2 - - + +
195C VAL* 5.9 1.3 - - + -
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Residues in contact with PHE 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C MET* 3.8 25.5 - - - -
140C PRO 3.0 9.2 + - - +
141C SER 3.7 6.5 - - - +
142C GLY 3.3 0.2 - - - -
143C GLU* 1.3 76.5 - - - +
145C ALA* 1.3 62.0 + - - +
147C ILE* 3.2 9.3 + - + +
148C CYS* 3.1 46.3 + - - -
160C ILE* 5.5 1.8 - - + -
169C PHE* 4.2 15.7 - + - -
212C LEU* 3.9 24.0 - - + -
215C PHE* 5.3 1.3 - - + -
216C THR* 4.2 13.5 - - + -
225C VAL* 3.9 16.6 - - + -
227C LEU* 3.7 31.4 - - + -
235C LEU* 5.6 1.1 - - + -
237C VAL* 3.8 19.3 - - + -
239C TYR* 3.9 15.3 - - - -
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Residues in contact with ALA 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C SER 2.9 17.2 + - - +
142C GLY* 3.2 8.3 + - - +
144C PHE* 1.3 78.7 - - - +
146C ARG* 1.3 62.0 + - - +
148C CYS* 3.4 1.6 + - - +
149C ARG* 3.1 24.8 + - - +
213C ASN* 4.8 0.7 - - - +
216C THR* 3.8 22.1 - - + +
219C THR* 3.9 17.5 - - + +
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Residues in contact with ARG 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LYS* 5.1 0.2 - - - +
80A LYS 3.0 21.0 + - - -
81A CYS 3.4 6.1 + - - -
82A ALA 2.7 34.3 + - - -
83A GLY* 4.4 9.0 - - - -
84A ASN* 6.1 0.8 - - - +
110A LYS* 3.7 19.5 - - - +
142C GLY 2.9 12.9 + - - +
143C GLU* 3.2 14.1 + - - +
145C ALA* 1.3 74.1 - - - +
147C ILE* 1.3 66.6 + - - +
149C ARG* 3.1 33.3 + - - +
150C ASP* 2.8 45.6 + - - +
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Residues in contact with ILE 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LYS* 4.3 3.4 - - - +
143C GLU* 3.1 24.9 + - + +
144C PHE* 3.5 11.0 - - + +
146C ARG* 1.3 77.2 - - - +
148C CYS* 1.3 62.0 + - - +
150C ASP* 3.9 0.8 - - - +
151C LEU* 2.9 37.0 + - + +
158C VAL* 5.6 0.2 - - + -
169C PHE* 3.7 60.1 - - + -
180C ILE* 3.9 31.0 - - + -
182C LEU* 3.8 20.6 - - + -
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Residues in contact with CYS 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C PHE* 3.1 47.3 + - - -
145C ALA 3.9 5.6 - - - +
147C ILE* 1.3 77.9 - - - +
149C ARG* 1.3 60.3 + - - +
152C SER* 2.6 33.8 + - - -
169C PHE* 6.3 0.4 - - - -
209C LEU* 3.7 15.4 - - + +
212C LEU* 3.8 24.7 - - + -
213C ASN* 3.2 17.7 - - - +
216C THR* 4.3 8.7 - - + -
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Residues in contact with ARG 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LYS* 4.0 5.1 + - - +
145C ALA 3.1 17.9 + - - +
146C ARG* 3.1 46.2 - - - +
148C CYS* 1.3 75.0 - - - +
150C ASP* 1.3 83.0 + - - +
152C SER* 3.0 22.7 - - - -
153C HIS* 3.4 27.5 + - - +
213C ASN* 3.2 12.2 + - - +
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Residues in contact with ASP 150 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A LYS 4.1 1.2 - - - +
81A CYS* 3.6 41.9 - - + +
110A LYS* 5.2 1.0 + - - -
114A TYR* 4.7 4.9 - - - +
146C ARG* 2.8 47.8 + - - +
147C ILE* 3.9 3.5 - - - +
149C ARG* 1.3 99.2 + - - +
151C LEU* 1.3 60.1 + - - +
152C SER 2.8 11.6 + - - -
153C HIS* 2.8 28.8 + - - +
154C ILE* 3.7 4.3 + - - +
180C ILE* 5.1 3.9 - - + +
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Residues in contact with LEU 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A TYR* 4.5 7.0 - - + +
147C ILE* 2.9 27.7 + - + +
150C ASP* 1.3 72.5 - - - +
152C SER* 1.3 55.9 + - - +
154C ILE* 3.0 10.7 + - - +
155C GLY 2.9 27.7 + - - +
158C VAL* 3.4 33.0 - - + -
169C PHE* 3.6 24.2 - - + +
170C SER 4.0 4.7 - - - +
171C ALA* 3.7 17.3 - - + +
178C GLY* 4.4 17.0 - - - +
180C ILE* 3.6 28.9 - - + -
209C LEU* 3.6 14.4 - - + +
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Residues in contact with SER 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C CYS 2.6 19.4 + - - -
149C ARG* 3.0 15.5 - - - -
150C ASP 2.8 1.2 + - - -
151C LEU* 1.3 78.7 - - - +
153C HIS* 1.3 61.3 + - - -
155C GLY 3.3 18.4 + - - +
209C LEU* 3.8 9.9 - - - +
213C ASN* 2.7 24.8 + - - -
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Residues in contact with HIS 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LYS* 4.0 45.9 + - + +
80A LYS* 4.4 22.9 - - + +
81A CYS* 4.3 2.2 - - - -
149C ARG* 3.4 31.5 + - - +
150C ASP* 2.8 29.6 + - - +
152C SER* 1.3 77.1 - - - +
154C ILE* 1.3 66.4 + - + +
175C LEU* 3.8 15.8 - - - +
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Residues in contact with ILE 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ILE* 4.2 10.5 - - + +
81A CYS* 4.3 11.0 - - - -
114A TYR* 3.9 32.5 - - + -
150C ASP 3.8 8.3 - - - +
151C LEU* 3.0 15.6 + - - +
153C HIS* 1.3 85.4 - - + +
155C GLY* 1.3 57.5 + - - +
171C ALA* 4.0 10.5 - - + +
172C SER 4.2 0.2 - - - -
173C GLY* 3.1 27.4 + - - -
175C LEU* 4.1 27.1 - - + +
176C GLY 3.9 5.4 - - - +
177C ASN* 3.8 12.3 - - - -
178C GLY* 3.5 26.7 - - - +
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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