Contacts of the helix formed by residues 215 - 224 (chain A) in PDB entry 4O6M
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 GLY 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A ARG* 3.5 19.2 + - - -
160A SER* 4.7 0.9 - - - -
211A SER 3.9 3.7 + - - -
212A ILE 3.1 10.8 + - - -
213A ILE 3.0 1.4 - - - -
214A ASP* 1.3 77.7 - - - +
216A CYS* 1.3 62.1 + - - +
217A ASP* 3.2 3.1 + - - -
218A GLY* 3.5 2.8 + - - -
219A GLU* 3.3 30.4 + - - +
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Residues in contact with CYS 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A SER* 3.6 27.6 - - - -
163A ILE* 4.0 20.9 - - - -
164A SER* 3.4 22.7 - - - +
167A LEU* 4.6 4.9 - - + -
177A ILE* 3.9 17.0 - - + -
213A ILE* 2.8 25.9 + - + +
215A GLY* 1.3 77.1 - - - +
217A ASP* 1.3 59.2 + - - +
219A GLU* 3.6 1.1 - - - -
220A ILE* 2.9 33.8 + - - +
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Residues in contact with ASP 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A PRO* 3.5 23.1 - - + +
177A ILE* 3.6 20.9 - - + +
178A THR* 2.6 31.4 + - - +
214A ASP* 2.6 19.9 - - - +
215A GLY* 3.9 1.6 - - - -
216A CYS* 1.3 79.2 - - - +
218A GLY* 1.3 74.0 + - - +
221A ALA* 3.0 30.1 + - - +
235A ASP* 2.9 9.6 - - - +
401A CA 2.3 23.1 - - - -
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Residues in contact with GLY 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A ARG* 5.9 1.1 - - - -
215A GLY 3.5 3.6 + - - -
216A CYS 3.3 0.2 - - - -
217A ASP* 1.3 86.9 + - - +
219A GLU* 1.3 63.4 + - - +
221A ALA* 3.4 6.2 + - - +
222A ARG* 3.1 34.4 + - - +
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Residues in contact with GLU 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A LEU* 3.7 26.2 - - + +
157A ARG* 3.3 27.3 + - - +
160A SER* 2.6 38.2 + - - +
161A LEU* 3.6 23.1 - - + +
164A SER* 2.5 38.0 + - - +
215A GLY 3.3 12.4 + - - +
216A CYS* 3.3 3.9 + - - +
218A GLY* 1.3 77.7 - - - +
220A ILE* 1.3 57.8 + - - +
222A ARG* 3.4 1.3 + - - +
223A LEU* 2.9 32.2 + - - +
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Residues in contact with ILE 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A SER* 3.5 35.0 - - - +
167A LEU* 3.9 10.3 - - + +
168A ALA* 3.7 24.9 - - + +
172A VAL 3.9 21.5 - - - +
174A PRO* 4.2 14.8 - - + -
177A ILE* 3.7 20.0 - - + -
216A CYS 2.9 21.3 + - - +
217A ASP 4.1 0.9 - - - +
219A GLU* 1.3 71.0 - - - +
221A ALA* 1.3 67.1 + - - +
223A LEU* 4.2 5.8 - - + -
224A LYS* 3.0 35.6 + - + +
226A MET* 4.7 0.6 - - - +
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Residues in contact with ALA 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A PRO* 3.6 21.5 - - + -
217A ASP 3.0 20.3 + - - +
218A GLY* 3.6 8.5 - - - +
219A GLU 3.3 0.2 - - - -
220A ILE* 1.3 78.4 - - - +
222A ARG* 1.3 58.1 + - + +
225A PHE* 3.0 7.6 + - - -
226A MET 2.6 30.0 + - - +
227A GLU* 3.5 26.4 - - + +
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Residues in contact with ARG 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ARG* 5.2 0.3 + - - -
62A ARG* 4.0 40.4 - - - +
134A LEU* 4.0 34.3 - - + +
135A ILE* 4.6 8.1 - - - +
218A GLY* 3.1 19.1 + - - +
219A GLU 4.0 0.2 - - - +
221A ALA* 1.3 75.8 - - + +
223A LEU* 1.3 65.4 + - - +
224A LYS 3.4 0.2 + - - -
225A PHE* 3.5 18.7 + - - -
227A GLU* 3.8 22.0 - - + +
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Residues in contact with LEU 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 3.6 33.9 - - + +
19A LEU* 4.2 0.7 - - - +
24A ARG* 2.8 48.6 + - - +
130A LEU* 3.8 18.2 - - + -
131A LEU* 4.3 7.0 - - + -
134A LEU* 3.9 25.6 - - + -
164A SER* 4.4 7.9 - - - +
168A ALA* 3.7 28.0 - - + -
219A GLU 2.9 18.7 + - - +
220A ILE* 3.9 9.4 - - + +
222A ARG* 1.3 77.3 - - - +
224A LYS* 1.3 59.3 + - + +
225A PHE* 3.5 1.1 + - - -
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Residues in contact with LYS 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU 4.6 3.6 - - - +
18A GLY* 4.3 19.1 + - - -
19A LEU* 4.1 19.9 - - + +
27A LYS* 5.2 2.4 - - - +
167A LEU 5.1 0.4 - - - +
168A ALA* 2.8 35.5 + - - +
170A THR 2.9 22.2 + - - -
171A SER* 4.9 2.2 - - - +
172A VAL 4.9 4.0 + - - +
220A ILE* 3.0 32.9 + - + +
223A LEU* 1.3 87.1 - - + +
225A PHE* 1.3 76.5 + - - +
226A MET* 3.2 27.1 - - + +
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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