Contacts of the helix formed by residues 220 - 230 (chain A) in PDB entry 2CXF
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 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A ARG* 3.2 41.3 + - - +
202A ILE* 5.2 1.9 - - - +
205A LYS* 4.6 7.2 + - - +
214A VAL 4.8 2.9 - - - +
215A ASN* 4.2 14.5 - - - +
216A ALA 3.0 21.6 + - - +
217A LEU 3.0 5.7 + - - +
218A MSE 4.6 1.0 - - - +
219A MSE 1.3 90.3 + - - +
221A GLU* 1.3 69.6 + - - +
222A GLU* 3.2 8.3 - - - +
223A GLY* 3.0 14.3 + - - -
224A ALA* 3.7 3.6 + - - +
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Residues in contact with GLU 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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91A MSE 5.5 2.9 - - - +
220A GLU* 1.3 77.0 + - - +
222A GLU* 1.3 72.7 + - - +
224A ALA* 3.0 10.9 + - + +
225A ILE* 2.9 46.3 + - + +
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Residues in contact with GLU 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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84A ALA 4.8 1.4 - - - +
87A ARG* 3.2 47.1 + - + +
88A MSE 4.2 6.3 + - - +
91A MSE 3.7 36.6 - - + +
217A LEU* 3.9 21.5 - - + +
220A GLU* 3.2 4.7 - - - +
221A GLU* 1.3 88.0 + - - +
223A GLY* 1.3 62.7 + - - +
225A ILE* 4.1 9.4 - - - -
226A ILE* 2.9 30.9 + - + +
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Residues in contact with GLY 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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202A ILE* 3.9 18.2 - - - +
217A LEU* 3.2 26.6 + - - -
218A MSE 4.4 5.7 - - - +
220A GLU 3.0 8.7 + - - -
222A GLU* 1.3 78.6 - - - +
224A ALA* 1.3 56.8 + - - +
226A ILE* 4.1 2.1 - - - +
227A ALA* 2.9 30.7 + - - +
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Residues in contact with ALA 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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202A ILE* 4.0 22.9 - - + +
220A GLU 3.7 4.5 + - - +
221A GLU* 3.0 11.2 + - + +
223A GLY* 1.3 71.5 - - - +
225A ILE* 1.3 58.9 + - + +
227A ALA* 3.2 6.8 + - - +
228A GLY* 2.7 34.5 + - - -
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Residues in contact with ILE 225 (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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91A MSE 4.1 22.0 - - + -
95A LYS* 4.7 4.3 - - - +
221A GLU* 2.9 46.5 + - + +
222A GLU* 3.5 9.6 - - - +
224A ALA* 1.3 76.7 - - + +
226A ILE* 1.3 65.2 + - - +
228A GLY* 2.9 12.8 + - - -
229A LEU* 3.0 35.4 + - + +
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Residues in contact with ILE 226 (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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91A MSE 3.8 39.7 - - + +
94A ALA* 3.9 24.2 - - + -
95A LYS* 5.9 0.7 - - + -
98A ILE* 4.3 12.6 - - + -
126A MSE 4.5 16.4 - - + -
129A CYS* 4.5 10.3 - - + -
217A LEU* 4.2 19.1 - - + -
222A GLU 2.9 23.8 + - - +
223A GLY* 4.1 2.5 - - - +
225A ILE* 1.3 72.0 - - + +
227A ALA* 1.3 58.2 + - - +
229A LEU* 3.0 12.0 + - + +
230A LEU* 3.0 40.0 + - + +
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Residues in contact with ALA 227 (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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195A SER* 3.7 18.7 - - - +
198A MSE 4.0 22.2 - - + +
199A LYS* 4.1 18.5 - - + +
202A ILE* 4.6 3.1 - - + -
223A GLY 2.9 21.1 + - - +
224A ALA* 3.4 8.1 - - - +
226A ILE* 1.3 76.6 - - - +
228A GLY* 1.3 60.0 + - - +
229A LEU 3.5 0.2 + - - -
230A LEU* 3.7 20.0 + - - +
231A VAL* 4.4 1.6 - - - +
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Residues in contact with GLY 228 (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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224A ALA 2.7 17.8 + - - -
225A ILE 2.9 5.3 + - - -
227A ALA* 1.3 72.7 - - - +
229A LEU* 1.3 63.2 + - - +
231A VAL* 3.1 23.9 - - - +
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Residues in contact with LEU 229 (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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95A LYS* 4.2 29.8 - - + -
98A ILE* 3.7 22.9 - - + +
102A ILE* 5.1 0.2 - - - +
225A ILE* 3.0 35.3 + - + +
226A ILE* 3.0 12.0 + - + +
228A GLY* 1.3 82.0 - - - +
230A LEU* 1.3 56.6 + - - +
231A VAL 2.8 11.9 + - - -
232A GLY* 3.2 11.3 + - - -
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Residues in contact with LEU 230 (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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98A ILE* 3.4 23.1 - - + -
122A PHE* 3.7 16.2 - - + -
126A MSE 4.3 15.7 - - + -
194A LEU* 4.4 8.2 - - + +
195A SER* 3.2 28.3 + - - +
198A MSE 3.6 36.3 - - + -
226A ILE* 3.0 23.1 + - + +
227A ALA* 3.7 5.6 + - - +
228A GLY 3.6 0.4 - - - -
229A LEU* 1.3 75.8 - - - +
231A VAL* 1.3 61.3 + - - +
232A GLY 3.3 0.7 - - - -
233A LEU* 3.2 40.7 + - + +
234A ASN* 4.0 1.0 + - - +
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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