Contacts of the helix formed by residues 193 - 203 (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 LYS 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A GLU* 4.5 20.0 - - + +
188A ALA 3.2 1.2 + - - -
191A GLN* 2.9 31.8 - - + +
192A LYS* 1.3 81.9 - - - +
194A LEU* 1.3 65.9 + - - +
195A SER 3.4 1.8 - - - -
196A GLU* 2.9 29.9 + - + +
197A TYR* 2.9 55.4 + - + +
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Residues in contact with LEU 194 (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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122A PHE* 4.0 22.9 - - + -
126A MSE 5.4 4.5 - - + -
184A TRP* 4.8 0.4 - - + -
185A LEU* 4.3 30.5 - - + +
188A ALA* 3.0 32.6 + - + +
189A LEU* 3.9 26.7 - - + +
192A LYS 3.4 1.5 - - - -
193A LYS* 1.3 77.6 - - - +
195A SER* 1.3 65.8 + - - +
196A GLU 3.0 0.9 + - - -
197A TYR* 3.1 7.3 + - + +
198A MSE 3.1 43.5 + - + +
230A LEU* 4.4 11.7 - - + +
233A LEU* 4.8 7.0 - - + -
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Residues in contact with SER 195 (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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192A LYS 4.4 0.9 + - - -
194A LEU* 1.3 78.2 - - - +
196A GLU* 1.3 67.4 + - - +
198A MSE 3.8 1.0 + - - +
199A LYS* 3.3 16.3 + - - +
227A ALA 3.7 13.2 - - - +
230A LEU* 3.2 50.5 + - - +
231A VAL* 3.5 9.0 - - - +
234A ASN* 2.9 28.9 + - - -
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Residues in contact with GLU 196 (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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158A VAL* 3.1 34.8 - - + +
160A GLU* 4.1 5.8 - - - +
193A LYS* 2.9 38.7 + - - +
195A SER* 1.3 79.6 + - - +
197A TYR* 1.3 69.9 + - + +
199A LYS* 2.9 21.0 + - + +
200A ALA* 3.1 9.6 + - + +
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Residues in contact with TYR 197 (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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154A VAL* 3.4 25.2 - - + +
158A VAL* 3.5 29.6 - - + -
160A GLU* 2.8 34.5 + - + +
161A ALA* 3.3 21.0 - - + -
164A ILE* 4.2 5.4 - - + -
184A TRP* 4.2 6.3 - + - -
188A ALA* 3.9 21.8 - - + -
191A GLN* 2.9 16.2 + - - -
193A LYS* 2.9 45.9 + - + +
194A LEU* 3.6 3.6 - - - +
196A GLU* 1.3 73.5 - - - +
198A MSE 1.3 66.0 + - + +
200A ALA* 2.7 35.8 + - - +
201A LEU* 3.1 7.8 + - - +
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Residues in contact with MSE 198 (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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126A MSE 5.6 7.2 - - + +
130A LEU* 4.5 14.1 - - - -
151A LEU* 4.3 4.3 - - + -
154A VAL* 4.4 0.2 - - + -
184A TRP* 4.0 24.9 - - + -
185A LEU* 5.6 1.1 - - - -
194A LEU* 3.1 26.1 + - + +
195A SER 3.9 4.3 - - - +
197A TYR* 1.3 91.9 - - + +
199A LYS* 1.3 62.4 - - - +
201A LEU* 3.2 26.3 + - + +
202A ILE* 2.9 27.3 - - + +
218A MSE 4.2 19.5 - - - +
227A ALA* 4.0 15.7 - - + -
230A LEU* 3.6 22.0 - - + -
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Residues in contact with LYS 199 (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 3.3 10.0 + - - +
196A GLU* 2.9 13.9 + - - +
198A MSE 1.3 78.6 - - - +
200A ALA* 1.3 61.5 + - - +
202A ILE* 3.5 3.9 + - - +
203A ASN* 2.6 51.4 + - - +
227A ALA* 4.1 14.7 - - + +
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Residues in contact with ALA 200 (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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154A VAL* 5.9 1.1 - - + -
157A LEU* 4.0 17.3 - - + +
158A VAL* 4.1 23.1 - - + -
196A GLU* 3.1 8.2 + - + +
197A TYR* 2.7 22.3 + - - +
199A LYS* 1.3 74.5 - - - +
201A LEU* 1.3 62.2 + - + +
203A ASN* 3.4 9.2 + - - +
204A LYS* 3.2 25.3 - - - +
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Residues in contact with LEU 201 (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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150A PRO* 3.7 24.0 - - + +
151A LEU* 4.5 4.9 - - + -
153A LEU* 4.5 7.0 - - + -
154A VAL* 3.9 22.0 - - + +
157A LEU* 3.9 19.7 - - + -
197A TYR 3.1 8.2 + - - +
198A MSE 3.2 27.6 + - + +
200A ALA* 1.3 76.8 - - - +
202A ILE* 1.3 60.0 + - + +
204A LYS* 2.6 36.7 + - - +
208A LEU* 3.6 25.2 - - + +
218A MSE 3.7 22.2 - - + -
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Residues in contact with ILE 202 (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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198A MSE 2.9 22.1 + - + +
199A LYS* 4.0 7.4 - - - +
201A LEU* 1.3 73.1 - - + +
203A ASN* 1.3 62.8 + - - +
204A LYS 3.1 4.5 + - - -
205A LYS* 3.2 35.9 - - - +
208A LEU* 3.9 7.6 - - + -
218A MSE 3.6 47.6 - - + +
220A GLU 5.2 1.3 - - - +
223A GLY 3.9 24.0 - - - +
224A ALA* 4.1 24.7 - - + +
227A ALA* 4.6 2.2 - - + -
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Residues in contact with ASN 203 (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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199A LYS* 2.6 53.0 + - - +
200A ALA* 3.7 7.4 - - - +
201A LEU 3.0 1.6 + - - -
202A ILE* 1.3 81.7 - - - +
204A LYS* 1.3 77.4 + - - +
205A LYS 3.8 1.1 - - - -
206A GLU* 4.3 5.9 - - - +
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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