Contacts of the helix formed by residues 217 - 230 (chain A) in PDB entry 2L9N
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 PHE 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A ASP* 4.6 21.3 - - - -
193A LEU* 3.4 30.3 - - + -
194A ILE* 3.6 15.0 - - + -
213A ASP* 3.4 20.6 - - + -
214A PRO* 3.9 14.7 + - + -
216A CYS* 1.3 78.9 - - - +
218A ARG* 1.3 63.0 + - - +
219A GLU 2.8 7.2 + - - -
220A ILE* 3.1 38.7 + - + -
221A ASP* 3.0 33.0 + - - +
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Residues in contact with ARG 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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125A LYS* 4.5 24.6 - - + +
172A MET* 4.2 33.5 - - + +
174A LEU* 4.7 18.6 - - + +
213A ASP* 2.9 23.6 + - - +
214A PRO 3.8 11.1 + - - +
215A GLY* 4.7 8.3 - - - +
216A CYS 3.2 0.6 - - - -
217A PHE* 1.3 76.5 - - - +
219A GLU* 1.3 66.0 + - - +
221A ASP* 3.8 2.5 - - - -
222A GLU* 3.0 42.1 + - - +
237A LEU* 5.0 9.7 - - - +
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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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124A THR 3.2 9.0 - - - +
125A LYS* 3.1 48.8 + - - +
126A ARG* 5.9 0.2 - - - -
127A PRO* 5.1 7.6 - - + -
215A GLY 4.6 1.1 - - - +
216A CYS 3.5 12.6 + - - +
217A PHE 2.8 1.6 + - - -
218A ARG* 1.3 89.4 + - - +
220A ILE* 1.3 68.0 + - + +
221A ASP 3.1 0.2 + - - -
222A GLU* 3.9 2.9 - - - +
223A LEU* 3.0 27.3 + - - +
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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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127A PRO* 5.7 5.6 - - + -
193A LEU* 3.9 19.7 - - + -
216A CYS 4.9 2.9 - - - +
217A PHE* 3.1 41.1 + - + +
219A GLU* 1.3 78.0 - - + +
221A ASP* 1.3 56.6 + - - +
223A LEU* 3.7 8.2 - - + +
224A ILE* 2.8 40.1 + - + +
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Residues in contact with ASP 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 LEU* 3.8 9.8 - - + +
193A LEU* 3.0 33.5 - - - +
194A ILE* 3.6 15.8 - - - +
211A LEU* 4.3 0.7 - - - +
213A ASP* 3.7 12.7 - - - +
217A PHE* 3.0 36.7 + - - +
218A ARG* 3.6 8.3 - - - +
220A ILE* 1.3 73.1 - - - +
222A GLU* 1.3 59.2 + - - +
223A LEU 3.0 1.7 + - - -
224A ILE* 3.2 1.6 - - - +
225A LYS* 2.7 61.2 + - - +
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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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176A PHE* 5.7 5.4 - - + -
218A ARG* 3.0 28.3 + - - +
219A GLU* 4.0 2.7 - - - +
221A ASP* 1.3 78.9 - - - +
223A LEU* 1.3 58.2 + - - +
225A LYS* 4.4 6.6 - - - +
226A LYS* 3.0 59.9 + - - +
229A LYS* 4.6 5.9 + - - -
235A GLU* 5.1 4.7 - - - +
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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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219A GLU 3.0 18.7 + - - +
220A ILE* 3.7 8.5 - - + +
221A ASP 3.0 0.6 - - - -
222A GLU* 1.3 78.1 + - - +
224A ILE* 1.3 76.1 + - + +
226A LYS* 3.9 3.8 + - - +
227A GLU* 3.0 30.9 + - + +
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Residues in contact with ILE 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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189A LYS* 4.3 27.1 - - + -
190A LEU* 3.9 10.3 - - + -
193A LEU* 3.5 33.4 - - + -
220A ILE* 2.8 30.3 - - + +
221A ASP* 3.2 6.7 - - - +
223A LEU* 1.3 88.5 - - + +
225A LYS* 1.3 86.1 + - + +
227A GLU* 3.2 11.7 + - - +
228A THR* 2.5 43.5 + - + +
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Residues in contact with LYS 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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174A LEU* 3.9 8.4 - - - +
176A PHE* 3.2 54.6 - - + -
186A LEU* 3.9 3.7 - - + +
190A LEU* 3.4 25.8 - - + -
211A LEU* 3.1 41.6 - - - +
221A ASP* 2.7 50.2 + - - +
222A GLU* 4.2 3.4 - - - +
224A ILE* 1.3 79.7 - - + +
226A LYS* 1.3 52.6 + - - +
228A THR* 2.6 18.3 + - - -
229A LYS* 2.7 29.7 + - - +
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Residues in contact with LYS 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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176A PHE* 5.1 0.8 - - - -
222A GLU* 3.0 44.3 + - - +
223A LEU* 3.9 4.1 + - - +
225A LYS* 1.3 75.7 - - - +
227A GLU* 1.3 64.3 + - - +
229A LYS* 3.2 31.2 - - - +
230A GLY* 3.0 25.8 + - - -
231A LYS 4.4 0.2 + - - -
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Residues in contact with GLU 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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185A LYS* 4.9 9.0 - - - -
223A LEU* 3.0 24.6 + - + +
224A ILE* 3.7 10.9 - - - +
226A LYS* 1.3 83.9 - - - +
228A THR* 1.3 67.1 + - - +
230A GLY* 4.1 6.4 + - - -
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Residues in contact with THR 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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182A GLU* 4.4 11.4 - - - +
185A LYS* 4.2 34.6 - - + +
186A LEU* 3.1 24.0 - - - +
189A LYS* 3.6 36.6 - - + -
224A ILE* 2.5 32.8 + - - +
225A LYS* 2.6 19.6 + - - -
227A GLU* 1.3 82.9 - - - +
229A LYS* 1.3 59.6 + - - +
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Residues in contact with LYS 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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176A PHE* 5.0 1.1 - - + -
182A GLU* 4.5 13.0 - - - +
186A LEU* 3.5 8.9 - - + +
222A GLU* 4.6 4.0 + - - -
225A LYS 2.7 30.4 + - - +
226A LYS* 3.2 34.1 - - - +
228A THR* 1.3 74.1 + - - +
230A GLY* 1.3 67.7 + - - +
231A LYS* 3.5 26.9 - - - +
232A GLY* 2.8 16.5 + - - -
233A SER* 2.8 35.8 + - - +
235A GLU* 2.6 40.8 + - - +
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Residues in contact with GLY 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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226A LYS 3.0 16.0 + - - -
227A GLU 4.1 5.6 + - - -
228A THR 3.4 2.4 - - - -
229A LYS* 1.3 76.7 - - - +
231A LYS* 1.3 78.6 + - - +
232A GLY* 2.8 3.5 + - - -
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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