Contacts of the helix formed by residues 218 - 230 (chain A) in PDB entry 2JEF
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 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A LYS* 2.9 18.9 + - - -
215A GLY 4.9 0.4 + - - -
216A MET 3.7 0.4 - - - -
217A ILE* 1.3 81.1 - - - +
219A GLU* 1.3 66.6 + - - -
220A ALA 3.4 0.2 - - - -
221A LYS 4.2 0.7 - - - -
222A ALA* 3.0 26.0 + - - +
11T C 3.4 23.1 - - - -
12T T 5.8 1.8 - - - -
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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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210A PHE* 4.3 5.0 - - + -
214A LYS* 2.5 55.6 + - + +
218A GLY* 1.3 71.4 - - - -
220A ALA* 1.3 65.5 + - - +
222A ALA* 3.4 3.0 + - - +
223A LYS* 3.0 60.2 + - + +
11T C 2.9 10.5 + - - +
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Residues in contact with ALA 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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219A GLU* 1.3 76.3 - - - +
221A LYS* 1.3 63.5 + - - +
223A LYS* 3.3 5.8 + - - +
224A TYR* 3.0 22.8 + - - +
10T C 3.4 38.6 - - - +
11T C 2.6 22.9 + - - +
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Residues in contact with LYS 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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185A GLY* 3.7 21.8 - - - +
186A ILE* 4.1 17.0 - - + -
190A THR* 2.8 32.7 + - + +
217A ILE* 3.6 39.3 + - + +
218A GLY 3.6 1.2 + - - -
220A ALA* 1.3 78.1 - - - +
222A ALA* 1.3 64.5 + - - +
224A TYR* 3.2 16.5 + - + +
225A LEU* 3.0 25.1 + - + +
11P T 4.8 5.6 + - - -
12P T 4.9 5.4 - - - -
10T C 5.0 1.9 + - - +
11T C 4.2 0.6 + - - -
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Residues in contact with ALA 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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210A PHE* 3.9 18.2 - - + -
213A LEU* 4.0 14.2 - - + +
214A LYS* 3.9 19.3 - - - +
217A ILE* 3.8 9.6 - - + +
218A GLY 3.0 20.7 + - - +
219A GLU 3.5 4.5 - - - +
221A LYS* 1.3 78.2 - - - +
223A LYS* 1.3 55.8 + - - +
225A LEU* 3.5 0.6 + - - -
226A ILE* 3.0 36.9 + - - +
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Residues in contact with LYS 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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210A PHE* 3.9 22.2 - - + -
219A GLU* 3.0 54.0 + - + +
220A ALA* 3.9 6.1 - - - +
222A ALA* 1.3 72.8 - - - +
224A TYR* 1.3 58.8 + - - +
226A ILE* 4.1 5.3 - - - +
227A SER* 3.0 32.7 + - - -
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Residues in contact with TYR 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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149A VAL* 3.5 19.4 - - + +
183A VAL* 4.0 10.7 - - + +
184A PRO* 2.7 35.7 + - - +
185A GLY* 4.8 4.0 - - - -
186A ILE* 4.7 4.5 - - + -
220A ALA 3.0 14.2 + - - +
221A LYS* 3.3 21.8 - - + +
223A LYS* 1.3 77.7 - - - +
225A LEU* 1.3 74.3 + - + +
227A SER* 3.5 5.3 - - - -
228A LEU* 3.1 44.3 + - + +
233A TYR* 3.7 30.9 - + - -
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Residues in contact with LEU 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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180A ILE* 3.8 11.2 - - + -
183A VAL* 4.2 8.7 - - + -
186A ILE* 3.9 23.6 - - + -
194A LEU* 3.9 30.7 - - + -
202A LEU* 3.6 25.1 - - + +
205A THR* 3.9 18.5 + - + -
213A LEU* 5.3 1.8 - - + -
217A ILE* 3.9 21.1 - - + -
221A LYS 3.0 13.2 + - - +
222A ALA* 4.1 2.9 - - - +
224A TYR* 1.3 85.9 - - + +
226A ILE* 1.3 66.7 + - - +
228A LEU* 3.1 6.1 + - + +
229A ALA* 2.9 23.9 + - - +
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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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205A THR* 3.8 20.2 - - - +
206A LEU* 4.0 7.4 - - + -
210A PHE* 3.2 40.6 - - + -
213A LEU* 3.9 17.7 - - + -
222A ALA 3.0 22.0 + - - +
223A LYS* 4.1 4.7 - - - +
225A LEU* 1.3 75.3 - - - +
227A SER* 1.3 65.2 + - - +
229A ALA* 3.0 4.8 + - - +
230A ARG* 2.9 61.0 + - - +
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Residues in contact with SER 227 (chain A).
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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223A LYS 3.0 21.2 + - - -
224A TYR* 3.5 6.3 - - - -
226A ILE* 1.3 79.5 - - - +
228A LEU* 1.3 58.0 + - - +
230A ARG* 3.5 4.9 + - - +
232A GLU* 2.8 41.0 + - - +
233A TYR* 3.0 27.3 + - - -
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Residues in contact with LEU 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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149A VAL* 3.8 15.9 - - + -
150A PHE* 3.8 29.5 - - + -
175A ILE* 3.5 15.1 - - - +
183A VAL* 4.1 15.0 - - + -
202A LEU* 4.2 14.7 - - + +
224A TYR* 3.1 55.1 + - + +
225A LEU* 3.1 9.2 + - + +
227A SER* 1.3 74.1 - - - +
229A ALA* 1.3 65.2 + - - +
231A ASP* 3.1 11.6 + - - -
233A TYR* 3.3 36.1 - - + +
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Residues in contact with ALA 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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175A ILE* 3.5 26.3 - - - +
202A LEU* 3.4 32.7 - - + +
203A VAL* 4.3 1.1 - - - +
205A THR* 3.5 7.2 - - - +
206A LEU* 3.8 22.1 - - + +
225A LEU 2.9 12.1 + - - +
226A ILE 3.0 8.7 + - - +
228A LEU* 1.3 76.5 - - - +
230A ARG* 1.3 58.3 + - - +
231A ASP 3.0 3.7 + - - -
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Residues in contact with ARG 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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206A LEU* 3.9 22.6 - - + +
226A ILE* 2.9 40.7 + - - +
227A SER* 3.9 4.0 - - - +
228A LEU 3.2 0.6 - - - -
229A ALA* 1.3 74.6 - - - +
231A ASP* 1.3 71.2 + - - +
232A GLU* 3.0 39.0 + - + +
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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