Contacts of the helix formed by residues 218 - 234 (chain A) in PDB entry 4DJH
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 ASP 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A PRO* 3.4 15.9 - - + +
216A ASP 3.0 7.4 + - - +
217A ASP* 1.3 75.8 - - - +
219A TYR* 1.3 65.0 + - - +
220A SER* 3.0 4.7 + - - -
221A TRP* 3.1 24.9 + - - +
222A TRP* 3.2 25.0 + - + +
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Residues in contact with TYR 219 (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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211A SER* 3.3 20.8 + - - -
212A LEU* 3.1 23.6 + - - +
213A GLN* 4.7 1.3 - - - -
214A PHE* 3.6 33.7 - + - +
215A PRO 2.8 14.6 + - - +
216A ASP* 5.0 2.0 - - - +
217A ASP 3.1 8.0 - - - +
218A ASP* 1.3 77.1 - - - +
220A SER* 1.3 56.3 + - - +
223A ASP* 2.7 69.6 + - + +
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Residues in contact with SER 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ASP 3.1 18.8 + - - -
218A ASP* 4.1 3.3 + - - -
219A TYR* 1.3 84.5 - - - +
221A TRP* 1.3 62.1 + - - +
223A ASP* 3.8 2.8 - - - +
224A LEU* 2.9 31.3 + - - +
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Residues in contact with TRP 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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218A ASP* 3.1 20.9 + - - +
220A SER* 1.3 79.1 + - - +
222A TRP* 1.3 115.2 + + - +
224A LEU* 3.0 14.8 + - + +
225A PHE* 2.5 70.2 + + + +
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Residues in contact with TRP 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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214A PHE* 3.3 35.1 - + + -
215A PRO* 4.0 27.2 - - + +
218A ASP* 3.2 24.7 + - + +
221A TRP* 1.3 113.0 - + - +
223A ASP* 1.3 56.9 + - - +
225A PHE* 3.4 27.6 - + - +
226A MET* 2.7 35.1 + - + +
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Residues in contact with ASP 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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214A PHE* 3.9 15.8 - - + -
219A TYR* 2.7 56.4 + - + +
220A SER* 3.8 4.0 - - - +
222A TRP* 1.3 73.6 - - - +
224A LEU* 1.3 58.7 + - - +
226A MET* 3.8 1.4 - - - +
227A LYS* 2.8 75.2 + - - +
298A ALA* 4.9 3.6 - - - +
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Residues in contact with LEU 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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220A SER 2.9 19.5 + - - +
221A TRP* 3.4 13.2 - - + +
223A ASP* 1.3 75.9 + - - +
225A PHE* 1.3 68.1 + - - +
227A LYS* 4.7 3.1 - - + -
228A ILE* 3.1 41.5 + - + +
295A LEU* 6.1 0.2 - - + -
298A ALA* 4.2 26.5 - - + +
299A LEU* 3.6 31.4 - - + -
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Residues in contact with PHE 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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221A TRP* 2.5 56.6 + + + +
222A TRP* 3.4 30.5 - + - +
224A LEU* 1.3 73.5 - - - +
226A MET* 1.3 75.9 + - + +
228A ILE* 3.8 4.9 - - - +
229A CYS* 3.1 47.6 + - - -
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Residues in contact with MET 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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139A TYR* 4.5 11.7 - - + +
189A VAL* 6.0 6.3 - - + -
192A SER* 4.6 13.2 - - - +
196A LEU* 4.4 10.8 - - + -
212A LEU* 3.7 29.8 - - - -
214A PHE* 4.0 20.4 - - + -
222A TRP* 2.7 21.4 + - + +
223A ASP* 3.8 2.7 - - - +
225A PHE* 1.3 85.5 - - + +
227A LYS* 1.3 60.1 - - + +
229A CYS* 2.9 8.7 + - + +
230A VAL* 2.8 38.9 + - + +
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Residues in contact with LYS 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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139A TYR* 5.6 3.6 - - - +
223A ASP* 2.8 54.9 + - - +
224A LEU* 4.2 3.8 - - - +
226A MET* 1.3 76.2 - - + +
228A ILE* 1.3 62.9 + - + +
230A VAL* 3.4 3.5 + - - +
231A PHE* 3.1 21.8 + - - +
294A ILE* 3.6 25.7 - - + +
295A LEU* 4.7 5.4 - - + +
297A GLU* 3.2 28.3 + - - +
298A ALA* 4.1 18.8 - - + +
1300A JDC 3.7 25.4 + - + +
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Residues in contact with ILE 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 LEU* 3.1 46.3 + - + +
225A PHE* 3.8 4.7 - - - +
227A LYS* 1.3 73.9 - - - +
229A CYS* 1.3 68.3 + - - +
231A PHE* 3.0 9.7 + - + +
232A ILE* 2.9 36.8 + - + +
295A LEU* 4.3 17.0 - - + -
299A LEU* 4.4 10.1 - - + -
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Residues in contact with CYS 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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143A PHE* 5.4 1.1 - - - -
225A PHE* 3.1 46.3 + - - +
226A MET* 2.9 11.7 + - + +
228A ILE* 1.3 78.3 - - - +
230A VAL* 1.3 63.2 + - + +
232A ILE* 3.1 5.3 + - - -
233A PHE* 2.8 50.2 + - + +
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Residues in contact with VAL 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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139A TYR* 4.1 20.9 - - + -
142A MET* 3.9 8.7 - - + -
143A PHE* 4.2 19.5 - - + -
189A VAL* 6.0 0.9 - - + -
226A MET* 2.8 27.3 + - + +
227A LYS 3.5 3.1 - - - +
229A CYS* 1.3 73.6 - - + +
231A PHE* 1.3 57.3 + - - +
234A ALA* 2.7 40.9 + - + +
235A PHE 3.7 0.3 + - - -
291A HIS* 3.8 14.3 - - + -
1300A JDC 3.2 45.3 - - + +
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Residues in contact with PHE 231 (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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227A LYS 3.1 10.1 + - - +
228A ILE* 3.0 9.3 + - + +
230A VAL* 1.3 82.6 - - - +
232A ILE* 1.3 66.7 + - + +
235A PHE* 3.3 26.6 - + - +
236A VAL* 3.0 49.8 + - + -
291A HIS* 3.8 33.0 - - + +
292A ILE* 4.6 10.5 - - + -
295A LEU* 3.6 41.5 - - + -
1300A JDC 6.5 0.2 - - + -
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Residues in contact with ILE 232 (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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228A ILE* 2.9 31.9 + - + +
229A CYS* 3.5 7.9 - - - +
231A PHE* 1.3 87.8 - - + +
233A PHE* 1.3 76.9 + - + +
236A VAL* 3.3 16.1 + - + -
237A ILE* 2.9 50.7 + - + +
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Residues in contact with PHE 233 (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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143A PHE* 4.0 18.2 - + + -
147A PHE* 3.6 17.4 - + + -
229A CYS* 2.8 51.7 + - + +
232A ILE* 1.3 85.0 - - + +
234A ALA* 1.3 57.6 + - - +
235A PHE 3.2 4.5 - - - -
237A ILE* 3.9 23.7 - - + +
238A PRO* 3.1 21.0 - - - +
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Residues in contact with ALA 234 (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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142A MET* 4.3 7.2 - - + +
143A PHE* 3.8 33.7 - - + -
146A ILE* 3.7 27.2 - - + +
230A VAL* 2.7 29.1 + - + +
233A PHE* 1.3 73.1 - - - +
235A PHE* 1.3 61.6 + - - +
238A PRO* 3.8 4.7 - - - -
283A PHE* 5.7 1.4 - - - -
291A HIS* 3.8 15.3 + - + -
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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