Contacts of the helix formed by residues 216 - 229 (chain B) in PDB entry 5EJC
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 PRO 216 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215B LEU* 1.3 87.6 - - + +
217B GLU* 1.3 66.2 + - - +
218B SER* 3.3 9.9 - - - +
219B SER* 3.1 11.4 + - - +
220B LEU* 2.9 22.9 + - - -
268B GLN* 3.6 33.4 - - + +
271B SER* 3.1 32.5 - - - +
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Residues in contact with GLU 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B LYS 4.8 0.5 - - - +
140B ALA* 3.4 39.4 - - + +
143B GLU* 3.8 31.4 - - + +
144B MSE 3.7 18.7 - - + +
213B GLY* 5.1 6.2 + - - -
215B LEU 4.2 7.6 - - - +
216B PRO* 1.3 74.1 - - - +
218B SER* 1.3 65.0 + - - +
220B LEU* 4.0 8.2 - - + +
221B GLN* 3.1 30.8 + - - +
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Residues in contact with SER 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B PRO* 4.3 11.3 - - - +
217B GLU* 1.3 78.7 - - - +
219B SER* 1.3 65.9 + - - +
221B GLN* 3.4 29.2 + - - +
222B ARG* 4.1 9.5 + - - +
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Residues in contact with SER 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LEU* 5.1 1.3 - - - -
216B PRO* 3.1 9.0 + - - +
218B SER* 1.3 81.1 + - - +
220B LEU* 1.3 68.4 + - - +
221B GLN 3.2 0.2 - - - -
222B ARG* 3.0 29.0 + - - +
223B VAL 3.6 2.4 + - - -
271B SER* 3.6 18.4 + - - -
272B ASP* 3.6 28.2 + - - +
275B VAL* 3.9 26.3 - - - +
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Residues in contact with LEU 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B ALA* 4.4 4.9 - - + -
144B MSE 3.8 13.0 - - + -
210B CYS 3.4 20.6 - - - +
211B PHE* 3.7 30.5 - - + +
212B ALA* 3.9 7.6 - - - -
213B GLY 5.0 0.2 - - - +
215B LEU* 4.1 20.6 - - + +
216B PRO 2.9 16.4 + - - +
217B GLU* 3.4 7.2 + - + +
219B SER* 1.3 76.8 - - - +
221B GLN* 1.3 58.1 + - - +
223B VAL* 2.9 32.4 + - + +
224B TRP* 3.0 42.6 + - + +
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Residues in contact with GLN 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B SER* 5.5 2.4 + - - -
56B ARG* 3.6 45.6 + - - +
60B TRP* 3.6 2.3 - - + -
144B MSE 3.8 39.6 - - - +
217B GLU 3.1 16.3 + - - +
218B SER* 3.4 28.8 + - - +
220B LEU* 1.3 75.9 - - - +
222B ARG* 1.3 59.5 + - + +
224B TRP* 3.1 5.4 + - - +
225B ASP* 2.9 34.3 + - - +
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Residues in contact with ARG 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B PRO* 4.5 23.2 - - + +
56B ARG* 4.1 14.8 - - - +
218B SER 4.1 13.6 + - - +
219B SER* 3.0 14.8 + - - +
221B GLN* 1.3 77.2 - - + +
223B VAL* 1.3 59.9 + - - +
225B ASP* 3.6 22.7 - - - +
226B LYS* 3.6 16.1 + - - +
272B ASP* 3.1 43.1 + - - +
275B VAL* 3.7 25.7 - - + +
276B SER* 3.1 19.7 + - - +
279B ILE* 4.3 15.5 - - + +
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Residues in contact with VAL 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B PHE* 5.0 1.8 - - + -
215B LEU* 4.8 4.5 - - + -
219B SER 4.2 0.7 - - - +
220B LEU* 2.9 21.6 + - + +
222B ARG* 1.3 76.7 - - - +
224B TRP* 1.3 67.3 + - + +
226B LYS* 3.0 25.0 + - - +
227B VAL* 3.3 8.4 + - + +
234B ILE* 4.5 10.1 - - + -
235B LEU* 3.9 28.0 - - + -
238B VAL* 4.0 24.5 - - + -
275B VAL* 3.7 34.1 - - + -
279B ILE* 5.6 2.0 - - + -
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Residues in contact with TRP 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B TRP* 3.8 14.1 - + + -
137B ILE* 3.8 18.8 - - + -
140B ALA* 3.8 20.4 - - + -
141B MSE 3.8 30.7 - - + -
144B MSE 3.7 27.1 - - + -
158B PHE* 3.7 31.4 - + + -
209B ARG 4.1 4.9 - - - -
210B CYS* 3.0 32.8 + - + +
212B ALA* 4.1 9.4 - - + -
220B LEU* 3.0 35.0 + - + +
221B GLN* 3.1 6.9 + - - +
223B VAL* 1.3 81.9 - - + +
225B ASP* 1.3 66.1 + - - +
227B VAL* 3.7 11.4 - - + -
228B VAL* 2.9 28.2 + - - +
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Residues in contact with ASP 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B SER* 4.1 8.1 - - - +
50B PRO* 4.0 4.3 - - - +
51B LEU* 3.2 39.2 + - + +
56B ARG* 3.0 32.8 + - - -
60B TRP* 3.1 19.7 + - - +
63B LEU* 5.5 0.2 - - - +
221B GLN 2.9 16.1 + - - +
222B ARG* 3.6 17.2 - - - +
224B TRP* 1.3 76.1 - - - +
226B LYS* 1.3 67.8 + - + +
228B VAL* 4.0 2.8 - - - +
229B SER* 3.0 28.3 + - - -
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Residues in contact with LYS 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B SER 2.9 24.7 + - - +
47B GLN* 3.3 17.2 + - - +
48B ARG 4.5 1.0 + - - -
49B PHE* 3.1 25.1 + - - +
50B PRO* 3.9 8.3 - - - +
222B ARG 3.6 19.0 + - - +
223B VAL* 3.0 9.8 + - - +
225B ASP* 1.3 77.6 - - - +
227B VAL* 1.3 64.5 + - - +
229B SER* 2.9 16.9 + - - -
230B GLY 3.2 0.5 + - - -
231B SER 3.2 21.0 + - - +
234B ILE* 4.0 20.2 - - + -
279B ILE* 4.2 26.6 - - + +
282B TRP* 3.6 27.4 - - + -
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Residues in contact with VAL 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B PHE* 3.5 27.8 - - + -
161B GLN* 3.7 4.5 - - - +
162B LEU* 4.5 8.7 - - + -
166B TYR* 2.7 41.8 + - + -
210B CYS* 5.2 2.5 - - + -
223B VAL 3.7 11.9 - - - +
224B TRP* 3.3 15.1 + - + +
226B LYS* 1.3 73.6 - - - +
228B VAL* 1.3 63.8 + - - +
230B GLY 3.4 0.5 + - - -
231B SER 3.3 8.7 - - - +
232B CYS* 5.1 3.1 - - + -
234B ILE* 3.9 9.4 - - + -
235B LEU* 3.9 31.2 - - + -
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Residues in contact with VAL 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B CYS* 5.6 0.3 - - - -
60B TRP* 4.1 34.1 - - + -
63B LEU* 3.8 35.6 - - + +
64B LEU* 4.1 23.8 - - + -
158B PHE* 4.0 22.4 - - + -
161B GLN* 3.5 21.0 + - - -
224B TRP* 2.9 21.0 + - + +
225B ASP 4.0 3.4 - - - +
227B VAL* 1.3 78.0 - - - +
229B SER* 1.3 57.1 + - - +
230B GLY* 3.0 5.9 + - - -
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Residues in contact with SER 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B CYS* 3.8 34.4 - - - +
46B SER* 3.6 24.1 - - - -
47B GLN* 2.5 36.0 + - - +
63B LEU* 4.2 10.3 - - - -
225B ASP 3.0 14.2 + - - -
226B LYS* 2.9 9.7 + - - -
228B VAL* 1.3 78.2 - - - +
230B GLY* 1.3 54.6 + - - +
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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