Contacts of the helix formed by residues 213 - 227 (chain A) in PDB entry 3EIJ
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 ALA 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A GLY 3.9 0.6 + - - -
212A LYS* 1.3 73.0 - - - +
214A SER* 1.3 59.6 + - - +
215A HIS 3.3 0.7 + - - -
216A ARG* 3.4 54.4 + - - +
217A GLU* 4.1 3.3 + - - +
353A GLU* 4.4 13.5 - - + +
358B HIS* 4.3 19.7 - - + +
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Residues in contact with SER 214 (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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212A LYS* 3.1 17.0 + - - +
213A ALA* 1.3 76.5 - - - +
215A HIS* 1.3 77.1 + - - +
216A ARG 3.2 0.4 + - - -
217A GLU* 3.5 8.1 + - - +
218A MET* 3.2 27.7 + - - +
358B HIS* 4.9 12.0 - - - -
397B THR* 5.4 2.3 + - - -
399B ASP* 3.2 33.1 + - - +
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Residues in contact with HIS 215 (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* 3.4 64.1 + + + +
177A GLU* 4.9 6.5 + - - -
207A LEU 5.5 0.2 - - - -
208A ALA* 4.0 10.1 - - - -
211A GLY* 3.8 9.6 - - - -
212A LYS* 3.0 57.0 + - + +
214A SER* 1.3 81.9 + - - +
216A ARG* 1.3 59.9 + - - +
218A MET* 3.8 4.8 - - - -
219A THR* 2.9 32.9 + - - -
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Residues in contact with ARG 216 (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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208A ALA* 4.1 16.0 + - + +
209A LEU* 5.0 5.2 + - - +
211A GLY 5.2 3.0 + - - -
212A LYS 4.1 6.9 + - - +
213A ALA* 3.5 45.0 + - - +
214A SER 3.2 0.6 - - - -
215A HIS* 1.3 75.1 - - - +
217A GLU* 1.3 66.1 + - - +
219A THR 3.3 0.9 + - - -
220A SER* 3.1 20.1 + - - -
260A LEU* 3.5 50.5 - - - +
263A GLN* 4.4 8.6 + - - +
264A PHE* 3.2 35.5 - - + -
353A GLU* 3.7 22.8 + - - -
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Residues in contact with GLU 217 (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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213A ALA 4.1 2.8 + - - +
214A SER* 3.5 12.6 + - - +
215A HIS 3.5 0.2 - - - -
216A ARG* 1.3 77.1 - - - +
218A MET* 1.3 64.7 + - + +
220A SER* 3.1 8.3 + - - -
221A LYS* 3.1 45.7 + - - +
267A ARG* 2.8 42.4 + - - -
399B ASP* 6.0 4.0 - - + -
403B ARG* 6.3 0.4 - - - -
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Residues in contact with MET 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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175A TYR* 2.4 64.1 + - + +
176A PHE* 3.5 26.9 - - + +
179A GLY* 3.7 19.1 - - - -
214A SER* 3.2 20.7 + - - +
215A HIS* 3.7 14.4 - - - +
216A ARG 3.3 0.2 - - - -
217A GLU* 1.3 77.9 - - + +
219A THR* 1.3 61.8 + - - +
221A LYS* 3.5 10.3 + - + +
222A LEU 3.1 9.4 + - - -
398B VAL* 4.1 12.1 - - + -
399B ASP* 4.2 25.1 - - + +
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Residues in contact with THR 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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175A TYR* 4.3 2.7 - - - -
176A PHE* 3.1 18.0 - - - -
204A ALA* 3.6 32.8 + - + +
205A VAL* 4.0 9.6 - - + -
208A ALA* 3.3 8.5 - - - +
215A HIS 2.9 21.3 + - - -
216A ARG 3.6 4.9 - - - -
217A GLU 3.2 0.2 - - - -
218A MET* 1.3 74.9 - - - +
220A SER* 1.3 59.7 + - - +
222A LEU* 3.0 8.8 + - + +
223A LEU* 2.9 39.5 + - + +
264A PHE* 3.8 18.2 - - + -
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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
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216A ARG 3.1 9.4 + - - -
217A GLU* 3.3 10.0 - - - -
219A THR* 1.3 76.9 - - - +
221A LYS* 1.3 62.1 + - - +
223A LEU* 3.3 10.4 + - - +
224A SER* 3.0 23.0 + - - -
264A PHE* 3.4 24.3 + - - -
267A ARG* 3.3 44.5 - - - +
271A ASP* 4.0 3.3 - - - +
273A ILE* 5.3 0.5 - - - +
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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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175A TYR* 4.0 5.6 - - - +
181A THR* 4.4 2.9 - - - +
217A GLU* 3.1 43.7 + - - +
218A MET* 3.6 15.4 - - + +
220A SER* 1.3 75.6 - - - +
222A LEU* 1.3 58.6 + - - +
224A SER* 3.4 5.2 + - - -
225A ASP* 3.0 39.8 + - - +
267A ARG* 3.7 17.3 - - - +
399B ASP* 4.6 11.3 + - - +
402B LYS* 4.2 28.3 - - - +
403B ARG* 4.5 23.7 - - - +
406B GLU* 4.0 17.7 + - - +
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Residues in contact with LEU 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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172A ILE* 5.2 10.1 - - + -
175A TYR* 3.8 24.0 + - + -
176A PHE* 6.1 0.2 - - + -
181A THR* 3.7 21.1 - - - +
184A VAL* 3.8 39.3 - - + -
200A VAL* 5.6 2.9 - - + -
204A ALA* 4.6 20.6 - - + -
218A MET 3.1 13.7 + - - +
219A THR* 3.0 11.8 + - - +
221A LYS* 1.3 77.9 - - - +
223A LEU* 1.3 59.4 + - + +
225A ASP* 3.4 0.7 + - - +
226A LEU* 2.9 57.3 + - + +
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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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200A VAL* 5.3 0.9 - - + -
201A PRO* 3.6 39.3 - - + -
204A ALA* 4.8 4.3 - - + -
205A VAL* 4.4 17.0 - - + -
219A THR* 2.9 29.3 + - + +
220A SER* 3.3 11.0 + - - +
222A LEU* 1.3 81.9 - - + +
224A SER* 1.3 62.0 + - - +
226A LEU* 3.5 6.5 + - + +
227A CYS* 3.1 27.2 + - - +
231A MET* 4.6 6.2 - - + +
236A VAL* 5.7 1.6 - - + -
240A PHE* 4.2 29.4 - - + -
264A PHE* 4.8 4.5 - - + +
268A ALA* 5.8 0.9 - - + -
273A ILE* 3.7 17.3 - - + +
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Residues in contact with SER 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 3.0 10.3 + - - -
221A LYS* 3.6 7.2 - - - -
223A LEU* 1.3 78.8 - - - +
225A ASP* 1.3 67.2 + - - +
227A CYS* 3.5 15.6 + - - +
267A ARG* 5.7 0.2 - - - -
271A ASP* 3.4 38.9 + - - +
273A ILE* 3.9 16.3 - - - +
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Residues in contact with ASP 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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181A THR* 2.9 44.9 + - + +
221A LYS* 3.0 20.8 + - - +
222A LEU 3.9 1.8 - - - +
224A SER* 1.3 82.1 + - - +
226A LEU* 1.3 64.3 + - - +
227A CYS 3.5 2.3 + - - +
229A THR* 3.4 16.8 + - - +
402B LYS* 5.1 5.5 + - - -
442B GLN* 4.2 4.5 + - - -
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Residues in contact with LEU 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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181A THR* 4.6 2.9 - - + +
184A VAL* 4.4 0.4 - - + -
185A ALA* 3.8 33.4 - - + +
188A LEU* 3.9 21.3 - - + -
200A VAL* 4.4 10.8 - - + -
222A LEU* 2.9 56.2 + - + +
223A LEU* 4.1 5.2 - - + +
225A ASP* 1.3 75.1 - - - +
227A CYS* 1.3 63.1 + - - +
229A THR* 3.2 3.2 + - - -
230A VAL* 3.1 47.2 + - + -
231A MET* 3.3 22.8 + - + -
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Residues in contact with CYS 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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223A LEU 3.1 18.9 + - - +
224A SER 3.5 9.6 - - - +
225A ASP 3.3 3.7 - - - +
226A LEU* 1.3 75.8 - - - +
228A GLY* 1.3 61.8 + - - +
229A THR* 4.4 0.5 + - - -
231A MET* 3.2 13.0 - - - +
233A THR* 3.7 33.4 - - - -
236A VAL* 3.8 24.0 - - + -
273A ILE* 3.7 24.6 - - + +
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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