Contacts of the helix formed by residues 214 - 228 (chain D) in PDB entry 3EXG
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 ARG 214 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120D ALA* 5.8 1.6 + - - +
148D TRP* 4.2 3.1 + - - -
172D ASN* 3.7 21.7 + - - +
174D LEU* 3.6 46.2 - - - +
175D MET* 3.6 33.2 - - - +
213D SER* 1.3 81.9 + - - +
215D PRO* 1.3 70.1 - - + +
216D VAL 2.8 6.9 + - - -
217D GLY* 3.0 15.2 + - - -
218D HIS* 3.6 33.4 + - - +
313D ILE* 5.3 11.5 - - - +
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Residues in contact with PRO 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D SER* 4.0 4.7 - - - +
212D HIS 3.5 15.0 - - - +
213D SER* 4.5 1.8 - - - -
214D ARG* 1.3 96.1 - - + +
216D VAL* 1.3 52.7 + - - -
217D GLY 3.3 0.2 - - - -
218D HIS* 2.8 40.8 + - + +
219D CYS* 3.0 14.2 + - - -
262D VAL* 4.2 18.4 - - + -
263D GLU* 4.4 4.3 - - - -
264D GLY* 3.9 27.1 - - - +
313D ILE* 6.0 2.5 - - + -
314D PRO* 4.6 10.1 - - + -
319D ILE* 4.7 0.7 - - - +
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Residues in contact with VAL 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D TRP* 3.7 33.0 - - + -
201D GLU* 4.5 6.5 - - + -
211D SER* 3.6 38.9 + - - +
212D HIS* 3.7 5.6 - - - +
213D SER 3.1 20.0 + - - +
214D ARG 2.8 4.2 + - - -
215D PRO* 1.3 72.8 - - - +
217D GLY* 1.3 62.1 + - - +
219D CYS* 3.2 10.1 + - - +
220D LEU* 3.1 21.5 + - + +
235D VAL* 4.8 7.9 - - + -
236D ILE 4.6 0.7 - - - +
237D ASN* 4.2 22.4 - - + -
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Residues in contact with GLY 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D TRP* 3.6 25.0 - - - +
214D ARG 3.0 11.2 + - - -
216D VAL* 1.3 77.1 - - - +
218D HIS* 1.3 68.3 + - - +
220D LEU* 3.3 6.3 + - - +
221D GLU* 3.1 25.9 + - - +
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Residues in contact with HIS 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D ARG* 3.6 49.7 + - + +
215D PRO* 2.8 23.2 + - + +
217D GLY* 1.3 77.7 - - - +
219D CYS* 1.3 52.9 + - - +
221D GLU* 3.2 20.4 - - - +
222D ALA* 2.8 30.5 + - - +
313D ILE* 6.3 1.6 - - + -
314D PRO 3.7 20.2 + - - +
315D GLN* 5.9 0.4 - - - -
316D VAL* 3.2 27.4 + - + +
319D ILE* 4.0 12.4 - - + +
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Residues in contact with CYS 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D VAL* 3.6 28.8 - - + +
211D SER* 3.7 23.8 - - - -
215D PRO 3.0 15.8 + - - -
216D VAL 3.3 8.5 - - - +
218D HIS* 1.3 76.5 - - - +
220D LEU* 1.3 53.9 + - - +
222D ALA* 3.1 5.4 + - - +
223D ALA* 2.7 35.3 + - - +
235D VAL* 4.0 19.2 - - + +
262D VAL* 3.9 14.1 - - - -
319D ILE* 4.1 11.9 - - - -
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Residues in contact with LEU 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D TRP* 3.4 37.9 - - + -
201D GLU* 4.0 19.1 - - + +
202D ARG* 4.1 14.0 - - + -
216D VAL* 3.1 15.5 + - + +
217D GLY* 3.3 5.8 + - - +
219D CYS* 1.3 74.1 - - - +
221D GLU* 1.3 57.6 + - - +
223D ALA* 3.2 5.7 + - - +
224D ALA* 2.8 31.2 + - - +
235D VAL* 3.7 32.3 - - + -
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Residues in contact with GLU 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217D GLY 3.1 12.4 + - - +
218D HIS* 3.2 37.8 - - - +
220D LEU* 1.3 76.7 - - - +
222D ALA* 1.3 63.4 + - - +
224D ALA* 3.2 6.2 + - - +
225D VAL* 2.9 26.8 + - + +
316D VAL* 3.8 17.3 - - + +
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Residues in contact with ALA 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218D HIS 2.8 17.3 + - - +
219D CYS 3.1 8.0 + - - +
221D GLU* 1.3 73.1 - - - +
223D ALA* 1.3 52.4 + - - +
225D VAL* 2.9 4.7 + - - +
226D LEU* 2.7 39.1 + - - +
316D VAL* 4.2 5.8 - - + +
319D ILE* 4.0 21.1 - - + -
320D ILE* 3.7 31.8 - - + +
323D ILE* 5.1 5.8 - - + -
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Residues in contact with ALA 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D ARG* 3.6 35.9 + - - +
219D CYS 2.7 19.0 + - - +
220D LEU 3.6 4.0 - - - +
222D ALA* 1.3 72.5 - - - +
224D ALA* 1.3 62.0 + - - +
226D LEU* 3.9 1.8 - - - +
227D SER* 3.1 24.3 + - - -
231D VAL 4.6 1.6 - - - +
233D CYS* 4.1 23.0 - - - -
235D VAL* 4.0 13.2 - - + -
323D ILE* 6.0 0.2 - - - +
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Residues in contact with ALA 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D ARG* 5.0 2.4 - - - +
220D LEU 2.8 16.5 + - - +
221D GLU* 3.8 4.7 - - - +
222D ALA 3.2 0.2 - - - -
223D ALA* 1.3 75.5 - - - +
225D VAL* 1.3 66.6 + - - +
226D LEU 3.2 0.3 + - - -
227D SER* 3.3 17.4 + - - -
228D LYS* 3.7 12.9 + - - +
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Residues in contact with VAL 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D GLU* 2.9 16.8 + - + +
222D ALA 2.9 8.5 + - - +
224D ALA* 1.3 77.8 - - - +
226D LEU* 1.3 63.5 + - + +
227D SER 3.5 0.5 + - - -
228D LYS* 3.5 37.4 + - - +
229D GLU* 3.6 18.6 - - - +
316D VAL* 5.5 3.4 - - + -
320D ILE* 3.9 25.4 - - + -
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Residues in contact with LEU 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222D ALA 2.7 17.1 + - - +
223D ALA* 4.1 4.7 - - - +
225D VAL* 1.3 76.9 - - + +
227D SER* 1.3 63.4 + - - +
229D GLU* 3.1 39.1 + - - +
231D VAL* 3.3 39.6 + - + +
233D CYS* 4.3 9.0 - - - -
320D ILE* 4.3 21.8 - - + +
323D ILE* 3.6 43.3 - - + -
324D LYS* 4.5 18.4 - - + +
329D ILE* 5.7 0.9 - - + -
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Residues in contact with SER 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D ARG* 3.8 12.8 + - - -
223D ALA 3.1 16.9 + - - -
224D ALA* 3.3 11.7 + - - -
226D LEU* 1.3 73.8 - - - +
228D LYS* 1.3 55.0 + - - +
229D GLU 2.6 16.2 + - - -
230D GLY* 2.8 13.9 + - - +
231D VAL 3.4 9.6 - - - +
232D GLU* 3.4 22.1 - - - +
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Residues in contact with LYS 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224D ALA 3.7 7.5 + - - +
225D VAL* 3.5 39.4 + - - +
226D LEU 3.2 0.2 - - - -
227D SER* 1.3 78.9 + - - +
229D GLU* 1.3 60.5 - - + +
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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