Contacts of the helix formed by residues 214 - 228 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148L TRP* 3.9 10.4 + - - -
172L ASN* 3.6 20.4 - - - +
174L LEU* 3.7 48.4 + - - +
175L MET* 4.1 20.9 - - - +
213L SER* 1.3 79.9 + - - +
215L PRO* 1.3 73.8 - - + +
216L VAL 2.7 2.3 + - - -
217L GLY* 2.7 17.2 + - - -
218L HIS* 3.7 33.2 + - + -
313L ILE* 5.4 11.7 - - - +
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Residues in contact with PRO 215 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211L SER* 3.7 13.2 - - - +
212L HIS 3.3 17.5 - - - +
213L SER* 4.2 2.5 - - - -
214L ARG* 1.3 95.6 - - + +
216L VAL* 1.3 62.5 + - - -
218L HIS* 2.7 30.2 + - + +
219L CYS* 3.1 13.2 + - - -
262L VAL* 4.3 15.5 - - + -
263L GLU* 4.3 0.9 - - - -
264L GLY* 4.0 25.8 - - - +
313L ILE* 6.6 0.4 - - + -
314L PRO* 4.6 11.0 - - + -
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Residues in contact with VAL 216 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148L TRP* 3.7 33.7 - - + -
201L GLU* 4.5 7.0 - - + -
211L SER* 3.7 17.5 + - - +
212L HIS* 3.7 27.6 - - - +
213L SER 2.9 20.4 + - - +
214L ARG 2.7 4.4 + - - -
215L PRO* 1.3 74.9 - - - +
217L GLY* 1.3 61.7 + - - +
219L CYS* 3.3 5.9 + - - +
220L LEU* 3.1 23.5 + - + +
235L VAL* 4.6 6.5 - - + +
237L ASN* 3.8 25.6 - - + +
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Residues in contact with GLY 217 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148L TRP* 3.5 25.8 - - - +
214L ARG 2.7 17.6 + - - -
216L VAL* 1.3 74.0 - - - +
218L HIS* 1.3 57.1 + - - -
220L LEU* 3.5 6.6 + - - +
221L GLU* 3.2 24.4 + - - +
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Residues in contact with HIS 218 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214L ARG* 3.7 40.0 + - + -
215L PRO* 2.7 27.9 + - + +
217L GLY* 1.3 70.8 - - - +
219L CYS* 1.3 62.2 + - - +
221L GLU* 3.2 23.7 - - - +
222L ALA* 2.8 27.9 + - - +
313L ILE* 5.8 2.2 - - + +
314L PRO* 4.1 20.5 + - - +
315L GLN* 5.9 0.7 - - - -
316L VAL* 3.9 19.1 - - + +
319L ILE* 3.9 17.8 - - + +
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Residues in contact with CYS 219 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209L VAL* 3.6 20.3 - - + +
211L SER* 3.7 13.5 - - - -
215L PRO 3.1 15.6 + - - -
216L VAL 3.4 7.4 - - - +
218L HIS* 1.3 74.0 - - - +
220L LEU* 1.3 54.7 + - - +
221L GLU 3.0 1.6 - - - -
222L ALA* 3.6 5.2 - - - +
223L ALA* 2.7 36.9 + - - +
235L VAL* 4.0 17.4 - - + +
262L VAL* 3.6 39.5 - - - -
319L ILE* 4.3 7.0 - - - -
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Residues in contact with LEU 220 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148L TRP* 3.6 31.0 - - + -
201L GLU* 3.7 23.1 - - + +
202L ARG* 4.2 16.0 - - + -
216L VAL* 3.1 14.9 + - + +
217L GLY* 3.6 9.6 - - - +
218L HIS 3.3 0.2 - - - -
219L CYS* 1.3 75.7 - - - +
221L GLU* 1.3 61.3 + - - +
223L ALA* 3.5 4.8 + - - +
224L ALA* 3.2 21.3 + - - +
235L VAL* 3.7 27.6 - - + -
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Residues in contact with GLU 221 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217L GLY 3.2 11.8 + - - +
218L HIS* 3.2 33.0 - - - +
220L LEU* 1.3 77.5 - - - +
222L ALA* 1.3 65.8 + - - +
224L ALA* 3.1 16.8 + - - +
225L VAL* 3.2 17.2 + - + +
316L VAL* 4.1 16.8 - - + +
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Residues in contact with ALA 222 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218L HIS 2.8 16.5 + - - +
219L CYS 3.7 3.4 - - - +
221L GLU* 1.3 73.3 - - - +
223L ALA* 1.3 66.1 + - - +
225L VAL* 2.9 5.1 + - - +
226L LEU* 2.9 29.1 + - + +
316L VAL* 3.8 14.7 - - + +
319L ILE* 4.2 20.2 - - + -
320L ILE* 3.7 26.4 - - + +
323L ILE* 5.4 2.2 - - + -
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Residues in contact with ALA 223 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202L ARG* 3.5 33.2 + - - -
219L CYS 2.7 21.8 + - - +
220L LEU 3.6 4.9 - - - +
221L GLU 3.2 0.2 - - - -
222L ALA* 1.3 72.3 - - - +
224L ALA* 1.3 56.9 + - - +
226L LEU* 3.2 3.0 + - - +
227L SER* 3.0 30.7 + - - -
231L VAL 4.4 1.7 - - - +
233L CYS* 4.2 21.7 - - + -
235L VAL* 4.1 11.9 - - + -
323L ILE* 6.1 0.2 - - - +
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Residues in contact with ALA 224 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202L ARG* 5.0 3.3 - - - +
220L LEU 3.2 9.5 + - - +
221L GLU* 3.1 11.4 + - - +
223L ALA* 1.3 73.8 - - - +
225L VAL* 1.3 68.1 + - + +
226L LEU 2.9 3.0 + - - -
227L SER* 3.2 18.4 + - - -
228L LYS* 3.5 13.1 + - - +
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Residues in contact with VAL 225 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221L GLU* 3.2 12.7 + - + +
222L ALA* 2.9 9.6 + - - +
224L ALA* 1.3 79.6 - - + +
226L LEU* 1.3 63.5 + - + +
228L LYS* 3.5 27.4 - - - +
229L GLU* 3.5 17.6 - - - +
316L VAL* 5.2 4.3 - - + -
320L ILE* 3.7 29.8 - - + -
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Residues in contact with LEU 226 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222L ALA 2.9 17.2 + - - +
223L ALA* 3.7 4.5 - - - +
224L ALA 3.0 0.2 - - - -
225L VAL* 1.3 77.1 - - + +
227L SER* 1.3 62.0 + - - +
228L LYS 3.1 1.8 - - - -
229L GLU* 2.7 33.8 + - - +
231L VAL* 3.3 34.2 + - + +
233L CYS* 3.8 17.0 - - - -
320L ILE* 3.9 31.4 - - + -
323L ILE* 3.7 39.3 - - + -
324L LYS* 4.5 20.4 - - + +
329L ILE* 5.5 0.2 - - + -
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Residues in contact with SER 227 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202L ARG* 3.7 19.9 + - - -
223L ALA 3.0 9.4 + - - -
224L ALA* 3.2 10.9 + - - -
226L LEU* 1.3 72.0 - - - +
228L LYS* 1.3 59.5 + - - +
229L GLU 2.7 10.9 + - - -
230L GLY* 3.0 11.4 + - - -
231L VAL 3.3 13.0 + - - +
232L GLU* 3.3 23.9 - - - +
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Residues in contact with LYS 228 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224L ALA 3.5 9.7 + - - +
225L VAL* 3.5 24.7 - - - +
226L LEU 3.1 0.2 - - - -
227L SER* 1.3 77.8 + - - +
229L GLU* 1.3 63.6 + - + +
230L GLY 3.7 0.4 - - - -
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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