Contacts of the helix formed by residues 214 - 228 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120F ALA* 5.1 6.1 + - - +
148F TRP* 3.8 10.7 + - - -
172F ASN* 3.5 20.5 + - - +
174F LEU* 3.5 46.7 - - - +
175F MET* 3.7 25.2 - - + +
213F SER* 1.3 81.9 + - - +
215F PRO* 1.3 70.0 - - + +
216F VAL 2.9 1.7 + - - -
217F GLY* 3.1 14.9 + - - -
218F HIS* 3.9 33.6 + - + -
313F ILE* 5.3 12.7 - - - +
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Residues in contact with PRO 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172F ASN* 5.6 0.2 - - - +
211F SER* 3.8 14.1 - - - +
212F HIS 3.3 14.8 - - - +
213F SER* 3.4 4.7 - - - -
214F ARG* 1.3 94.8 - - + +
216F VAL* 1.3 61.4 + - - +
217F GLY 3.2 0.2 - - - -
218F HIS* 2.9 30.2 + - + +
219F CYS* 3.0 15.2 + - - -
262F VAL* 4.0 15.7 - - + -
263F GLU 4.4 0.9 - - - -
264F GLY* 3.9 27.8 - - - +
314F PRO* 5.4 7.0 - - + -
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Residues in contact with VAL 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148F TRP* 3.6 33.4 - - + -
201F GLU* 4.6 6.1 - - + -
211F SER* 3.5 39.9 - - - +
212F HIS* 3.6 3.6 - - - +
213F SER 2.9 15.2 + - - +
215F PRO* 1.3 77.2 - - - +
217F GLY* 1.3 62.6 + - - +
219F CYS* 3.0 15.8 + - - +
220F LEU* 3.2 14.7 + - + +
235F VAL* 4.7 8.5 - - + -
236F ILE 4.4 1.1 - - - +
237F ASN* 3.7 27.4 - - + +
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Residues in contact with GLY 217 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148F TRP* 3.4 28.1 - - - +
214F ARG 3.1 10.0 + - - -
216F VAL* 1.3 78.4 - - - +
218F HIS* 1.3 60.8 + - - +
219F CYS 3.2 0.2 + - - -
220F LEU* 3.4 4.9 + - - +
221F GLU* 3.1 31.6 + - - +
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Residues in contact with HIS 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214F ARG* 3.9 45.3 + - + +
215F PRO* 2.9 24.2 + - + +
217F GLY* 1.3 76.7 - - - +
219F CYS* 1.3 61.3 + - - +
221F GLU* 3.4 25.2 + - - +
222F ALA* 3.1 22.5 + - - +
313F ILE* 5.8 3.6 - - + -
314F PRO 4.1 18.8 + - - -
315F GLN* 5.9 0.4 - - - -
316F VAL* 3.9 21.3 - - + +
319F ILE* 3.8 18.6 - - + +
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Residues in contact with CYS 219 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209F VAL* 3.8 15.5 - - + -
211F SER* 4.1 10.1 - - - -
215F PRO 3.0 17.9 + - - -
216F VAL* 3.0 8.0 + - - +
218F HIS* 1.3 75.0 - - - +
220F LEU* 1.3 53.7 + - - +
222F ALA* 2.9 7.6 + - - +
223F ALA* 2.6 35.7 + - - +
235F VAL* 3.8 23.1 - - + +
262F VAL* 3.5 39.0 - - - -
319F ILE* 4.0 7.0 - - - -
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Residues in contact with LEU 220 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148F TRP* 3.5 37.2 - - + -
201F GLU* 3.9 20.6 - - + +
202F ARG* 4.0 15.5 + - + +
216F VAL* 3.2 9.5 + - + +
217F GLY 3.4 5.1 + - - +
219F CYS* 1.3 76.9 - - - +
221F GLU* 1.3 61.7 + - - +
223F ALA* 3.8 5.8 - - - +
224F ALA* 3.1 22.9 + - - +
235F VAL* 3.7 32.1 - - + -
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Residues in contact with GLU 221 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217F GLY 3.1 18.9 + - - +
218F HIS* 3.4 32.4 - - - +
219F CYS 3.1 0.2 - - - -
220F LEU* 1.3 76.3 - - - +
222F ALA* 1.3 62.3 + - - +
224F ALA* 3.4 11.2 - - - +
225F VAL* 3.4 20.1 - - - +
316F VAL* 4.1 17.5 - - + +
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Residues in contact with ALA 222 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218F HIS 3.1 13.5 + - - +
219F CYS* 2.9 10.0 + - - +
221F GLU* 1.3 75.1 - - - +
223F ALA* 1.3 66.3 + - - +
224F ALA 3.0 2.7 + - - -
225F VAL* 3.2 6.2 + - - +
226F LEU* 3.1 29.1 + - + +
316F VAL* 3.7 22.0 - - + +
319F ILE* 4.4 13.0 - - + -
320F ILE* 3.9 16.1 - - + +
323F ILE* 5.1 2.2 - - + -
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Residues in contact with ALA 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202F ARG* 3.4 36.0 + - - +
219F CYS 2.6 20.8 + - - +
220F LEU* 3.8 4.5 - - - +
222F ALA* 1.3 71.4 - - - +
224F ALA* 1.3 62.0 + - - +
226F LEU* 3.4 2.0 + - - +
227F SER* 3.0 26.0 + - - -
231F VAL 4.3 1.4 - - - +
233F CYS* 3.8 28.5 - - + -
235F VAL* 4.0 5.4 - - + -
323F ILE* 6.2 0.2 - - - -
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Residues in contact with ALA 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202F ARG* 4.8 2.7 - - - +
220F LEU 3.1 12.4 + - - +
221F GLU* 3.4 13.0 - - - +
222F ALA 3.0 0.2 - - - -
223F ALA* 1.3 76.6 - - - +
225F VAL* 1.3 64.3 + - + +
227F SER* 3.0 22.5 + - - -
228F LYS* 3.7 16.1 + - - +
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Residues in contact with VAL 225 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221F GLU 3.4 14.6 - - - +
222F ALA* 3.2 7.8 + - - +
224F ALA* 1.3 77.1 - - + +
226F LEU* 1.3 62.3 + - + +
228F LYS* 3.7 25.2 + - - +
229F GLU* 4.0 13.6 - - - +
316F VAL* 5.3 3.1 - - + -
320F ILE* 3.8 29.4 - - + -
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Residues in contact with LEU 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222F ALA 3.1 19.9 + - - +
223F ALA* 3.9 3.8 - - - +
224F ALA 3.1 1.0 - - - -
225F VAL* 1.3 75.6 - - + +
227F SER* 1.3 58.8 + - - +
228F LYS 3.1 5.6 - - - -
229F GLU* 3.0 34.2 + - - +
230F GLY 3.4 0.2 + - - -
231F VAL* 3.0 45.9 + - + +
233F CYS* 3.8 11.2 - - - -
320F ILE* 4.3 26.7 - - + -
323F ILE* 3.7 44.0 - - + -
324F LYS* 4.4 12.3 - - + -
329F ILE* 5.6 0.2 - - + -
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Residues in contact with SER 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202F ARG* 3.3 24.7 + - - -
223F ALA 3.0 7.0 + - - -
224F ALA* 3.0 15.6 + - - -
226F LEU* 1.3 77.0 - - - +
228F LYS* 1.4 57.2 + - - +
229F GLU 3.1 1.8 - - - -
230F GLY* 3.3 11.7 + - - -
231F VAL 3.3 9.2 + - - +
232F GLU* 3.1 26.0 - - - +
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Residues in contact with LYS 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224F ALA* 4.2 16.0 + - - +
225F VAL* 3.7 17.5 - - - +
226F LEU 3.1 0.6 - - - -
227F SER* 1.4 75.9 + - - +
229F GLU* 1.3 62.4 + - + +
230F GLY 3.5 1.1 - - - -
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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