Contacts of the helix formed by residues 209 - 222 (chain F) in PDB entry 5UHG
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 SER 209 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272C GLU* 4.5 12.8 + - - -
289C LYS* 5.1 2.4 - - - +
203D ARG* 5.5 0.4 - - - +
207F ASP 3.3 9.4 + - - -
208F GLU* 1.3 79.4 - - - +
210F GLU* 1.3 65.3 + - - +
211F ALA* 3.1 13.3 + - - -
212F LEU* 3.5 14.3 + - - +
213F ARG* 3.4 18.7 + - - +
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Residues in contact with GLU 210 (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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210D ASP* 3.9 26.6 - - - +
208F GLU 4.0 0.4 + - - +
209F SER* 1.3 73.1 - - - +
211F ALA* 1.3 62.0 + - - +
213F ARG* 3.4 7.9 + - - +
214F GLN* 3.1 33.6 + - + +
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Residues in contact with ALA 211 (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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272C GLU* 4.0 21.1 - - - +
275C LEU* 5.9 0.7 - - + -
279C ARG* 4.9 5.8 + - - +
209F SER* 3.1 8.4 - - - -
210F GLU* 1.3 78.7 - - - +
212F LEU* 1.3 51.2 + - - +
214F GLN* 3.3 6.3 + - - +
215F ALA* 2.8 37.0 + - - +
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Residues in contact with LEU 212 (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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275C LEU* 4.0 28.2 - - + +
287C PRO* 3.3 27.1 - - + +
288C THR* 5.4 0.9 - - - -
289C LYS* 3.3 49.6 - - + +
208F GLU* 5.7 4.9 - - + -
209F SER* 3.5 16.5 + - - +
210F GLU 3.4 0.4 - - - -
211F ALA* 1.3 78.8 - - - +
213F ARG* 1.3 55.8 + - - +
215F ALA* 3.5 5.8 - - - -
216F ARG* 2.7 45.2 + - + +
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Residues in contact with ARG 213 (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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214D ARG* 3.6 49.0 - - - +
208F GLU* 4.2 22.4 + - + +
209F SER 3.4 10.9 + - - +
210F GLU* 3.7 12.3 - - - +
211F ALA 3.3 0.4 - - - -
212F LEU* 1.3 80.7 - - - +
214F GLN* 1.3 64.2 + - + +
216F ARG* 3.4 41.9 + - - +
217F LYS* 3.8 20.1 + - - +
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Residues in contact with GLN 214 (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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210F GLU* 3.1 22.7 + - + +
211F ALA* 3.7 5.2 - - - +
213F ARG* 1.3 78.1 - - + +
215F ALA* 1.3 59.9 + - - +
216F ARG 3.1 2.4 + - - -
217F LYS* 3.3 9.2 + - - +
218F ASP* 3.0 39.0 + - - +
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Residues in contact with ALA 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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275C LEU* 5.9 2.7 - - + -
279C ARG* 3.4 43.3 - - - +
287C PRO* 3.6 14.3 - - + +
211F ALA 2.8 19.0 + - - +
212F LEU* 3.7 7.9 - - + +
214F GLN* 1.3 76.3 - - - +
216F ARG* 1.3 61.1 + - - +
218F ASP* 3.7 12.8 - - - +
219F ALA* 3.4 17.7 + - - +
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Residues in contact with ARG 216 (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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286C PRO* 4.6 13.8 - - + +
287C PRO* 3.5 25.8 - - + +
208F GLU* 5.8 2.0 + - - -
212F LEU* 2.7 24.6 + - + +
213F ARG* 3.4 36.1 - - - +
214F GLN 3.1 0.2 - - - -
215F ALA* 1.3 79.1 - - - +
217F LYS* 1.3 58.8 + - - +
219F ALA* 3.6 2.1 + - - +
220F GLU* 3.2 29.0 + - + +
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Residues in contact with LYS 217 (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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218D ARG* 6.1 6.1 - - - +
237D ASP* 2.4 34.5 + - - +
239D ASN* 5.5 3.8 - - - +
213F ARG* 3.8 13.5 + - - +
214F GLN* 3.3 11.7 + - - +
216F ARG* 1.3 77.6 - - - +
218F ASP* 1.3 65.7 + - - +
220F GLU* 4.1 12.4 + - - +
221F LEU* 3.1 34.7 + - + +
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Residues in contact with ASP 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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279C ARG* 5.8 3.0 + - - -
214F GLN* 3.0 29.8 + - - +
215F ALA* 3.7 11.2 - - - +
216F ARG 3.2 0.2 - - - -
217F LYS* 1.3 80.5 - - - +
219F ALA* 1.3 63.5 + - - +
221F LEU* 3.9 4.1 - - - +
222F THR* 3.1 23.4 + - - -
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Residues in contact with ALA 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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278C TYR* 5.7 1.1 - - + -
279C ARG* 5.5 9.6 - - + -
282C ARG 5.3 0.4 - - - +
283C PRO* 5.0 5.2 - - + -
284C GLY* 3.1 29.1 + - - +
285C GLU 3.3 24.9 - - - +
287C PRO* 4.3 4.3 - - + -
215F ALA 3.4 14.2 + - - +
216F ARG 4.0 3.1 - - - +
217F LYS 3.4 0.2 - - - -
218F ASP* 1.3 77.1 - - - +
220F GLU* 1.3 67.4 + - - +
222F THR* 3.0 15.7 + - - +
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Residues in contact with GLU 220 (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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284C GLY 4.2 10.5 - - - +
285C GLU 4.6 1.7 + - - +
286C PRO* 5.3 14.1 - - + -
237D ASP* 5.2 5.5 - - - +
239D ASN* 4.7 13.0 + - - -
216F ARG* 3.2 18.6 + - + +
217F LYS* 4.3 13.6 + - - +
219F ALA* 1.3 79.5 - - - +
221F LEU* 1.3 68.4 + - - +
222F THR 3.8 5.2 - - - +
233F LYS* 4.0 19.4 - - + -
237F LYS* 4.0 23.8 + - + +
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Residues in contact with LEU 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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236D VAL* 3.5 46.3 - - + +
237D ASP* 3.6 38.8 - - + +
217F LYS* 3.1 25.8 + - + +
218F ASP* 3.9 4.5 - - - +
219F ALA 3.0 1.0 + - - -
220F GLU* 1.3 86.0 + - - +
222F THR* 1.3 69.2 + - - +
223F ALA* 3.5 4.0 + - - +
233F LYS* 5.5 0.9 - - - -
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Residues in contact with THR 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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283C PRO* 4.7 15.9 - - + +
284C GLY* 3.3 19.9 - - - +
127D LYS* 4.6 12.1 - - - +
236D VAL* 5.6 0.4 - - - -
218F ASP 3.1 13.9 + - - -
219F ALA* 3.0 17.2 + - - +
220F GLU 3.8 4.4 - - - +
221F LEU* 1.3 83.6 - - - +
223F ALA* 1.3 69.3 + - - +
233F LYS* 4.3 3.0 - - - -
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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