Contacts of the helix formed by residues 210 - 222 (chain L) in PDB entry 3Q3G
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 HIS 210 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98J TYR 5.5 1.0 + - - -
99J SER* 5.8 1.0 - - - -
100J TYR* 4.8 15.2 - + - -
61K LYS* 4.8 6.0 + - - -
176L TYR* 3.5 6.5 - - - -
177L SER 2.8 17.1 + - - +
178L GLU* 3.7 29.4 + - + -
180L PHE* 3.4 20.8 - - + -
208L ARG* 4.3 11.3 - - + +
209L THR* 1.3 87.4 - - - +
211L THR* 1.3 60.4 + - - +
213L THR* 3.6 1.2 + - - -
214L GLY 3.2 16.1 + - - -
246L PHE 3.2 15.1 + - - -
247L GLY* 3.4 18.6 + - - -
248L ASP* 3.0 30.6 - - - +
249L PRO* 4.1 11.9 - - + +
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Residues in contact with THR 211 (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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138L LEU* 4.5 1.4 - - + +
176L TYR* 2.8 35.2 + - + +
209L THR* 3.3 14.4 - - - +
210L HIS* 1.3 68.0 - - - +
212L ALA* 1.3 59.2 + - - +
214L GLY* 3.3 2.3 + - - -
215L ILE* 3.0 48.5 + - + +
239L VAL* 4.6 8.7 - - + -
241L THR* 4.4 4.3 + - + -
243L GLY 4.6 0.7 + - - -
245L LYS* 3.6 9.6 + - - +
248L ASP* 3.2 1.8 + - - -
252L TYR* 3.3 26.0 + - - +
283L GLU* 4.9 0.2 + - - -
287L ILE* 4.0 13.2 - - + -
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Residues in contact with ALA 212 (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 THR* 1.3 69.2 - - - +
213L THR* 1.4 64.1 + - - +
215L ILE* 3.1 5.3 + - - -
216L ARG 3.0 19.6 + - - -
245L LYS* 3.8 10.0 - - + +
248L ASP* 2.9 15.1 + - - +
250L LEU* 3.5 19.1 - - + +
251L GLY 3.5 21.8 - - - +
252L TYR* 3.9 13.8 - - + -
255L VAL* 3.2 18.5 - - + +
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Residues in contact with THR 213 (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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180L PHE* 3.6 30.7 - - + -
210L HIS* 3.6 2.9 + - - -
212L ALA* 1.4 74.7 - - - +
214L GLY* 1.3 57.2 + - - +
216L ARG* 3.5 3.1 + - + +
217L LYS* 3.0 42.7 + - + +
248L ASP* 2.5 28.1 + - - -
249L PRO* 3.9 9.8 - - + +
250L LEU* 3.4 26.9 - - + +
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Residues in contact with GLY 214 (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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138L LEU* 3.6 11.4 - - - -
174L MET* 3.5 10.1 - - - +
176L TYR* 4.4 3.8 - - - -
180L PHE* 3.4 21.7 - - - -
210L HIS 3.2 10.8 + - - -
211L THR 3.6 4.0 - - - -
212L ALA 3.2 0.6 - - - -
213L THR* 1.3 74.7 - - - +
215L ILE* 1.4 56.9 + - - +
217L LYS 3.3 1.4 + - - -
218L VAL* 3.0 32.2 + - - +
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Residues in contact with ILE 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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138L LEU* 3.8 17.3 - - + -
211L THR* 3.0 25.0 + - + +
212L ALA* 3.1 1.5 + - - +
214L GLY* 1.4 70.1 - - - +
216L ARG* 1.4 65.6 + - - +
218L VAL* 3.3 4.9 + - - +
219L VAL* 3.0 31.7 + - + +
237L LEU* 4.5 17.0 - - + -
239L VAL* 4.8 1.6 - - + -
252L TYR* 3.9 28.3 - - + -
255L VAL* 3.5 19.7 - - + -
256L ILE* 4.5 14.6 - - + -
259L ALA* 4.7 7.6 - - + -
266L ARG* 5.1 3.4 - - - -
287L ILE* 3.9 25.1 - - + -
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Residues in contact with ARG 216 (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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212L ALA 3.0 12.2 + - - +
213L THR* 3.7 9.0 - - - +
215L ILE* 1.4 74.3 - - - +
217L LYS* 1.3 62.3 + - + +
219L VAL* 3.3 5.9 + - - +
220L ARG* 2.8 80.9 + - - +
250L LEU* 3.5 34.2 - - + +
254L ASP* 2.8 39.6 + - - +
255L VAL* 3.4 13.5 - - + +
258L GLU* 3.8 9.3 + - - +
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Residues in contact with LYS 217 (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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174L MET* 3.8 16.0 - - + +
180L PHE* 3.6 42.2 - - + +
213L THR* 3.0 29.0 + - + +
214L GLY 3.7 4.9 - - - +
216L ARG* 1.3 77.5 - - + +
218L VAL* 1.3 55.3 + - - +
220L ARG* 4.9 2.0 - - - -
221L GLU* 2.8 66.6 + - - +
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Residues in contact with VAL 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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136L ALA* 4.3 7.0 - - + -
138L LEU* 3.7 31.6 - - + -
174L MET* 4.1 6.3 - - + -
214L GLY 3.0 16.6 + - - +
215L ILE* 3.6 9.4 - - - +
217L LYS* 1.3 76.1 - - - +
219L VAL* 1.4 59.7 + - + +
222L LEU* 3.0 54.8 + - + +
223L PHE* 3.2 17.8 + - + -
237L LEU* 3.6 31.2 - - + -
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Residues in contact with VAL 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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215L ILE* 3.0 24.3 + - + +
216L ARG* 3.7 5.4 - - - +
218L VAL* 1.4 80.5 - - + +
220L ARG* 1.3 56.4 + - + +
223L PHE* 3.6 11.1 - - - +
237L LEU* 5.6 1.1 - - + -
255L VAL 5.5 1.3 - - - +
258L GLU* 4.3 25.6 - - + +
259L ALA* 3.9 19.1 - - + +
262L GLU* 4.2 29.2 - - + -
264L VAL* 3.9 24.5 - - + -
615L EDO 2.8 31.5 - - - +
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Residues in contact with ARG 220 (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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216L ARG* 2.8 65.9 + - - +
217L LYS* 4.5 2.9 - - - +
219L VAL* 1.3 73.5 - - + +
221L GLU* 1.3 65.1 + - + +
224L ASN* 3.6 8.3 + - - +
258L GLU* 2.8 37.6 + - - +
615L EDO 3.6 18.6 + - - -
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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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174L MET* 5.6 1.2 - - - +
182L ILE* 3.6 29.7 - - + +
217L LYS* 2.8 59.9 + - - +
220L ARG* 1.3 79.6 - - + +
222L LEU* 1.4 62.1 + - - +
223L PHE 3.5 0.2 - - - -
224L ASN* 3.3 7.1 - - - +
227L ASN* 2.7 31.7 + - - +
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Residues in contact with LEU 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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136L ALA* 4.0 25.1 - - + -
137L PHE 4.5 2.2 - - - +
172L SER* 3.4 24.9 - - - +
173L LEU 4.2 4.3 - - - +
174L MET* 3.8 20.2 - - + +
182L ILE* 3.7 38.6 - - + -
185L THR* 5.1 3.8 - - + -
186L PHE* 3.3 24.6 - - + -
217L LYS 3.7 0.4 + - - +
218L VAL* 3.0 47.4 + - + +
221L GLU* 1.4 75.3 - - - +
223L PHE* 1.4 55.9 + - + +
224L ASN 3.2 7.5 + - - +
227L ASN* 4.4 5.8 - - - +
229L ALA* 3.8 1.6 - - - +
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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