Contacts of the helix formed by residues 210 - 222 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98F TYR 5.1 1.4 + - - -
99F SER* 5.5 0.2 - - - -
100F TYR* 4.5 17.7 - + - -
61H LYS* 5.0 3.6 + - - -
176I TYR* 3.5 5.4 - - - -
177I SER 2.8 16.4 + - - +
178I GLU* 3.7 28.3 + - + -
180I PHE* 3.4 21.2 - - + -
208I ARG* 4.3 11.7 - - + +
209I THR* 1.3 75.8 - - - +
211I THR* 1.4 60.2 + - - +
213I THR* 4.4 0.9 - - - -
214I GLY 3.2 16.1 + - - -
246I PHE 3.2 23.6 + - - -
247I GLY* 3.4 18.7 + - - -
248I ASP* 3.0 32.2 - - - +
249I PRO* 4.1 12.5 - - + +
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Residues in contact with THR 211 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138I LEU* 4.4 1.5 - - + +
176I TYR* 3.2 31.9 + - + +
209I THR* 3.3 8.7 - - - +
210I HIS* 1.4 68.2 - - - +
212I ALA* 1.4 55.8 + - - +
214I GLY* 3.0 4.5 + - - -
215I ILE* 2.9 52.1 + - + +
239I VAL* 4.6 9.0 - - + -
241I THR* 4.5 3.6 + - + +
243I GLY 4.7 1.4 + - - -
245I LYS* 3.3 18.0 + - - +
248I ASP* 3.2 1.6 + - - -
252I TYR* 3.2 23.7 + - - +
283I GLU* 4.6 0.2 + - - -
287I ILE* 4.1 12.3 - - + -
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Residues in contact with ALA 212 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211I THR* 1.4 71.7 - - - +
213I THR* 1.4 58.1 + - - +
215I ILE* 3.1 4.4 + - - +
216I ARG 3.0 24.3 + - - -
245I LYS* 3.9 11.9 - - + +
248I ASP* 2.9 13.5 + - - +
250I LEU* 3.4 22.0 - - + +
251I GLY 3.7 8.5 - - - +
252I TYR* 3.9 8.2 - - + -
255I VAL* 3.4 33.8 - - + +
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Residues in contact with THR 213 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180I PHE* 3.6 31.4 - - + -
210I HIS* 4.0 2.7 - - - -
212I ALA* 1.4 75.3 - - - +
214I GLY* 1.3 56.8 + - - +
216I ARG* 3.5 3.2 + - + +
217I LYS* 3.0 43.7 + - + +
248I ASP* 2.5 28.1 + - - -
249I PRO* 3.9 11.2 - - + +
250I LEU* 3.4 26.0 - - + +
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Residues in contact with GLY 214 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138I LEU* 3.8 13.0 - - - -
174I MET* 3.5 8.1 - - - +
176I TYR* 4.4 2.5 - - - -
180I PHE* 3.5 22.8 - - - -
210I HIS 3.2 7.9 + - - -
211I THR 3.0 8.1 + - - -
213I THR* 1.3 72.9 - - - +
215I ILE* 1.4 56.4 + - - +
217I LYS 3.3 0.7 + - - -
218I VAL* 3.0 33.1 + - - +
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Residues in contact with ILE 215 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138I LEU* 3.6 19.5 - - + -
211I THR* 2.9 26.8 + - + +
212I ALA* 3.1 6.3 + - - +
214I GLY* 1.4 71.0 - - - +
216I ARG* 1.4 65.0 + - - +
218I VAL* 3.3 5.9 + - - +
219I VAL* 3.0 31.8 + - + +
237I LEU* 4.5 13.2 - - + -
239I VAL* 4.7 5.2 - - + -
252I TYR* 3.8 29.6 - - + -
255I VAL* 4.5 11.7 - - + +
256I ILE* 4.5 15.0 - - + -
259I ALA* 4.7 9.6 - - + -
266I ARG* 4.8 3.4 - - - -
287I ILE* 3.9 19.3 - - + +
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Residues in contact with ARG 216 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212I ALA 3.0 6.6 + - - +
213I THR* 3.7 9.6 - - - +
215I ILE* 1.4 74.2 - - - +
217I LYS* 1.3 56.7 + - + +
219I VAL* 3.3 6.8 + - - +
220I ARG* 2.8 84.2 + - - +
250I LEU* 3.4 39.1 - - - +
254I ASP* 2.7 31.9 + - - +
255I VAL* 3.5 23.9 - - + +
258I GLU* 3.8 9.4 + - - +
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Residues in contact with LYS 217 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174I MET* 3.8 15.0 - - + +
180I PHE* 3.6 42.2 - - + +
213I THR* 3.0 30.4 + - + +
214I GLY 3.3 4.9 + - - +
216I ARG* 1.3 74.8 - - + +
218I VAL* 1.3 57.8 + - - +
220I ARG* 4.6 1.8 - - - +
221I GLU* 2.8 66.8 + - - +
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Residues in contact with VAL 218 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136I ALA* 4.3 0.9 - - + -
137I PHE 4.7 0.4 - - - +
138I LEU* 3.6 30.5 - - + -
174I MET* 4.1 7.6 - - + -
214I GLY 3.0 17.4 + - - +
215I ILE* 3.3 10.1 + - - +
217I LYS* 1.3 75.7 - - - +
219I VAL* 1.4 60.2 + - + +
222I LEU* 3.0 55.1 + - + +
223I PHE* 3.1 24.7 + - + -
237I LEU* 3.6 31.2 - - + -
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Residues in contact with VAL 219 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215I ILE* 3.0 24.9 + - + +
216I ARG* 3.7 6.5 - - - +
218I VAL* 1.4 78.5 - - + +
220I ARG* 1.3 61.0 + - - +
223I PHE* 3.4 29.5 - - + +
237I LEU* 5.6 0.4 - - + -
255I VAL 5.5 1.3 - - - +
258I GLU* 4.3 25.1 - - + +
259I ALA* 3.9 27.4 - - + +
262I GLU* 4.2 31.2 - - + +
264I VAL* 4.3 16.6 - - + -
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Residues in contact with ARG 220 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216I ARG* 2.8 69.9 + - + +
217I LYS* 4.5 2.5 - - - +
219I VAL* 1.3 74.5 - - + +
221I GLU* 1.3 62.8 + - + +
223I PHE 4.7 0.5 - - - +
224I ASN* 3.6 19.1 - - - +
258I GLU* 2.8 36.9 + - - +
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Residues in contact with GLU 221 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174I MET* 5.7 1.1 - - - +
182I ILE* 3.6 29.6 - - + +
217I LYS* 2.8 61.5 + - - +
220I ARG* 1.3 77.8 - - + +
222I LEU* 1.4 62.3 + - + +
223I PHE 3.4 1.3 - - - -
224I ASN* 3.4 5.8 - - - +
227I ASN* 2.7 32.6 + - - +
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Residues in contact with LEU 222 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136I ALA* 4.1 15.3 - - + -
137I PHE 4.4 1.1 - - - +
172I SER* 3.9 33.6 + - - +
173I LEU 4.4 3.6 - - - +
174I MET* 3.9 20.0 - - + +
182I ILE* 3.8 41.1 - - + -
184I PHE 4.5 0.2 - - - +
185I THR* 5.1 3.4 - - + -
186I PHE* 3.3 26.1 - - + -
217I LYS 4.9 0.9 - - - +
218I VAL* 3.0 44.1 + - + +
221I GLU* 1.4 75.9 - - - +
223I PHE* 1.4 57.8 + - + +
224I ASN 3.2 7.8 + - - +
227I ASN* 4.1 6.6 - - + +
229I ALA* 3.8 1.7 - - - +
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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